Contacts of the strand formed by residues 92 - 99 (chain S) in PDB entry 2A3W
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 VAL 92 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37S PHE 4.1 0.2 - - - +
38S ARG* 3.2 7.6 - - - +
39S ALA* 2.9 49.0 + - + +
65S LYS* 6.2 0.4 - - - +
71S TYR* 3.6 23.6 - - + +
86S GLU* 4.4 4.7 - - + +
90S ALA 4.3 6.1 - - - +
91S PRO* 1.3 76.3 - - - +
93S HIS* 1.3 66.3 + - - +
94S ILE* 3.7 24.7 - - + -
109S ILE* 3.7 24.5 - - + -
110S ASN* 3.6 10.1 - - - +
203S TRP* 4.8 0.6 - - - -
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Residues in contact with HIS 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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36S CYS* 4.0 11.3 - - - +
37S PHE* 3.7 10.8 + - - -
38S ARG* 3.6 38.8 - - + +
92S VAL* 1.3 73.9 - - - +
94S ILE* 1.3 63.2 + - - +
95S CYS* 3.4 31.6 + - - -
108S TRP* 3.5 4.8 + - - +
109S ILE* 3.5 2.8 - - - -
110S ASN* 2.8 39.3 + - - +
111S GLY 4.9 3.2 + - - -
156S ASP* 5.1 4.1 + - + +
169S ILE* 4.5 1.0 - - + +
172S ALA* 3.8 12.0 + - + +
173S TYR* 3.5 52.4 - + + +
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Residues in contact with ILE 94 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35S LEU 3.7 0.5 - - - +
36S CYS* 3.0 4.5 - - - +
37S PHE* 2.9 73.2 + - + +
39S ALA* 4.7 2.5 - - + -
49S LEU* 3.8 11.7 - - + -
63S VAL* 4.9 2.7 - - + -
71S TYR* 3.7 17.9 - - + -
92S VAL* 3.7 26.5 - - + -
93S HIS* 1.3 79.1 - - - +
95S CYS* 1.3 74.4 + - - +
96S VAL* 4.7 1.3 - - + +
107S PHE* 4.3 16.8 - - + -
108S TRP 3.4 2.7 - - - -
109S ILE* 3.9 21.8 - - + -
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Residues in contact with CYS 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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34S THR* 4.9 0.4 - - + -
35S LEU 3.1 4.3 - - - -
36S CYS* 2.0 47.1 - - - -
93S HIS* 3.4 20.4 + - - -
94S ILE* 1.3 74.3 - - - +
96S VAL* 1.3 61.2 + - - +
106S GLU 4.2 0.9 - - - -
107S PHE* 3.5 5.4 - - - -
108S TRP* 2.8 44.3 + - + +
169S ILE* 3.8 33.0 - - + -
172S ALA* 4.4 2.2 - - - -
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Residues in contact with VAL 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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33S PHE* 3.9 10.3 - - + -
34S THR* 3.4 2.4 - - - -
35S LEU* 2.8 55.6 + - + +
37S PHE* 5.5 0.4 - - + -
63S VAL* 3.9 27.8 - - + -
73S LEU* 3.9 29.2 - - + -
94S ILE* 5.2 2.2 - - + -
95S CYS* 1.3 76.0 - - - +
97S SER* 1.3 65.7 + - - +
105S ALA* 5.3 0.4 - - + -
106S GLU 3.2 10.5 - - - +
107S PHE* 3.7 31.0 - - + -
169S ILE* 6.2 0.2 - - - -
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Residues in contact with SER 97 (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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33S PHE* 3.2 14.4 - - - -
34S THR* 3.7 16.6 - - - -
96S VAL* 1.3 79.1 - - - +
98S TRP* 1.3 61.7 + - - +
104S ILE 4.4 1.1 + - - -
105S ALA* 3.3 5.2 - - - +
106S GLU* 2.9 54.3 + - - +
108S TRP* 5.6 0.9 - - - -
163S VAL* 3.8 22.5 - - - +
164S LEU 4.9 2.9 - - - -
169S ILE* 5.6 4.5 - - - -
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Residues in contact with TRP 98 (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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30S LEU 4.1 4.3 - - - -
31S GLN 3.5 17.0 - - - -
32S ASN* 3.5 4.7 - - - -
33S PHE* 3.1 63.4 + + + +
73S LEU* 4.1 6.5 - - + -
75S ILE* 3.9 25.4 - - + -
97S SER* 1.3 75.3 - - - +
99S GLU* 1.3 65.1 - - - +
100S SER* 3.7 11.2 - - - -
103S GLY 3.3 18.8 + - - -
104S ILE 3.4 8.1 - - - -
105S ALA* 4.3 1.8 - - + -
119S LEU* 3.0 36.9 + - + +
120S ARG 3.3 22.7 - - - -
123S TYR* 3.2 26.0 - + - -
125S VAL* 3.5 22.4 - - + -
163S VAL* 3.9 4.5 - - - +
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Residues in contact with GLU 99 (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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199R LYS* 2.7 28.6 + - - -
32S ASN* 3.5 17.7 - - - +
98S TRP* 1.3 79.3 - - - +
100S SER* 1.3 51.8 + - - +
101S SER* 3.6 22.0 + - - +
102S SER* 2.6 26.7 + - - +
103S GLY* 2.7 37.2 + - - -
104S ILE* 3.2 9.4 + - + +
163S VAL* 3.7 21.2 - - + +
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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