Contacts of the helix formed by residues 85 - 93 (chain P) in PDB entry 2X86
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 ASP 85 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83P GLU* 2.9 22.9 + - - +
84P TRP* 1.3 74.8 - - - +
86P GLY* 1.3 57.1 + - - +
87P LYS* 2.9 12.4 + - - +
88P TYR* 2.7 33.4 + - + +
89P MET* 2.9 28.5 + - - +
139P VAL* 5.1 0.4 - - - -
34Q LYS* 3.2 37.1 + - + +
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Residues in contact with GLY 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84P TRP 3.0 9.1 + - - -
85P ASP* 1.3 70.2 + - - +
87P LYS* 1.3 60.7 + - - +
89P MET* 4.1 1.3 - - - -
90P MET* 2.8 36.2 + - - +
139P VAL* 4.1 16.4 - - - -
33Q LEU* 2.9 26.2 + - - -
34Q LYS 3.3 0.6 + - - -
36Q GLY* 4.0 9.0 - - - -
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Residues in contact with LYS 87 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85P ASP* 2.9 9.3 + - - +
86P GLY* 1.3 76.8 - - - +
88P TYR* 1.3 63.1 + - - +
90P MET* 3.9 2.9 - - - +
91P ASP* 3.0 44.4 + - - +
32Q ASN* 4.4 8.3 - - - +
33Q LEU* 3.3 10.7 + - - +
34Q LYS* 3.9 22.2 - - + +
50Q TYR* 6.5 0.2 - - - -
52Q ASP* 3.6 38.4 + - + +
54Q GLU* 5.4 4.6 - - - +
55Q ASP* 5.5 1.2 + - - -
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Residues in contact with TYR 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53P LYS* 3.0 25.9 + - - -
78P CYS* 3.6 32.9 - - + +
83P GLU* 4.6 14.1 - - + -
85P ASP* 2.7 29.7 + - + +
87P LYS* 1.3 74.4 - - - +
89P MET* 1.3 67.6 + - - +
91P ASP* 3.1 6.7 + - + +
92P ASN* 2.8 55.3 + - + +
400P NAP 3.4 10.4 + - - -
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Residues in contact with MET 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78P CYS* 3.9 16.8 - - - +
80P SER 3.9 10.3 - - - +
83P GLU* 3.4 48.5 - - + +
85P ASP 2.9 16.4 + - - +
86P GLY* 3.3 8.3 + - - +
88P TYR* 1.3 79.5 - - - +
90P MET* 1.3 57.7 + - - +
92P ASN* 5.0 0.4 - - - -
93P ASN* 2.8 59.7 + - - +
139P VAL* 3.8 13.9 - - + +
140P PHE* 3.9 16.8 - - - +
143P SER* 3.6 20.4 - - - +
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Residues in contact with MET 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86P GLY* 2.8 24.3 + - - +
87P LYS* 4.1 2.7 - - - +
89P MET* 1.3 73.1 - - - +
91P ASP* 1.3 57.5 + - - +
94P TYR* 3.2 28.7 + - + +
95P GLN* 2.8 29.2 + - - +
139P VAL* 5.0 4.0 - - - -
142P TYR* 4.0 21.3 - - + -
143P SER* 3.9 23.1 - - - -
146P LEU* 3.6 33.0 - - + -
33Q LEU* 3.7 19.7 - - + -
50Q TYR* 4.2 28.3 - - + -
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Residues in contact with ASP 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57P LEU* 6.1 0.2 - - - +
87P LYS* 3.0 41.4 + - - +
88P TYR* 3.7 6.6 - - + +
90P MET* 1.3 77.2 - - - +
92P ASN* 1.3 60.2 + - + +
95P GLN* 3.3 19.9 - - - +
96P TYR* 2.9 31.0 + - - +
52Q ASP* 5.3 3.7 - - - +
55Q ASP* 4.3 14.3 - - - +
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Residues in contact with ASN 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53P LYS* 2.8 27.7 + - - +
74P HIS* 5.7 0.5 + - - -
76P GLY 5.1 0.7 - - - +
77P ALA* 3.8 1.2 - - - -
78P CYS* 3.2 8.1 - - - +
88P TYR* 2.8 47.9 + - + +
89P MET 4.4 0.2 - - - +
91P ASP* 1.3 77.1 - - + +
93P ASN* 1.3 72.3 + - - +
96P TYR* 3.1 22.9 - - - +
400P NAP 2.9 37.4 + - - -
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Residues in contact with ASN 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76P GLY 5.8 0.7 - - - -
77P ALA* 3.4 11.7 - - + +
78P CYS* 2.8 46.3 + - - -
89P MET* 2.8 28.6 + - - +
92P ASN* 1.3 84.0 + - - +
94P TYR* 1.3 64.1 + - - +
97P SER* 2.8 33.1 + - - -
140P PHE* 4.0 8.5 - - - -
143P SER* 3.2 29.0 + - - +
144P LYS* 4.6 7.1 - - + +
147P PHE* 6.0 0.2 - - - -
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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