Contacts of the helix formed by residues 1056 - 1071 (chain A) in PDB entry 3U44
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 THR1056 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055A LEU* 1.3 76.4 - - - +
1057A ALA* 1.3 72.3 + - - +
1058A ALA* 3.6 13.7 + - + +
1059A GLU* 2.9 38.9 + - + +
1060A LYS* 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1057 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056A THR* 1.3 77.3 + - - +
1058A ALA* 1.3 57.5 + - - +
1060A LYS* 3.8 10.7 - - - +
1061A GLY* 3.1 23.4 + - - -
1175A SER* 4.6 4.7 + - - -
1177A ARG* 5.9 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1058 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056A THR* 3.0 13.2 + - + +
1057A ALA* 1.3 76.9 - - - +
1059A GLU* 1.3 66.5 + - + +
1061A GLY* 3.2 3.0 + - - -
1062A THR* 3.0 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1059 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1051A MET* 6.0 1.4 - - - +
1054A GLY 4.6 1.2 - - - +
1055A LEU* 3.3 32.6 - - + +
1056A THR* 2.9 34.8 + - + +
1058A ALA* 1.3 77.0 - - + +
1060A LYS* 1.3 66.3 + - - +
1062A THR* 3.4 8.0 + - - -
1063A ALA* 3.1 21.5 + - - +
1099A GLN* 4.1 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1060 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055A LEU* 4.5 11.1 - - + +
1056A THR 2.9 15.9 + - - +
1057A ALA* 3.8 10.8 - - - +
1059A GLU* 1.3 77.1 - - - +
1061A GLY* 1.3 63.6 + - - +
1063A ALA* 3.1 9.3 + - - +
1064A MET* 2.9 32.8 + - + +
1102A ALA* 2.7 41.9 + - + +
1103A ILE* 4.7 0.4 - - - +
1104A ASP* 4.4 15.6 - - - +
1107A GLU* 5.0 9.0 - - - -
1175A SER* 5.3 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1061 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057A ALA 3.1 13.8 + - - -
1058A ALA* 3.2 4.2 + - - -
1060A LYS* 1.3 76.7 - - - +
1062A THR* 1.3 56.3 + - - +
1064A MET* 3.2 5.5 + - - +
1065A HIS* 2.9 30.1 + - - +
1175A SER* 3.5 31.6 - - - -
1224A PHE* 5.2 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1062 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1058A ALA 3.0 14.6 + - - -
1059A GLU* 3.7 10.3 - - - -
1060A LYS 3.3 0.2 - - - -
1061A GLY* 1.3 74.4 - - - +
1063A ALA* 1.3 62.8 + - - +
1065A HIS* 3.3 8.8 + - + +
1066A THR* 3.0 32.5 + - - +
1099A GLN* 4.7 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1063 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055A LEU* 5.5 0.2 - - + -
1059A GLU 3.1 12.6 + - - +
1060A LYS* 3.1 13.3 + - + +
1062A THR* 1.3 74.4 - - - +
1064A MET* 1.3 65.7 + - - +
1065A HIS 3.3 0.7 + - - -
1066A THR* 3.3 14.4 + - - -
1067A VAL* 3.4 16.6 + - - +
1095A LEU* 4.3 5.1 - - + +
1099A GLN* 3.7 44.8 - - + +
1102A ALA* 5.7 0.7 - - + -
1103A ILE* 4.2 9.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1064 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060A LYS* 2.9 34.3 + - + +
1061A GLY* 3.6 8.3 - - - +
1063A ALA* 1.3 76.2 - - - +
1065A HIS* 1.3 63.7 + - - +
1067A VAL* 3.5 5.8 + - - +
1068A MET* 3.4 18.9 + - - +
1103A ILE* 3.5 33.0 - - + -
1104A ASP 3.6 20.6 - - - +
1107A GLU* 4.2 15.5 - - + +
1108A ILE* 3.4 30.2 - - + +
1175A SER* 5.2 2.0 - - - +
1224A PHE* 4.0 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1065 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061A GLY 2.9 16.6 + - - +
1062A THR* 3.4 10.5 - - + +
1064A MET* 1.3 75.2 - - - +
1066A THR* 1.3 69.9 + - - +
1068A MET* 3.2 15.8 + - - +
1069A GLN* 3.3 27.7 + - + +
1129A GLU* 3.7 31.9 + - - -
1157A ILE* 6.1 0.2 - - + -
1159A ASP* 3.2 27.1 + - - +
1173A TYR* 4.2 30.1 - + + -
1224A PHE* 4.8 6.2 - + + -
77B GLN* 6.1 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1066 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062A THR* 3.0 18.8 + - - +
1063A ALA* 3.3 9.4 + - - -
1065A HIS* 1.3 82.5 + - - +
1067A VAL* 1.3 65.3 + - - +
1069A GLN* 3.0 15.0 + - - +
1070A HIS* 3.2 38.3 + - + +
1089A LEU* 4.6 5.6 - - + -
1094A LEU* 4.2 23.6 + - + +
1095A LEU* 4.4 9.5 - - + +
1099A GLN* 5.8 0.3 + - - -
77B GLN* 5.5 10.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1067 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063A ALA 3.4 7.3 + - - +
1064A MET 3.7 7.2 - - - +
1065A HIS 3.3 0.6 - - - -
1066A THR* 1.3 76.4 - - - +
1068A MET* 1.3 59.3 + - - +
1070A HIS* 2.8 20.1 + - - +
1071A ILE* 2.9 17.0 + - + +
1082A ALA* 5.2 0.9 - - + +
1085A THR* 4.6 11.3 - - + +
1086A VAL* 4.0 14.1 - - + -
1089A LEU* 3.8 23.8 - - + -
1095A LEU* 4.5 1.1 - - + -
1103A ILE* 3.3 34.8 - - + -
1108A ILE* 3.4 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1068 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1064A MET 3.4 8.1 + - - +
1065A HIS* 3.2 11.0 + - - +
1067A VAL* 1.3 81.3 - - - +
1069A GLN* 1.3 60.0 + - - +
1071A ILE* 3.2 23.2 - - - +
1073A LEU* 5.3 0.2 - - - +
1108A ILE* 3.8 28.7 - - + +
1111A PHE* 4.2 15.5 - - + -
1112A PHE* 3.7 31.9 - - - -
1128A ARG* 3.4 6.9 + - - -
1173A TYR* 3.4 47.6 + - + +
1222A TYR* 4.5 0.7 - - + -
1224A PHE* 3.6 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1069 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1065A HIS* 3.4 26.7 - - + +
1066A THR* 3.0 9.7 + - - +
1068A MET* 1.3 76.6 - - - +
1070A HIS* 1.3 66.5 + - + +
1071A ILE 3.5 0.2 - - - -
1128A ARG* 3.3 44.1 + - + +
1129A GLU* 2.7 33.7 + - + +
1159A ASP* 2.8 36.7 + - - +
1173A TYR* 3.4 23.1 - - - -
78B HIS* 5.1 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1070 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1066A THR* 3.2 30.7 + - + +
1067A VAL 2.8 7.6 + - - +
1069A GLN* 1.3 82.7 - - + +
1071A ILE* 1.3 67.3 + - - +
1072A PRO* 3.4 7.8 - - - +
1085A THR* 4.1 9.5 - - + +
1089A LEU* 3.7 26.4 - - + +
1094A LEU* 3.3 20.6 - - + +
1128A ARG* 4.8 2.4 + - - +
77B GLN* 3.3 20.8 + - + -
78B HIS* 3.2 39.2 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1071 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067A VAL* 2.9 18.7 + - + +
1068A MET* 3.2 19.1 - - - +
1070A HIS* 1.3 77.5 - - - +
1072A PRO* 1.3 70.2 - - + +
1073A LEU* 3.9 2.9 - - + -
1077A PRO* 4.3 23.3 - - + -
1081A GLU 4.6 1.6 - - - +
1082A ALA* 4.2 20.6 - - + +
1085A THR* 3.4 30.1 - - + +
1108A ILE* 5.1 4.0 - - + -
1112A PHE* 3.2 33.9 - - + -
1128A ARG* 2.8 35.8 + - - +
----------------------------------------------------------
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