Contacts of the helix formed by residues 1077 - 1088 (chain A) in PDB entry 4Z4Q
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 GLY1077 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1076A HIS* 1.3 80.1 - - - +
1078A ASP* 1.3 66.1 + - - -
1079A SER* 3.3 5.5 + - - -
1080A SER* 3.3 18.6 + - - -
1081A ILE* 3.4 10.8 + - - +
1117B ARG* 3.7 28.4 - - - +
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Residues in contact with ASP1078 (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 VAL* 3.9 14.4 - - + -
1070A MET* 3.1 30.6 - - + +
1077A GLY* 1.3 67.9 - - - -
1079A SER* 1.3 78.4 + - - +
1081A ILE* 2.9 2.9 + - - +
1082A TYR* 2.7 26.5 + - - +
1116A MET* 3.8 25.7 - - + +
1063B ALA* 5.9 0.2 - - + -
1116B MET* 5.3 6.8 - - + +
1117B ARG* 3.6 29.2 + - - +
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Residues in contact with SER1079 (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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1077A GLY* 3.3 3.0 + - - -
1078A ASP* 1.3 86.9 + - - +
1080A SER* 1.3 68.1 + - - +
1082A TYR* 4.8 4.0 - - - -
1083A ASP* 2.8 40.6 + - - -
1117B ARG* 5.4 6.3 + - - +
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Residues in contact with SER1080 (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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1040A VAL* 5.1 3.1 - - - -
1074A HIS* 5.4 5.2 - - - -
1076A HIS* 5.3 6.9 - - - +
1077A GLY* 3.3 14.7 + - - -
1078A ASP 3.3 0.4 - - - -
1079A SER* 1.3 80.0 + - - +
1081A ILE* 1.3 66.4 + - - +
1083A ASP* 3.3 5.1 + - - +
1084A ALA* 3.0 24.6 + - - +
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Residues in contact with ILE1081 (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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1040A VAL* 4.3 7.4 - - + -
1044A ILE* 3.6 10.6 - - + +
1066A VAL* 4.2 13.5 - - + +
1069A ILE* 3.7 48.2 - - + -
1070A MET* 3.9 33.7 - - + +
1074A HIS* 3.6 29.2 - - + -
1076A HIS 4.1 10.3 - - - +
1077A GLY 3.4 5.3 + - - +
1078A ASP* 2.9 10.3 + - - +
1080A SER* 1.3 73.8 - - - +
1082A TYR* 1.3 65.2 + - - +
1084A ALA* 3.3 2.8 + - - +
1085A MET* 3.1 18.1 + - + +
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Residues in contact with TYR1082 (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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1062A SER* 3.6 9.4 - - - -
1066A VAL* 4.1 19.7 - - + +
1078A ASP* 2.7 20.4 + - - +
1079A SER* 4.0 3.8 - - - +
1081A ILE* 1.3 76.3 - - - +
1083A ASP* 1.3 72.3 + - - +
1085A MET* 3.0 12.3 + - - +
1086A VAL* 2.8 51.3 + - + +
1101A MET* 4.0 5.2 - - + -
1104A ASN 5.0 0.3 + - - -
1113A PRO* 5.2 2.9 - - + -
1114A ALA 2.8 29.5 + - - -
1115A ALA* 3.6 3.3 - - - -
1116A MET* 3.5 37.9 - - + -
1119A THR* 2.8 35.6 + - - +
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Residues in contact with ASP1083 (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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1079A SER* 2.8 35.8 + - - +
1080A SER* 3.9 4.3 - - - +
1082A TYR* 1.3 80.7 - - - +
1084A ALA* 1.3 56.6 + - - +
1086A VAL* 3.2 9.5 + - - +
1087A ARG* 3.0 27.7 + - - +
1113A PRO* 5.8 4.0 - - - +
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Residues in contact with ALA1084 (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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1040A VAL* 4.1 21.1 - - + -
1041A GLN* 5.1 3.9 + - + +
1044A ILE* 3.6 14.1 - - + -
1080A SER 3.0 16.9 + - - +
1081A ILE 3.5 4.5 - - - +
1083A ASP* 1.3 73.3 - - - +
1085A MET* 1.3 65.8 + - - +
1086A VAL 3.1 1.6 - - - -
1087A ARG* 3.3 6.9 + - - +
1088A MET* 3.1 32.2 + - + +
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Residues in contact with MET1085 (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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1044A ILE* 3.6 16.9 - - + +
1048A MET* 4.4 11.9 - - - +
1062A SER* 4.7 5.4 - - - +
1065A SER* 4.4 18.2 - - - -
1066A VAL* 4.2 21.8 - - - -
1069A ILE* 5.3 2.7 - - - -
1081A ILE 3.1 12.9 + - - +
1082A TYR* 3.0 18.7 + - + +
1084A ALA* 1.3 77.2 - - - +
1086A VAL* 1.3 62.4 + - - +
1088A MET* 3.4 21.3 + - - +
1089A SER* 3.5 11.4 + - - -
1099A VAL* 4.1 13.2 - - + +
1101A MET* 4.0 17.9 - - + +
1121A ALA* 4.8 7.0 - - - -
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Residues in contact with VAL1086 (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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1082A TYR* 2.8 58.2 + - + +
1083A ASP* 3.5 9.6 - - - +
1084A ALA 3.1 0.4 - - - -
1085A MET* 1.3 74.9 - - - +
1087A ARG* 1.3 61.4 + - - +
1089A SER* 2.7 31.8 + - - -
1090A GLN* 2.9 15.9 - - - +
1101A MET* 4.0 10.8 - - - -
1105A ASN* 3.8 25.4 - - + +
1113A PRO* 3.8 23.3 - - + -
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Residues in contact with ARG1087 (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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1041A GLN* 5.3 9.9 - - - +
1083A ASP 3.0 15.8 + - - +
1084A ALA* 3.8 6.5 - - - +
1086A VAL* 1.3 77.3 - - - +
1088A MET* 1.3 60.2 + - + +
1089A SER 2.8 6.6 + - - -
1090A GLN* 3.0 32.9 + - - +
1093A LYS* 3.9 30.6 + - + +
1094A ASN* 3.0 26.8 + - - +
1167A SER* 6.1 2.6 - - - +
1168A THR* 4.0 26.8 + - - +
1261A TYR* 3.7 21.0 + - - -
1262A GLU* 4.0 7.5 + - - +
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Residues in contact with MET1088 (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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1041A GLN* 3.9 43.1 - - + +
1044A ILE* 3.1 50.0 - - + -
1045A LEU* 4.6 11.9 - - - -
1084A ALA 3.1 17.8 + - - +
1085A MET* 3.8 6.3 - - - +
1086A VAL 3.2 0.4 - - - -
1087A ARG* 1.3 75.0 - - + +
1089A SER* 1.3 57.4 + - - +
1090A GLN 3.5 0.4 - - - -
1094A ASN* 3.6 14.4 - - - +
1097A ILE* 3.4 7.5 - - - +
1098A LEU* 3.2 29.2 + - + -
1099A VAL* 3.2 33.7 + - + +
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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