Contacts of the helix formed by residues 87 - 96 (chain S) in PDB entry 5JPQ
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 SER 87 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84S GLU* 3.8 31.6 - - - -
85S PRO 3.3 4.0 + - - -
86S TYR* 1.3 81.1 - - - +
88S LYS* 1.3 65.5 + - - +
89S VAL* 3.3 10.5 + - - -
90S SER* 3.4 12.3 + - - -
91S ARG* 3.3 19.6 + - - +
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Residues in contact with LYS 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86S TYR 3.9 0.2 + - - -
87S SER* 1.3 73.7 - - - +
89S VAL* 1.3 57.5 + - - +
91S ARG* 3.5 7.3 + - - +
92S ILE* 2.8 28.3 + - - +
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Residues in contact with VAL 89 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5S TYR* 4.0 26.7 - - + -
16S TYR* 4.9 11.4 - - + -
17S ASP 4.9 5.2 - - - +
18S GLU* 5.8 3.4 - - - +
20S GLY* 5.7 4.7 - - - -
87S SER* 3.2 7.0 - - - -
88S LYS* 1.3 76.3 - - - +
90S SER* 1.3 58.7 + - - +
92S ILE* 3.1 9.1 + - - +
93S PHE* 2.8 30.3 + - - +
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Residues in contact with SER 90 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66S GLU* 5.5 10.1 - - - -
85S PRO 4.8 7.0 - - - -
86S TYR* 5.2 1.3 - - - -
87S SER* 3.4 22.7 + - - -
89S VAL* 1.3 77.4 - - - +
91S ARG* 1.3 60.5 + - - +
93S PHE* 3.7 6.9 - - - +
94S ARG* 3.3 21.7 + - - +
169W PHE 5.8 0.2 - - - -
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Residues in contact with ARG 91 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86S TYR 5.6 0.4 - - - +
87S SER 3.3 10.8 + - - +
88S LYS* 3.5 10.3 - - - +
89S VAL 3.2 0.2 - - - -
90S SER* 1.3 76.3 - - - +
92S ILE* 1.3 65.4 + - - +
94S ARG* 2.9 7.3 + - - +
95S GLU* 2.8 25.1 + - - +
146W ASN* 5.2 2.7 - - - +
168W LYS 5.4 4.7 - - - +
169W PHE 4.8 14.1 - - - +
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Residues in contact with ILE 92 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20S GLY* 5.0 17.9 - - - +
88S LYS 2.8 20.5 + - - +
89S VAL* 3.1 10.3 + - - +
91S ARG* 1.3 72.6 - - - +
93S PHE* 1.3 63.1 + - - +
95S GLU* 3.6 16.2 + - - +
96S SER* 3.7 10.0 + - - -
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Residues in contact with PHE 93 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7S ILE* 5.0 16.6 - - + -
89S VAL 2.8 15.9 + - - +
90S SER* 3.7 9.0 - - - +
92S ILE* 1.3 78.0 - - - +
94S ARG* 1.3 61.8 + - - +
96S SER* 3.3 14.5 + - - -
97S LEU* 3.4 10.6 + - - +
100S VAL* 5.6 2.4 - - - +
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Residues in contact with ARG 94 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90S SER 3.3 13.4 + - - +
91S ARG* 2.9 6.2 + - - +
93S PHE* 1.3 75.0 - - + +
95S GLU* 1.3 64.9 + - - +
96S SER 3.1 2.7 - - - -
97S LEU* 3.2 20.6 + - - +
98S PRO 4.9 0.3 - - - -
144W VAL 5.1 2.5 - - - +
145W GLU* 3.9 10.3 - - - +
146W ASN* 3.3 35.9 + - + +
169W PHE 5.7 3.8 - - - +
170W PHE* 6.4 0.2 - - - -
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Residues in contact with GLU 95 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91S ARG 2.8 15.7 + - - +
92S ILE* 3.7 11.2 - - - +
93S PHE 3.3 0.2 - - - -
94S ARG* 1.3 77.7 - - - +
96S SER* 1.3 58.0 + - - +
97S LEU 3.4 0.8 + - - -
98S PRO* 5.2 1.4 - - - +
146W ASN* 4.1 10.9 - - + +
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Residues in contact with SER 96 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92S ILE 3.7 8.3 + - - -
93S PHE* 3.3 10.3 + - - -
94S ARG 3.1 0.4 - - - -
95S GLU* 1.3 78.4 - - - +
97S LEU* 1.3 53.8 + - - +
98S PRO* 3.5 3.4 - - - -
99S LYS* 3.1 13.1 + - - +
100S VAL* 2.8 39.9 + - - +
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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