Contacts of the helix formed by residues 1061 - 1080 (chain A) in PDB entry 5IYB
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 SER1061 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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994A PHE* 4.6 1.7 - - - -
996A ILE* 3.9 22.4 - - - +
1002A SER* 5.0 4.9 - - - -
1003A ASP* 3.9 15.3 - - - -
1004A LEU* 4.4 4.0 - - - -
1059A ARG 3.6 1.8 + - - -
1060A LEU* 1.3 76.8 - - - +
1062A GLY* 1.3 55.8 + - - +
1063A GLU* 3.8 11.2 - - - +
1064A ALA* 3.2 22.7 + - - +
1065A PHE* 2.7 32.9 + - - +
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Residues in contact with GLY1062 (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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1003A ASP* 3.7 12.3 + - - -
1004A LEU* 3.9 21.5 - - - +
1008A LYS* 4.7 15.4 - - - -
1061A SER* 1.3 73.3 - - - +
1063A GLU* 1.3 59.4 + - - +
1065A PHE* 3.3 4.7 + - - +
1066A ASP* 2.9 25.8 + - - +
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Residues in contact with GLU1063 (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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994A PHE* 3.9 22.1 - - + -
1061A SER* 3.8 11.8 + - - +
1062A GLY* 1.3 70.7 - - - +
1064A ALA* 1.3 63.7 + - - +
1066A ASP* 3.1 9.3 + - + +
1067A TRP* 2.8 31.0 + - - +
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Residues in contact with ALA1064 (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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990A ALA* 4.4 6.7 - - + +
994A PHE* 3.6 34.3 - - + -
996A ILE* 5.0 0.9 - - + -
1060A LEU* 4.4 15.3 - - + -
1061A SER* 3.2 30.3 + - - +
1062A GLY 3.3 0.2 - - - -
1063A GLU* 1.3 83.5 - - - +
1065A PHE* 1.3 60.6 + - - +
1067A TRP* 3.5 2.6 + - - +
1068A LEU* 3.0 22.6 + - - +
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Residues in contact with PHE1065 (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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1004A LEU* 4.3 15.5 - - + -
1008A LYS* 4.4 14.6 - - + -
1009A VAL* 3.8 54.1 - - + -
1012A GLY* 4.7 0.9 - - - -
1013A VAL* 4.5 2.7 - - + -
1049A LEU* 4.0 14.1 - - + -
1054A MET* 3.9 32.3 - - + -
1060A LEU* 4.8 4.9 - - + +
1061A SER 2.7 17.8 + - - +
1062A GLY 3.5 8.7 - - - +
1063A GLU 3.2 0.2 - - - -
1064A ALA* 1.3 75.3 - - - +
1066A ASP* 1.3 57.8 + - - +
1068A LEU* 3.1 8.8 + - + +
1069A LEU* 3.0 64.4 + - + +
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Residues in contact with ASP1066 (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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1008A LYS* 4.4 17.8 + - - -
1062A GLY 2.9 13.8 + - - +
1063A GLU* 3.1 14.1 + - + +
1065A PHE* 1.3 79.2 - - - +
1067A TRP* 1.3 61.3 + - - +
1069A LEU* 3.4 14.7 + - - +
1070A GLY* 3.2 16.8 + - - -
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Residues in contact with TRP1067 (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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599A HIS* 6.0 2.9 - + - -
986A MET* 4.2 7.4 - - + -
989A ASN* 4.4 12.3 - - + -
990A ALA* 4.0 33.7 - - + -
993A ILE* 4.1 24.5 - - + -
994A PHE* 3.6 33.7 - + + -
1063A GLU 2.8 10.7 + - - +
1064A ALA 3.8 0.9 - - - +
1066A ASP* 1.3 69.6 - - - +
1068A LEU* 1.3 69.8 + - + +
1070A GLY* 3.1 4.6 + - - +
1071A GLU* 2.8 66.2 + - + +
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Residues in contact with LEU1068 (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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983A LEU* 5.3 0.4 - - - +
986A MET* 3.9 41.7 - - + +
987A ILE* 3.9 16.2 - - + +
990A ALA* 4.7 4.5 - - + -
1049A LEU* 4.0 17.0 - - + -
1054A MET* 3.8 28.7 - - + -
1060A LEU* 4.1 7.0 - - + -
1064A ALA 3.0 15.0 + - - +
1065A PHE* 3.1 13.9 + - + +
1067A TRP* 1.3 86.5 - - + +
1069A LEU* 1.3 61.3 + - - +
1071A GLU* 3.4 3.2 + - + +
1072A ILE* 3.0 33.9 + - + +
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Residues in contact with LEU1069 (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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1012A GLY* 4.2 20.6 - - - +
1013A VAL* 5.4 0.7 - - - -
1015A GLU* 6.3 0.2 - - + -
1016A LEU* 3.5 39.9 - - + +
1019A LYS* 6.4 0.2 - - - +
1049A LEU* 4.8 6.3 - - + -
1065A PHE* 3.0 56.8 + - + +
1066A ASP* 3.8 15.3 - - - +
1067A TRP 3.2 0.2 - - - -
1068A LEU* 1.3 76.2 - - + +
1070A GLY* 1.3 57.7 + - - +
1072A ILE* 3.9 0.4 - - + -
1073A GLU* 2.9 34.3 + - - +
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Residues in contact with GLY1070 (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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1066A ASP 3.2 8.3 + - - -
1067A TRP* 3.1 8.3 + - - -
1069A LEU* 1.3 80.0 - - - +
1071A GLU* 1.3 56.2 + - - +
1073A GLU* 3.7 9.7 - - - +
1074A SER* 3.0 28.1 + - - -
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Residues in contact with GLU1071 (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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659A GLU* 4.1 10.0 - - - +
986A MET* 3.9 24.3 - - + +
1067A TRP* 2.8 56.7 + - + +
1068A LEU* 3.8 7.2 - - + +
1070A GLY* 1.3 73.9 - - - +
1072A ILE* 1.3 66.0 + - - +
1074A SER* 2.9 19.2 + - - -
1075A LYS* 2.6 47.8 + - - +
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Residues in contact with ILE1072 (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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981A CYS* 4.8 5.2 - - + -
983A LEU* 3.7 32.5 - - + -
986A MET* 4.3 16.2 - - - -
1016A LEU* 4.4 18.6 - - + -
1020A LEU* 4.9 5.8 - - + -
1041A PHE* 4.4 18.8 - - + -
1045A LEU* 4.3 5.8 - - + -
1049A LEU* 4.2 19.5 - - + -
1068A LEU* 3.0 39.1 + - + +
1069A LEU* 4.1 2.5 - - - +
1071A GLU* 1.3 74.8 - - - +
1073A GLU* 1.3 64.2 + - - +
1075A LYS* 4.4 0.4 - - - +
1076A PHE* 3.0 25.7 + - + +
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Residues in contact with GLU1073 (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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1016A LEU* 4.2 7.2 - - + +
1019A LYS* 3.5 50.8 + - + +
1020A LEU* 4.2 13.4 - - + +
1069A LEU* 2.9 20.4 + - - +
1070A GLY* 3.7 9.0 - - - +
1072A ILE* 1.3 78.4 - - - +
1074A SER* 1.3 63.0 + - - +
1076A PHE* 4.1 0.9 - - - +
1077A ASN* 3.2 31.7 + - - +
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Residues in contact with SER1074 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1070A GLY 3.0 15.9 + - - -
1071A GLU* 2.9 23.2 + - - -
1073A GLU* 1.3 78.2 - - - +
1075A LYS* 1.3 74.1 + - - +
1077A ASN* 3.4 3.7 + - - +
1078A GLN* 3.0 25.1 + - - +
56F TYR* 6.1 0.7 - - - -
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Residues in contact with LYS1075 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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658A LEU 4.9 12.6 - - - +
659A GLU* 4.6 12.1 + - - +
981A CYS* 4.0 11.5 - - + -
986A MET* 3.7 25.6 - - + -
1071A GLU* 2.6 45.0 + - - +
1072A ILE 4.4 0.2 - - - +
1074A SER* 1.3 86.0 + - - +
1076A PHE* 1.3 64.9 + - - +
1078A GLN* 3.5 21.7 + - - +
1079A ALA* 3.0 23.0 + - - +
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Residues in contact with PHE1076 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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896A LEU* 4.5 16.6 - - + +
980A PRO* 3.6 30.5 - - + -
981A CYS* 3.5 11.3 - - - -
1020A LEU* 3.6 49.1 - - + -
1021A VAL 5.5 0.2 - - - -
1022A ILE* 3.8 23.1 - - + -
1038A THR* 4.7 10.1 - - + -
1041A PHE* 3.7 33.7 - + + -
1072A ILE* 3.0 21.8 + - + +
1075A LYS* 1.3 78.1 - - - +
1077A ASN* 1.3 65.9 + - + +
1079A ALA* 3.0 17.5 + - + +
1080A ILE* 3.6 6.9 + - + +
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Residues in contact with ASN1077 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1019A LYS 4.9 9.7 + - - -
1020A LEU* 6.3 1.1 - - + +
1021A VAL 5.1 8.7 + - - +
1073A GLU* 3.2 24.9 + - - +
1074A SER* 3.8 4.3 - - - +
1075A LYS 3.4 0.2 - - - -
1076A PHE* 1.3 82.4 - - - +
1078A GLN* 1.3 61.0 + - - +
1079A ALA 3.4 0.3 + - - -
1080A ILE* 3.4 24.9 - - - +
56F TYR* 3.1 49.9 + - + +
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Residues in contact with GLN1078 (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 SER 3.0 16.1 + - - +
1075A LYS* 3.7 28.9 - - - +
1077A ASN* 1.3 76.4 - - - +
1079A ALA* 1.3 62.3 + - - +
1080A ILE* 3.4 6.9 + - - +
1082A HIS* 4.5 10.1 + - - +
56F TYR* 5.0 3.3 - - - -
126F THR* 5.9 2.2 - - - +
127F ASP* 2.8 41.3 + - + +
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Residues in contact with ALA1079 (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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896A LEU* 4.3 9.9 - - + +
897A ALA* 3.5 23.8 + - - +
900A SER* 4.6 19.4 - - - +
901A VAL* 6.1 0.7 - - + -
980A PRO* 4.1 24.7 - - + -
1075A LYS 3.0 13.9 + - - +
1076A PHE 3.0 12.6 + - - +
1078A GLN* 1.3 74.7 - - - +
1080A ILE* 1.3 68.2 + - - +
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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
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895A GLY* 3.1 21.8 - - - +
896A LEU* 3.5 18.1 - - + +
897A ALA* 4.4 1.6 - - - +
1022A ILE* 3.7 40.6 - - + +
1076A PHE* 3.6 6.5 + - + +
1077A ASN* 3.4 22.4 - - - +
1078A GLN 3.6 3.8 - - - +
1079A ALA* 1.3 82.7 - - - +
1081A ALA* 1.3 72.1 + - - +
1082A HIS* 3.6 15.7 - - + -
54F THR* 5.7 6.5 - - - +
56F TYR* 5.8 3.1 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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