Contacts of the helix formed by residues 1067 - 1091 (chain F) in PDB entry 1NYE
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN1067 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825E LYS* 3.0 39.0 + - - +
878E ALA* 6.1 0.2 - - - -
1054F TYR* 4.6 4.3 - - - -
1058F THR 3.4 10.5 - - - +
1059F ARG* 4.3 9.4 - - + -
1065F GLY 3.4 14.2 - - - +
1066F THR* 1.3 78.9 - - - +
1068F PRO* 1.3 75.4 - - + +
1069F GLU* 3.2 11.1 + - - +
1070F GLU* 2.9 41.6 + - - +
1071F LEU* 3.3 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1068 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875E ALA* 3.7 22.8 - - + +
878E ALA* 4.3 7.4 - - + -
879E CYS* 3.8 24.5 - - + +
947E VAL* 3.9 15.0 - - + -
1054F TYR* 4.6 8.5 - - + -
1059F ARG* 2.8 42.0 - - - +
1067F ASN* 1.3 84.5 - - + +
1069F GLU* 1.3 64.6 + - - +
1071F LEU* 3.1 5.1 + - + +
1072F ILE* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1069 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823E ILE* 6.3 0.7 - - + -
825E LYS* 3.5 20.7 + - + -
946E PRO* 4.3 3.3 - - - +
947E VAL* 4.6 1.4 - - - +
1059F ARG* 2.6 40.0 + - - +
1067F ASN* 3.2 13.1 + - - +
1068F PRO* 1.3 74.7 - - - +
1070F GLU* 1.3 53.0 - - - +
1072F ILE* 3.1 9.1 + - - +
1073F GLY 2.7 31.5 + - - -
1104F VAL* 3.6 30.3 - - + +
1106F LEU* 4.1 30.6 - - + +
1115F ILE* 3.4 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1070 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825E LYS* 4.2 9.0 - - + -
826E LYS 3.6 16.2 - - - +
827E GLY* 4.3 2.8 - - - -
844E THR* 2.9 30.2 + - + +
845E GLU* 3.2 11.5 - - + +
846E SER* 2.9 40.7 + - - -
1065F GLY 3.7 3.1 - - - +
1066F THR* 3.4 22.7 - - - +
1067F ASN* 2.9 30.1 - - - +
1069F GLU* 1.3 76.9 - - - +
1071F LEU* 1.3 62.2 + - + +
1073F GLY* 3.2 1.9 + - - -
1074F ALA* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1071 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844E THR* 4.4 7.9 - - - +
848E VAL* 5.9 0.7 - - + -
849E LEU* 5.3 6.1 - - + -
871E LEU* 4.0 20.3 - - + +
874E ALA* 4.4 10.5 - - + +
875E ALA* 3.9 32.3 - - + +
878E ALA* 5.7 0.4 - - + -
1042F VAL* 4.4 15.0 - - + -
1049F LEU* 4.5 13.2 - - + -
1066F THR* 3.4 33.0 - - + -
1067F ASN 3.3 13.7 + - - +
1068F PRO* 3.1 6.5 + - + +
1070F GLU* 1.3 82.3 - - - +
1072F ILE* 1.3 58.5 + - - +
1074F ALA* 3.4 6.9 + - - +
1075F ALA* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1072 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872E ILE* 5.0 14.8 - - + -
875E ALA* 3.6 14.6 - - + -
947E VAL* 3.7 37.5 - - + -
950E VAL* 6.1 0.9 - - + -
1068F PRO 3.0 18.6 + - - +
1069F GLU* 3.4 7.4 - - - +
1071F LEU* 1.3 74.1 - - - +
1073F GLY* 1.3 66.3 + - - +
1075F ALA* 3.2 7.0 + - - +
1076F HIS* 2.8 23.2 + - - +
1104F VAL* 4.7 2.2 - - + -
1115F ILE* 4.0 22.4 - - + -
1118F ILE* 4.2 22.9 - - + -
1147F VAL* 5.1 1.7 - - + +
1151F LEU* 4.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1073 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827E GLY* 4.1 8.5 - - - -
1069F GLU 2.7 16.2 + - - -
1070F GLU 3.2 2.7 + - - -
1072F ILE* 1.3 73.3 - - - +
1074F ALA* 1.3 61.7 + - - +
1076F HIS* 3.2 2.6 + - - +
1077F ALA* 3.0 20.8 + - - +
1102F ALA* 3.3 21.1 - - - +
1104F VAL* 3.5 22.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1074 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827E GLY* 3.8 10.1 - - - -
828E GLN 4.3 4.7 - - - +
829E ALA* 4.7 0.5 - - - +
842E VAL* 4.5 7.2 - - + +
843E SER 3.8 18.8 - - - +
844E THR* 4.3 7.9 - - - +
849E LEU* 4.6 12.3 - - + -
871E LEU* 4.7 7.0 - - + -
1070F GLU 3.0 12.9 + - - +
1071F LEU* 3.7 9.6 - - - +
1073F GLY* 1.3 76.7 - - - +
1075F ALA* 1.3 63.5 + - - +
1077F ALA* 3.3 1.7 + - - +
1078F ALA* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1075 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868E PRO* 3.5 35.1 - - + +
871E LEU* 3.8 11.8 - - + +
872E ILE* 4.0 17.0 - - + -
1071F LEU 3.0 18.1 + - - +
1072F ILE 3.6 4.0 - - - +
1074F ALA* 1.3 77.0 - - - +
1076F HIS* 1.3 53.5 + - - +
1078F ALA* 3.3 2.5 + - - +
1079F CYS* 2.7 39.2 + - - +
1147F VAL* 4.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1076 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1072F ILE 2.8 19.9 + - - +
1073F GLY* 3.6 7.6 - - - +
1075F ALA* 1.3 72.0 - - - +
1077F ALA* 1.3 53.3 + - - +
1079F CYS* 3.6 1.0 - - - +
1080F PHE* 2.8 36.3 + - - +
1102F ALA* 4.6 1.3 - - + -
1118F ILE* 3.0 43.9 - - + +
1120F LEU* 4.1 17.0 - - + +
1145F CYS* 4.5 2.0 - - - -
1147F VAL* 3.5 27.7 - - + +
1148F SER* 2.7 32.8 + - - -
1151F LEU* 4.1 2.9 - - + -
1155F ILE* 3.8 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1077 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828E GLN* 4.2 4.7 - - - -
829E ALA* 3.7 18.8 - - + +
1073F GLY 3.0 15.5 + - - +
1074F ALA 3.7 4.0 - - - +
1076F HIS* 1.3 74.4 - - - +
1078F ALA* 1.3 55.0 + - - +
1080F PHE* 3.0 5.4 + - - +
1081F SER* 2.7 37.8 + - - -
1100F THR* 3.5 20.8 + - - +
1101F THR 4.7 0.4 - - - -
1102F ALA* 4.0 15.8 - - + +
1120F LEU* 4.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1078 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829E ALA* 3.4 5.5 - - - +
842E VAL* 3.2 33.9 - - + -
854E TYR* 2.8 36.2 + - + -
868E PRO* 4.1 9.0 - - + -
871E LEU* 5.7 0.7 - - + -
1074F ALA 2.9 12.5 + - - +
1075F ALA* 3.7 4.5 - - - +
1077F ALA* 1.3 75.4 - - - +
1079F CYS* 1.3 63.2 + - - +
1082F MET* 3.1 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1079 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859E ARG* 3.1 26.2 + - - +
868E PRO* 3.7 10.7 - - + +
1075F ALA 2.7 21.5 + - - +
1076F HIS 3.6 3.4 - - - +
1078F ALA* 1.3 75.5 - - - +
1080F PHE* 1.3 60.9 + - - +
1082F MET* 3.9 2.2 - - - +
1083F ALA* 3.0 23.6 + - - +
1145F CYS* 3.7 11.0 - - - -
1146F PRO* 3.7 9.9 - - - -
1147F VAL* 3.4 41.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1080 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1076F HIS* 2.8 21.9 + - + +
1077F ALA* 3.5 2.9 - - - +
1079F CYS* 1.3 72.0 - - - +
1081F SER* 1.3 67.1 + - - +
1083F ALA* 3.5 1.4 + - - +
1084F LEU* 3.1 28.5 + - + +
1100F THR* 3.8 31.9 - - + -
1120F LEU* 3.8 29.4 - - + -
1122F SER* 4.1 12.3 - - - -
1138F ILE* 4.0 25.1 - - + -
1141F ALA* 3.5 23.1 - - + -
1142F LYS* 3.7 26.9 - - + -
1145F CYS* 3.9 13.5 - - - -
1157F LEU* 4.2 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1081 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829E ALA* 3.8 8.4 + - - +
831E TRP* 4.2 13.0 - - - +
854E TYR* 3.8 13.5 - - - -
1077F ALA 2.7 26.2 + - - -
1080F PHE* 1.3 77.9 - - - +
1082F MET* 1.3 63.2 + - - +
1084F LEU* 3.3 6.4 + - - +
1085F SER* 3.2 18.5 + - - -
1098F ILE* 3.8 24.9 - - - +
1100F THR* 2.8 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1082 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831E TRP* 3.2 37.7 - - + -
835E ILE* 4.7 9.4 - - + +
854E TYR* 3.1 32.2 + - + -
855E GLY 3.3 24.2 - - - +
856E PHE* 4.6 8.7 - - + -
859E ARG* 3.6 32.1 - - - +
1078F ALA 3.1 13.4 + - - +
1079F CYS* 3.9 3.8 - - - +
1081F SER* 1.3 75.3 - - - +
1083F ALA* 1.3 65.2 + - - +
1085F SER* 3.2 5.2 + - - -
1086F LEU* 3.0 22.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1083 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859E ARG* 6.2 0.2 - - - +
1079F CYS 3.0 18.3 + - - +
1080F PHE 3.9 3.4 - - - +
1082F MET* 1.3 76.7 - - - +
1084F LEU* 1.3 57.7 + - - +
1086F LEU* 3.4 9.1 + - - +
1087F MET* 2.9 37.3 + - + +
1141F ALA* 4.4 8.5 - - + -
1145F CYS* 3.6 26.5 - - + +
1146F PRO* 5.2 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1084 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1080F PHE* 3.1 23.1 + - + +
1081F SER 3.3 9.4 - - - +
1082F MET 3.1 0.2 - - - -
1083F ALA* 1.3 74.2 - - - +
1085F SER* 1.3 66.0 + - - +
1087F MET* 3.3 2.1 + - - +
1088F LEU* 2.9 38.0 + - + +
1098F ILE* 3.4 29.6 - - + -
1124F VAL* 3.7 27.1 - - + -
1134F PHE* 4.4 3.1 - - + -
1137F ILE* 4.0 19.1 - - + -
1138F ILE* 3.3 34.8 - - + -
1141F ALA* 4.1 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1085 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831E TRP* 3.5 27.4 + - - -
833E GLY 3.3 19.1 + - - -
835E ILE* 3.5 21.8 + - - +
1081F SER 3.2 5.4 + - - -
1082F MET 3.2 8.6 + - - -
1084F LEU* 1.3 78.7 - - - +
1086F LEU* 1.3 64.8 + - - +
1088F LEU* 3.3 2.3 + - - +
1089F GLY* 2.9 18.7 + - - -
1095F PRO* 4.0 22.1 - - - +
1098F ILE* 4.1 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1086 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835E ILE* 3.4 32.3 - - + +
856E PHE* 6.0 3.8 - - + -
1082F MET* 3.0 13.7 + - + +
1083F ALA* 3.4 12.8 - - - +
1085F SER* 1.3 75.7 - - - +
1087F MET* 1.3 74.5 + - + +
1089F GLY* 3.0 13.0 + - - -
1090F GLU* 3.1 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1087 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083F ALA* 2.9 24.1 + - + +
1084F LEU* 3.7 1.8 - - - +
1086F LEU* 1.3 82.9 - - + +
1088F LEU* 1.3 65.1 + - - +
1090F GLU* 3.1 32.7 + - - +
1091F ALA* 3.3 10.9 + - - +
1137F ILE* 3.5 30.5 - - + +
1140F LYS* 3.5 43.1 - - + -
1141F ALA* 4.6 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1088 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1084F LEU* 2.9 42.0 + - + +
1085F SER 3.6 3.6 - - - +
1087F MET* 1.3 70.8 - - - +
1089F GLY* 1.3 63.9 + - - +
1091F ALA* 2.9 16.7 + - + +
1092F GLY 3.3 0.2 + - - -
1093F PHE* 3.0 29.3 + - + +
1095F PRO* 3.7 35.2 - - + -
1098F ILE* 4.4 0.9 - - + -
1126F VAL* 4.0 12.3 - - + -
1129F ILE* 3.6 28.9 - - + -
1134F PHE* 3.7 18.6 - - + -
1137F ILE* 4.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1089 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835E ILE* 4.1 15.3 - - - -
1085F SER 2.9 15.1 + - - -
1086F LEU 3.0 4.9 + - - -
1088F LEU* 1.3 76.1 - - - +
1090F GLU* 1.3 56.3 + - - +
1092F GLY* 2.8 21.7 + - - -
1093F PHE 3.2 12.5 + - - -
1094F THR* 5.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1090 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1086F LEU* 3.1 39.6 + - + +
1087F MET* 3.1 23.1 + - - +
1089F GLY* 1.3 72.6 - - - +
1091F ALA* 1.3 57.1 + - - +
1092F GLY 3.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1091 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087F MET 3.3 8.4 + - - +
1088F LEU* 2.9 12.8 + - + +
1090F GLU* 1.3 78.2 - - - +
1092F GLY* 1.3 60.5 + - - +
1093F PHE* 3.4 27.0 - - + -
1137F ILE* 4.6 17.7 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il