Contacts of the helix formed by residues 1061 - 1081 (chain A) in PDB entry 3U5P
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 GLU1061 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060A SER* 1.3 84.4 + - - +
1062A VAL* 1.3 52.4 + - - +
1064A GLN* 3.0 17.3 + - - +
1065A ALA* 2.7 35.2 + - - +
15I ALA* 5.1 2.9 - - + +
16I PRO* 4.4 18.1 - - + +
17I ARG 3.4 21.0 - - - +
18I ALY 5.1 2.6 - - - +
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Residues in contact with VAL1062 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981A GLU* 3.5 16.2 - - + -
982A PHE* 3.7 7.7 - - + -
1035A CYS* 3.9 7.0 - - - -
1060A SER* 3.3 7.5 + - - +
1061A GLU* 1.3 78.2 - - - +
1063A ALA* 1.3 58.1 + - - +
1065A ALA* 3.5 8.2 - - - +
1066A GLY* 2.8 25.1 + - - -
16I PRO* 4.1 1.3 - - - +
17I ARG 2.9 46.9 - - - +
18I ALY 3.9 42.0 - - + +
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Residues in contact with ALA1063 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035A CYS* 4.2 13.2 - - - +
1036A GLU* 5.7 2.4 - - - +
1039A ASN* 3.4 44.2 - - + +
1060A SER* 3.0 14.7 + - - +
1062A VAL* 1.3 80.0 - - - +
1064A GLN* 1.3 58.4 + - + +
1066A GLY* 3.4 2.6 + - - -
1067A LYS* 3.0 34.7 + - - +
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Residues in contact with GLN1064 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978A LEU* 5.6 0.2 - - - -
1060A SER 2.8 28.0 + - - +
1061A GLU* 3.2 13.6 - - - +
1063A ALA* 1.3 75.3 - - - +
1065A ALA* 1.3 65.5 + - - +
1067A LYS* 3.0 31.4 + - - +
1068A ALA* 3.1 13.7 + - - +
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Residues in contact with ALA1065 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978A LEU* 3.8 38.6 - - + +
981A GLU* 6.0 0.2 - - + -
982A PHE* 4.1 7.0 - - + -
1061A GLU 2.7 16.3 + - - +
1062A VAL* 3.5 8.1 - - - +
1064A GLN* 1.3 70.6 - - - +
1066A GLY* 1.3 64.5 + - - +
1068A ALA* 3.2 3.1 + - - +
1069A VAL* 2.9 27.5 + - - +
16I PRO* 4.1 20.0 - - + -
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Residues in contact with GLY1066 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982A PHE* 3.3 24.0 - - - -
1032A PHE* 4.1 9.7 - - - -
1035A CYS* 4.3 7.0 - - - -
1062A VAL 2.8 12.2 + - - -
1063A ALA 3.6 5.6 - - - -
1064A GLN 3.2 0.2 - - - -
1065A ALA* 1.3 75.3 - - - +
1067A LYS* 1.3 62.8 + - - +
1068A ALA 3.1 0.2 + - - -
1069A VAL* 3.2 1.0 + - - +
1070A ALA* 2.9 26.7 + - - +
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Residues in contact with LYS1067 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036A GLU* 6.0 4.0 - - - +
1039A ASN* 5.9 2.8 - - - +
1063A ALA* 3.0 19.7 + - - +
1064A GLN* 3.0 24.6 + - - +
1066A GLY* 1.3 74.5 - - - +
1068A ALA* 1.3 60.2 + - - +
1070A ALA* 3.4 5.6 + - - +
1071A LEU* 3.0 43.1 + - + +
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Residues in contact with ALA1068 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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976A HIS* 4.8 4.9 - - + +
978A LEU* 3.9 21.1 - - + -
1064A GLN 3.1 8.5 + - - +
1065A ALA 3.7 6.5 - - - +
1067A LYS* 1.3 78.1 - - - +
1069A VAL* 1.3 60.3 + - - +
1071A LEU* 3.2 9.6 + - - +
1072A TYR* 2.8 32.3 + - - +
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Residues in contact with VAL1069 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973A LEU* 4.5 16.8 - - + -
976A HIS* 3.7 32.5 - - + +
978A LEU* 3.9 20.2 - - + +
979A SER* 4.2 14.4 - - - +
982A PHE* 4.7 3.1 - - + -
1003A LEU* 6.4 0.4 - - + -
1032A PHE* 3.2 29.8 - - + -
1065A ALA 2.9 20.2 + - - +
1066A GLY 4.0 2.2 - - - +
1068A ALA* 1.3 75.0 - - - +
1070A ALA* 1.3 56.1 + - - +
1072A TYR* 3.9 7.3 - - - +
1073A PHE* 3.0 27.2 + - - +
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Residues in contact with ALA1070 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032A PHE* 3.7 34.3 - - + -
1066A GLY 2.9 17.9 + - - +
1067A LYS* 3.6 6.1 - - - +
1069A VAL* 1.3 74.9 - - - +
1071A LEU* 1.3 66.5 + - + +
1073A PHE* 3.4 5.9 - - - +
1074A GLU* 3.1 27.1 + - - +
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Residues in contact with LEU1071 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067A LYS* 3.0 33.2 + - + +
1068A ALA* 3.7 6.7 - - - +
1070A ALA* 1.3 76.3 - - + +
1072A TYR* 1.3 66.6 + - - +
1074A GLU* 3.0 22.3 + - + +
1075A ASP* 3.1 17.3 + - - +
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Residues in contact with TYR1072 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972A TYR* 3.2 53.9 + - + -
973A LEU* 4.3 10.1 - - + -
975A CYS* 6.0 0.2 - - - +
976A HIS* 3.4 38.4 - + + +
977A GLU* 6.0 0.4 - - - -
1068A ALA 2.8 20.9 + - - +
1069A VAL* 4.0 2.5 - - - +
1071A LEU* 1.3 73.7 - - - +
1073A PHE* 1.3 63.9 + - - +
1075A ASP* 3.7 12.2 - - + +
1076A LYS* 3.3 46.1 + - + +
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Residues in contact with PHE1073 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969A LEU* 3.8 33.9 - - + -
973A LEU* 3.9 30.5 - - + -
1024A PHE* 4.5 5.8 - + - -
1025A VAL* 4.6 7.9 - - + -
1028A VAL* 3.4 41.5 - - + -
1029A ARG* 4.5 12.3 - - + -
1032A PHE* 4.9 3.6 - + + -
1069A VAL 3.0 18.9 + - - +
1070A ALA* 3.4 7.9 - - - +
1072A TYR* 1.3 76.3 - - - +
1074A GLU* 1.3 70.9 + - - +
1076A LYS* 3.2 5.4 + - + -
1077A LEU* 2.7 54.4 + - + +
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Residues in contact with GLU1074 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029A ARG* 2.9 46.5 + - - +
1070A ALA 3.1 14.7 + - - +
1071A LEU* 3.0 18.9 + - + +
1073A PHE* 1.3 88.1 - - - +
1075A ASP* 1.3 68.0 + - - +
1077A LEU* 3.1 11.4 + - - +
1078A THR* 3.1 31.1 + - + +
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Residues in contact with ASP1075 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1071A LEU 3.1 14.2 + - - +
1072A TYR* 3.7 16.6 - - + +
1074A GLU* 1.3 72.4 - - - +
1076A LYS* 1.3 59.9 + - + +
1077A LEU 2.8 0.2 + - - -
1078A THR* 2.6 33.9 + - - -
1079A GLU* 2.8 20.0 + - - +
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Residues in contact with LYS1076 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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969A LEU* 3.3 19.1 - - + +
972A TYR* 3.4 58.2 + - + -
973A LEU* 6.1 0.2 - - + -
1072A TYR* 3.3 44.4 + - + +
1073A PHE* 3.2 8.5 + - + +
1075A ASP* 1.3 83.7 - - + +
1077A LEU* 1.3 59.2 + - - +
1079A GLU* 3.7 32.8 - - + +
1080A ILE* 3.3 18.7 + - - +
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Residues in contact with LEU1077 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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969A LEU* 3.8 22.0 - - + -
1025A VAL* 3.6 37.2 - - + -
1029A ARG* 3.5 28.5 - - - +
1073A PHE* 2.7 24.7 + - + +
1074A GLU* 3.4 17.3 - - - +
1075A ASP 2.8 4.8 + - - -
1076A LYS* 1.3 72.9 - - - +
1078A THR* 1.3 55.9 + - + +
1080A ILE* 5.1 0.4 - - - -
1081A TYR* 2.7 41.5 + - + +
1086A PHE* 4.0 23.3 - - + -
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Residues in contact with THR1078 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1074A GLU* 3.3 18.5 + - - +
1075A ASP* 2.6 22.5 + - - -
1077A LEU* 1.3 75.1 - - + +
1079A GLU* 1.3 60.0 + - - -
1081A TYR 3.4 19.5 - - - +
1082A SER* 4.1 7.8 + - - -
1085A THR* 5.8 8.3 - - + -
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Residues in contact with GLU1079 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972A TYR* 4.7 6.5 + - - -
1075A ASP* 2.8 15.0 + - - +
1076A LYS* 3.7 33.1 - - + +
1078A THR* 1.3 80.9 + - - +
1080A ILE* 1.3 70.0 + - + +
1081A TYR 3.6 0.4 + - - -
1082A SER* 4.7 7.6 + - - -
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Residues in contact with ILE1080 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934A ILE* 4.9 6.3 - - + -
965A LYS* 3.8 44.9 - - + +
968A ARG* 3.5 46.0 - - + +
969A LEU* 4.7 6.7 - - + -
972A TYR* 3.6 21.5 - - + +
1076A LYS 3.3 19.4 + - - +
1077A LEU 3.6 0.2 - - - -
1079A GLU* 1.3 89.2 - - + +
1081A TYR* 1.3 67.1 + - + +
1082A SER 4.0 0.9 - - - -
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Residues in contact with TYR1081 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962A ASP* 3.7 13.4 + - - -
965A LYS* 3.6 46.8 - - + +
966A CYS* 4.9 2.3 - - - -
969A LEU* 4.5 12.3 - - + -
1021A PRO* 3.5 25.4 - - + +
1025A VAL* 5.7 0.9 - - + -
1077A LEU* 2.7 28.0 + - + +
1078A THR* 3.4 16.7 - - - +
1080A ILE* 1.3 83.0 - - + +
1082A SER* 1.3 66.1 + - - +
1083A ASP* 3.5 8.5 - - - +
1084A ARG* 3.4 46.5 - - + +
1085A THR* 5.7 0.2 - - - +
1086A PHE* 3.5 32.5 - + + -
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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) + - + + + + + -
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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