Contacts of the strand formed by residues 92 - 99 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37F PHE 4.1 0.2 - - - +
38F ARG* 3.4 7.7 - - - +
39F ALA* 2.9 48.0 + - + +
65F LYS* 6.2 0.7 - - - +
71F TYR* 3.7 16.2 - - - +
86F GLU* 4.5 4.0 - - + +
90F ALA 4.4 6.1 - - - +
91F PRO* 1.3 76.9 - - - +
93F HIS* 1.3 67.0 - - - +
94F ILE* 3.8 24.4 + - + +
109F ILE* 3.6 30.3 - - + -
110F ASN* 3.5 9.2 - - - +
203F TRP* 4.8 0.4 - - - -
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Residues in contact with HIS 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F CYS* 4.0 12.2 - - + +
37F PHE* 3.6 15.3 + - - -
38F ARG* 3.8 34.5 - - + +
92F VAL* 1.3 76.2 - - - +
94F ILE* 1.3 62.1 + - - +
95F CYS* 3.3 34.0 + - - -
108F TRP 3.5 1.5 + - - +
109F ILE* 3.4 5.2 - - - -
110F ASN* 2.8 37.7 + - - +
111F GLY* 4.9 3.8 + - - -
156F ASP* 5.2 4.5 + - + +
169F ILE* 4.4 0.8 - - - +
172F ALA* 3.7 12.2 + - + +
173F TYR* 3.5 52.0 - + + +
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Residues in contact with ILE 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F LEU 3.7 0.5 - - - +
36F CYS* 3.1 3.5 - - - +
37F PHE* 2.9 73.6 + - + +
39F ALA* 4.7 2.9 - - + -
49F LEU* 3.8 11.4 - - + -
63F VAL* 5.0 1.8 - - + -
71F TYR* 3.6 23.3 - - + -
92F VAL* 3.8 26.7 - - + -
93F HIS* 1.3 80.7 - - - +
95F CYS* 1.3 72.7 + - - +
96F VAL* 4.8 1.1 - - + +
107F PHE* 4.3 16.4 - - + -
108F TRP 3.4 2.5 - - - -
109F ILE* 4.0 18.4 - - + -
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Residues in contact with CYS 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F THR* 4.8 0.4 - - + -
35F LEU 3.2 3.6 - - - -
36F CYS* 2.0 46.9 - - - -
93F HIS* 3.3 23.1 - - - -
94F ILE* 1.3 74.6 - - - +
96F VAL* 1.3 60.5 + - - +
106F GLU 3.7 0.4 - - - +
107F PHE* 3.4 5.0 - - - -
108F TRP* 2.7 47.6 + - + +
169F ILE* 3.8 32.3 - - + -
172F ALA* 4.4 2.9 - - - -
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Residues in contact with VAL 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F PHE* 3.9 10.2 - - + -
34F THR* 3.3 2.8 - - - -
35F LEU* 2.7 56.1 + - + +
37F PHE* 5.6 0.7 - - + -
63F VAL* 3.8 28.5 - - + -
73F LEU* 4.2 17.0 - - + -
94F ILE* 5.1 2.7 - - + -
95F CYS* 1.3 76.9 - - - +
97F SER* 1.3 68.8 + - - +
105F ALA* 5.2 0.4 - - + -
106F GLU 3.2 12.1 - - - +
107F PHE* 3.6 35.0 - - + -
169F ILE* 6.2 0.2 - - - -
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Residues in contact with SER 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F PHE* 3.1 15.5 - - - -
34F THR* 3.5 17.5 - - - -
96F VAL* 1.3 79.4 - - - +
98F TRP* 1.3 62.8 + - - +
104F ILE 5.2 1.0 + - - -
105F ALA* 3.2 6.5 - - - +
106F GLU* 3.0 50.3 + - - +
108F TRP* 5.2 1.9 + - - -
163F VAL* 3.6 23.2 - - - +
164F LEU 4.9 1.7 + - - -
169F ILE* 5.7 3.1 - - - -
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Residues in contact with TRP 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F LEU 4.0 4.9 - - - -
31F GLN 3.4 18.6 - - - -
32F ASN* 3.5 4.3 - - - -
33F PHE* 3.1 62.4 + + + +
73F LEU* 4.1 5.6 - - + -
75F ILE* 3.8 26.4 - - + +
97F SER* 1.3 76.6 - - - +
99F GLU* 1.3 64.1 + - - +
100F SER* 3.7 10.3 - - - -
103F GLY 3.3 18.5 + - - -
104F ILE 3.3 12.1 - - - -
105F ALA* 4.2 1.8 - - + -
119F LEU* 2.9 38.6 + - + +
120F ARG 3.2 23.3 - - - -
123F TYR 3.3 25.1 - - - -
125F VAL* 3.5 21.8 - - + -
163F VAL* 3.6 4.5 - - - +
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Residues in contact with GLU 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F ASN* 3.6 17.2 - - - +
98F TRP* 1.3 79.0 - - - +
100F SER* 1.3 54.6 + - - +
101F SER* 3.6 20.4 + - - +
102F SER* 2.6 26.7 + - - +
103F GLY* 2.7 36.7 + - - -
104F ILE* 3.1 10.7 + - + +
163F VAL* 3.8 21.1 - - + +
199J LYS* 2.7 27.0 + - - -
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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