Contacts of the helix formed by residues 1077 - 1088 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1117A ARG* 4.2 24.7 - - - -
1076B HIS* 1.3 79.4 - - - +
1078B ASP* 1.3 66.1 + - - -
1079B SER* 3.2 6.9 + - - -
1080B SER* 3.4 10.8 + - - -
1081B ILE* 3.3 18.9 + - - +
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Residues in contact with ASP1078 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116A MET* 4.8 8.6 - - + +
1117A ARG* 3.4 31.2 + - - +
1066B VAL* 3.8 14.2 - - + +
1070B MET* 3.1 29.9 - - + +
1077B GLY* 1.3 71.6 - - - -
1079B SER* 1.3 64.1 + - - +
1081B ILE* 3.1 4.0 + - - +
1082B TYR* 2.6 37.7 + - - +
1116B MET* 4.0 22.3 - - + +
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Residues in contact with SER1079 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117A ARG* 5.0 9.9 + - - -
1077B GLY* 4.8 3.8 - - - -
1078B ASP* 1.3 83.1 + - - +
1080B SER* 1.3 68.0 + - - +
1082B TYR* 4.4 5.8 - - - +
1083B ASP* 2.9 41.4 + - - -
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Residues in contact with SER1080 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040B VAL* 5.2 3.4 - - - -
1074B HIS* 5.5 4.5 - - - -
1076B HIS* 5.2 8.0 - - - +
1077B GLY* 3.4 14.5 + - - -
1078B ASP 3.3 0.4 - - - -
1079B SER* 1.3 81.7 + - - +
1081B ILE* 1.3 67.8 + - - +
1083B ASP* 3.9 4.1 - - - +
1084B ALA* 3.1 21.0 + - - +
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Residues in contact with ILE1081 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040B VAL* 4.4 7.9 - - + -
1044B ILE* 3.8 9.7 - - + +
1066B VAL* 4.2 13.9 - - + +
1069B ILE* 3.6 47.8 - - + -
1070B MET* 3.7 33.2 - - + +
1074B HIS* 3.6 29.2 - - + +
1076B HIS 4.1 1.8 - - - +
1077B GLY 3.3 14.7 + - - +
1078B ASP 3.1 6.1 + - - +
1080B SER* 1.3 78.9 - - - +
1082B TYR* 1.3 65.3 + - - +
1084B ALA* 3.2 2.6 + - - +
1085B MET* 3.1 19.5 + - + +
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Residues in contact with TYR1082 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062B SER* 3.6 16.2 - - - -
1066B VAL* 4.0 19.5 - - + +
1078B ASP 2.6 21.9 + - - +
1079B SER* 4.0 4.9 - - - +
1081B ILE* 1.3 72.6 - - - +
1083B ASP* 1.3 66.2 + - - +
1085B MET* 3.1 10.0 + - - +
1086B VAL* 2.9 55.5 + - + +
1101B MET* 4.2 7.8 - - + -
1104B ASN 5.2 0.2 + - - -
1113B PRO* 5.0 3.9 - - + +
1114B ALA 2.8 28.4 + - - -
1115B ALA* 3.7 2.9 - - - -
1116B MET* 3.4 42.8 - - + -
1119B THR* 2.9 22.6 + - - +
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Residues in contact with ASP1083 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1079B SER* 2.9 36.3 + - - +
1080B SER* 3.9 4.1 - - - +
1082B TYR* 1.3 87.9 - - - +
1084B ALA* 1.3 62.1 + - - +
1086B VAL* 3.3 9.7 + - - +
1087B ARG* 3.0 23.7 + - - +
1113B PRO* 5.9 2.9 - - - +
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Residues in contact with ALA1084 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040B VAL* 4.0 21.5 - - + -
1041B GLN* 5.1 6.0 + - + +
1044B ILE* 3.7 13.7 - - + -
1080B SER 3.1 17.3 + - - +
1081B ILE 3.5 4.0 - - - +
1083B ASP* 1.3 75.1 - - - +
1085B MET* 1.3 64.1 + - - +
1086B VAL 3.3 0.2 + - - -
1087B ARG* 3.4 8.3 + - - +
1088B MET* 3.0 29.2 + - - +
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Residues in contact with MET1085 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044B ILE* 3.6 25.2 - - + +
1048B MET* 4.5 10.1 - - - +
1062B SER* 4.7 5.6 - - - -
1065B SER* 4.4 22.4 - - - -
1066B VAL* 4.5 16.6 - - - -
1069B ILE* 5.5 2.9 - - - -
1081B ILE* 3.1 12.8 + - + +
1082B TYR* 3.3 17.5 - - + +
1084B ALA* 1.3 76.2 - - - +
1086B VAL* 1.3 63.9 + - - +
1088B MET* 3.4 17.1 + - - +
1089B SER* 3.6 10.2 + - - -
1099B VAL* 4.0 14.1 - - + +
1101B MET* 4.2 15.7 - - + -
1121B ALA* 4.7 7.9 - - - -
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Residues in contact with VAL1086 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082B TYR* 2.9 55.9 + - + +
1083B ASP* 3.3 11.4 - - - +
1084B ALA 3.1 0.2 - - - -
1085B MET* 1.3 73.4 - - - +
1087B ARG* 1.3 56.1 - - - +
1089B SER* 2.7 39.2 + - - -
1090B GLN* 3.2 13.4 - - - +
1101B MET* 4.2 9.6 - - - -
1105B ASN* 3.8 27.4 - - + +
1113B PRO* 4.0 21.5 - - + -
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Residues in contact with ARG1087 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041B GLN* 5.5 8.1 - - - +
1083B ASP 3.0 8.9 + - - +
1084B ALA* 3.7 9.6 - - - +
1086B VAL* 1.3 75.2 - - - +
1088B MET* 1.3 58.8 + - + +
1089B SER 2.8 10.7 + - - -
1090B GLN* 3.1 33.7 + - - +
1093B LYS* 3.9 35.2 + - + +
1094B ASN* 2.9 31.8 + - - +
1165B ASN 5.9 0.6 + - - -
1167B SER* 6.2 1.4 - - - +
1168B THR* 4.1 24.0 - - - +
1261B TYR* 3.9 18.6 + - - -
1262B GLU* 4.5 7.7 + - - -
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Residues in contact with MET1088 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041B GLN* 3.8 42.0 - - + +
1044B ILE* 3.2 37.5 - - + -
1045B LEU* 4.1 11.9 - - + -
1084B ALA 3.0 14.5 + - - +
1085B MET* 3.9 10.8 - - - +
1086B VAL 3.2 1.0 - - - -
1087B ARG* 1.3 75.6 - - + +
1089B SER* 1.3 57.0 + - - +
1090B GLN 3.6 0.2 - - - -
1094B ASN* 3.3 15.3 - - - +
1097B ILE* 3.4 6.2 - - - +
1098B LEU* 3.0 43.7 + - + -
1099B VAL* 3.1 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
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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