Contacts of the strand formed by residues 90 - 100 (chain F) in PDB entry 1VHA
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 TYR 90 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126D GLU* 4.7 3.8 + - - -
0F SER 3.8 21.6 + - - -
1F LEU 5.0 1.3 - - - -
3F ARG* 3.5 42.2 + - + +
53F ALA* 4.1 25.4 - - + -
82F PHE* 4.8 2.9 - - - -
85F VAL* 3.1 32.0 + - + +
86F GLN* 3.6 23.3 + - - +
88F LYS* 4.0 26.9 - - + -
89F GLY* 1.3 78.9 - - - +
91F LYS* 1.3 60.7 + - - +
155F LEU* 3.8 20.4 - - + -
156F ILE 3.6 1.3 - - - -
157F ARG* 3.8 35.9 + - + -
158F GLN* 4.7 3.6 - - - +
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Residues in contact with LYS 91 (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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82F PHE* 4.8 7.0 - - + -
90F TYR* 1.3 75.1 - - - +
92F ILE* 1.3 79.0 + - + +
122F GLN 5.9 2.9 - - - +
127F GLN* 5.9 1.3 - - - +
155F LEU* 3.4 6.5 - - - +
156F ILE* 2.7 60.8 + - - +
157F ARG 5.4 0.8 + - - -
158F GLN* 3.5 42.9 + - - +
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Residues in contact with ILE 92 (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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49F ILE* 4.7 8.7 - - + -
82F PHE* 3.3 36.8 - - + -
85F VAL* 5.1 2.5 - - + -
91F LYS* 1.3 87.5 - - + +
93F GLY* 1.3 72.2 + - - +
94F ASN* 3.8 12.1 - - - +
95F VAL* 4.8 9.6 - - + +
121F LEU* 4.3 27.1 - - + +
123F CYS* 4.1 28.6 - - + +
127F GLN* 3.1 20.0 + - + +
154F LEU 4.1 2.7 - - - +
155F LEU* 4.2 16.4 - - + -
156F ILE* 4.8 1.9 - - - +
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Residues in contact with GLY 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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0E SER* 4.0 9.0 + - - -
2E ILE 5.5 0.9 - - - -
3E ARG* 5.4 0.7 - - - -
91F LYS 3.4 3.6 + - - -
92F ILE* 1.3 70.7 - - - +
94F ASN* 1.3 62.6 + - - +
127F GLN* 3.1 26.5 + - - +
154F LEU* 2.7 23.3 + - - -
156F ILE* 3.4 30.7 - - - -
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Residues in contact with ASN 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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3E ARG* 2.7 50.7 - - - +
4E ILE* 2.8 54.5 + - - +
51E GLY 4.6 1.2 + - - -
52E ALA* 4.0 2.0 + - - +
92F ILE* 4.1 2.5 - - - -
93F GLY* 1.3 77.6 - - - +
95F VAL* 1.3 74.9 + - - +
127F GLN* 3.4 10.1 - - - +
153F ALA* 3.9 0.7 - - - -
154F LEU* 3.1 32.6 + - - +
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Residues in contact with VAL 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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3E ARG* 5.5 0.3 + - - -
45F LEU* 3.3 42.4 - - + -
49F ILE* 4.7 3.8 - - + -
92F ILE* 4.8 9.6 - - + -
94F ASN* 1.3 84.7 + - - +
96F ASP* 1.3 64.0 + - - +
97F ILE* 3.4 11.2 - - + -
117F ILE* 5.0 0.9 - - + -
121F LEU* 4.4 12.6 - - + -
127F GLN 2.8 15.4 + - - +
128F VAL* 4.4 19.5 - - + -
129F ASN* 2.9 27.9 + - - +
152F VAL 3.9 2.5 - - - +
153F ALA* 3.9 15.7 - - + -
154F LEU 5.8 0.2 - - - +
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Residues in contact with ASP 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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4E ILE 4.0 12.1 - - - +
5E GLY* 3.4 0.9 - - - -
6E HIS* 2.8 32.7 + - - +
51E GLY* 3.3 26.2 - - - +
94F ASN* 4.6 0.2 - - - +
95F VAL* 1.3 75.3 - - - +
97F ILE* 1.3 68.4 + - - +
98F THR* 5.3 0.6 + - - -
129F ASN* 2.7 28.5 + - - -
131F LYS* 3.5 9.9 - - - -
150F GLU 4.4 0.2 - - - +
151F ALA* 3.6 1.4 - - - -
152F VAL* 3.1 45.9 + - + +
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Residues in contact with ILE 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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41F ALA* 4.3 12.3 - - + +
45F LEU* 3.5 22.7 - - + -
95F VAL* 3.4 24.2 - - + -
96F ASP* 1.3 90.7 + - - +
98F THR* 1.3 61.2 + - - +
99F ILE* 4.0 15.7 - - + -
117F ILE* 5.8 3.1 - - + -
129F ASN 2.9 12.4 + - - +
130F VAL* 3.5 17.2 - - + -
131F LYS* 2.7 36.8 + - - +
149F CYS* 3.7 17.3 - - - -
150F GLU 3.7 1.3 - - - -
151F ALA* 3.4 26.2 - - + -
152F VAL 4.5 1.1 - - - +
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Residues in contact with THR 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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6E HIS* 3.3 26.2 + - - +
7E GLY* 4.8 0.2 - - - -
8E PHE* 4.4 17.3 - - + +
96F ASP* 5.3 0.5 + - - -
97F ILE* 1.3 72.2 - - - +
99F ILE* 1.3 61.9 + - - +
100F ILE* 3.7 4.8 + - + +
131F LYS* 3.1 34.9 - - + +
133F THR* 4.0 25.4 - - + -
149F CYS* 3.2 5.8 - - - -
150F GLU* 2.8 45.4 + - - +
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Residues in contact with ILE 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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40F VAL* 4.9 9.9 - - + -
41F ALA* 4.3 14.6 - - + -
97F ILE* 4.0 11.4 - - + -
98F THR* 1.3 74.5 - - - +
100F ILE* 1.3 62.0 + - - +
101F ALA* 3.9 11.2 + - + -
106F MSE 4.1 28.5 - - + -
110F ILE* 4.8 3.6 - - + -
113F MSE 4.1 17.9 - - + -
130F VAL* 3.8 23.3 - - + -
131F LYS 2.8 15.9 + - - +
132F ALA* 3.5 5.1 - - + +
133F THR* 2.9 30.5 + - - +
147F ILE* 5.8 3.1 - - + -
148F ALA 3.7 9.9 - - - +
149F CYS* 4.2 7.0 - - - -
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Residues in contact with ILE 100 (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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8E PHE* 3.4 41.3 - - + -
8F PHE* 5.3 6.3 - - + -
98F THR* 4.0 11.4 - - + +
99F ILE* 1.3 74.1 - - - +
101F ALA* 1.3 61.5 + - - +
133F THR* 3.5 10.3 - - + +
134F THR 4.8 0.7 - - - -
135F THR* 3.6 32.5 - - + +
141F THR* 3.7 11.8 - - + +
147F ILE* 3.7 0.2 - - - -
148F ALA* 2.6 54.9 + - + +
149F CYS 5.3 0.4 - - - -
150F GLU* 4.9 13.9 - - + +
170F ACY 4.2 11.0 - - + -
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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