Contacts of the strand formed by residues 92 - 99 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G PHE 4.1 0.2 - - - +
38G ARG* 3.3 7.1 - - - +
39G ALA* 3.0 46.2 + - + +
65G LYS* 6.3 0.2 - - - +
71G TYR* 3.7 17.9 - - + +
86G GLU* 4.5 4.3 - - + +
90G ALA 4.4 5.4 - - - +
91G PRO* 1.3 77.0 - - - +
93G HIS* 1.3 67.6 + - - +
94G ILE* 3.8 25.3 + - + -
109G ILE* 3.6 30.7 - - + -
110G ASN* 3.6 9.0 - - - +
203G TRP* 4.8 1.0 - - - -
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Residues in contact with HIS 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G CYS* 4.1 11.2 - - + +
37G PHE* 3.6 14.9 + - - -
38G ARG* 3.8 35.0 - - + +
92G VAL* 1.3 74.9 - - - +
94G ILE* 1.3 61.0 + - - +
95G CYS* 3.4 32.7 + - - -
108G TRP* 3.5 1.5 + - - +
109G ILE* 3.4 4.9 - - - -
110G ASN* 2.8 35.4 + - - -
111G GLY* 4.9 3.8 + - - -
156G ASP* 5.2 4.1 + - + +
169G ILE* 4.4 0.8 - - + +
172G ALA* 3.7 13.0 + - + +
173G TYR* 3.4 55.9 - + + +
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Residues in contact with ILE 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G LEU 3.8 0.7 - - - +
36G CYS* 3.1 4.2 - - - +
37G PHE* 2.9 71.0 + - + +
39G ALA* 4.7 2.9 - - + -
49G LEU* 4.1 11.2 - - + -
63G VAL* 5.0 2.5 - - + -
71G TYR* 3.6 22.9 - - + -
92G VAL* 3.8 21.8 - - + -
93G HIS* 1.3 78.7 - - - +
95G CYS* 1.3 67.2 + - - +
96G VAL* 4.8 1.6 - - + +
107G PHE* 4.2 22.4 - - + -
108G TRP 3.4 2.9 - - - -
109G ILE* 3.9 23.8 - - + -
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Residues in contact with CYS 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G LEU 3.2 3.8 - - - -
36G CYS* 2.0 47.3 - - - -
93G HIS* 3.4 22.2 - - - -
94G ILE* 1.3 73.3 - - - +
96G VAL* 1.3 60.1 + - - +
106G GLU 3.6 0.7 - - - +
107G PHE* 3.4 4.9 - - - -
108G TRP* 2.7 48.6 + - + +
169G ILE* 3.8 34.3 - - + -
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Residues in contact with VAL 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G PHE* 3.9 11.1 - - + -
34G THR* 3.3 2.9 - - - -
35G LEU* 2.7 56.5 + - + +
37G PHE* 5.7 0.4 - - + -
63G VAL* 3.9 26.9 - - + -
73G LEU* 4.2 18.4 - - + -
94G ILE* 5.4 2.0 - - + -
95G CYS* 1.3 76.7 - - - +
97G SER* 1.3 69.0 + - - +
105G ALA* 5.3 0.2 - - + -
106G GLU 3.1 11.9 - - - +
107G PHE* 3.7 35.9 - - + -
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Residues in contact with SER 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G PHE* 3.2 13.7 - - - -
34G THR* 3.4 18.4 - - - -
96G VAL* 1.3 78.5 - - - +
98G TRP* 1.3 61.7 + - - +
104G ILE 3.8 1.5 + - - +
105G ALA* 3.2 5.2 - - - +
106G GLU* 2.8 52.9 + - - +
108G TRP* 5.7 1.3 - - - -
163G VAL* 3.6 23.3 - - - +
164G LEU 4.8 2.5 - - - -
169G ILE* 5.4 3.6 - - - -
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Residues in contact with TRP 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G LEU 4.2 0.7 - - - -
31G GLN 3.6 17.7 - - - -
32G ASN* 3.4 5.0 - - - -
33G PHE* 3.0 63.8 + + + +
73G LEU* 4.2 6.3 - - + -
75G ILE* 3.8 26.7 - - + -
97G SER* 1.3 75.9 - - - +
99G GLU* 1.3 66.4 + - - +
100G SER* 3.7 11.2 - - - -
103G GLY 3.3 18.8 + - - -
104G ILE 3.3 9.2 - - - -
105G ALA* 4.2 2.0 - - + -
119G LEU* 3.0 36.7 + - + +
120G ARG 3.3 22.7 - - - -
123G TYR* 3.2 26.9 - + - -
125G VAL* 3.6 23.3 - - + -
163G VAL* 3.6 4.4 - - - +
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Residues in contact with GLU 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199F LYS* 2.8 28.8 + - - -
32G ASN* 3.7 17.8 - - - +
98G TRP* 1.3 78.0 + - - +
100G SER* 1.3 55.9 + - - +
101G SER* 3.5 21.8 + - - +
102G SER* 2.6 26.1 + - - +
103G GLY* 2.7 37.1 + - - -
104G ILE* 3.1 10.9 + - + +
163G VAL* 3.8 20.9 - - + +
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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