Contacts of the strand formed by residues 90 - 100 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A SER 3.2 33.5 + - - -
1A LEU 4.9 2.2 - - - -
3A ARG* 3.3 37.0 + - + +
53A ALA* 4.3 16.6 - - + -
82A PHE* 4.8 0.2 - - - -
85A VAL* 3.1 29.4 + - + +
86A GLN* 3.4 21.9 + - - +
88A LYS* 4.0 29.2 - - + -
89A GLY* 1.3 79.6 - - - +
91A LYS* 1.3 60.1 + - - +
155A LEU* 4.0 24.5 - - + -
156A ILE* 3.2 22.9 - - - +
157A ARG* 3.7 21.7 + - + -
158A GLN* 3.2 11.3 - - - +
126B GLU* 4.7 3.1 + - - -
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Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PHE* 4.5 10.3 - - + -
86A GLN* 5.0 2.7 - - - +
90A TYR* 1.3 72.4 - - - +
92A ILE* 1.3 75.5 + - - +
93A GLY* 3.6 0.4 + - - -
127A GLN* 4.9 6.1 - - - +
155A LEU* 3.7 6.7 - - - +
156A ILE* 2.8 45.8 + - + +
157A ARG 4.8 3.1 - - - -
158A GLN* 3.3 45.1 - - + +
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Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ILE* 4.4 7.2 - - + -
82A PHE* 3.2 36.2 - - + -
85A VAL* 5.4 0.4 - - + -
91A LYS* 1.3 90.4 + - - +
93A GLY* 1.3 64.7 + - - +
94A ASN* 3.4 24.0 - - - +
95A VAL* 4.4 11.0 - - + -
121A LEU* 4.1 27.3 + - + +
123A CYS* 4.3 23.6 - - + +
127A GLN* 3.1 27.9 + - + +
154A LEU 4.2 2.0 - - - +
155A LEU* 4.2 16.8 - - + -
156A ILE* 4.8 0.4 - - - -
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Residues in contact with GLY 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LYS 3.6 2.0 + - - -
92A ILE* 1.3 72.1 - - - +
94A ASN* 1.3 62.8 + - - +
127A GLN* 3.0 24.8 + - - +
154A LEU* 2.7 22.0 + - - -
155A LEU* 4.2 0.2 - - - +
156A ILE* 3.8 27.4 - - - -
0C SER* 5.0 5.2 - - - -
2C ILE 5.4 3.6 - - - -
3C ARG* 4.5 4.1 + - - -
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Residues in contact with ASN 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ILE* 3.7 3.8 - - - -
93A GLY* 1.3 80.5 - - - +
95A VAL* 1.3 72.6 + - - +
127A GLN 3.3 13.7 - - - +
153A ALA* 3.8 0.5 - - - -
154A LEU* 3.0 31.5 + - - +
2C ILE 4.2 0.2 - - - +
3C ARG* 3.3 32.5 - - - +
4C ILE* 3.0 46.1 + - - +
51C GLY 4.7 0.8 + - - -
52C ALA* 3.4 19.2 + - - +
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Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 3.9 25.6 - - + -
49A ILE* 4.6 1.6 - - + -
92A ILE* 4.4 21.8 - - + -
94A ASN* 1.3 87.5 + - - +
96A ASP* 1.3 61.5 + - - +
97A ILE* 5.0 4.3 - - + -
117A ILE* 4.8 1.6 - - + -
121A LEU* 4.5 8.1 - - + -
127A GLN 2.9 16.4 + - - +
128A VAL* 3.9 26.0 - - + -
129A ASN* 3.1 24.1 + - - +
152A VAL 3.5 8.5 - - - +
153A ALA* 3.8 20.4 - - + -
154A LEU 4.9 0.2 - - - +
4C ILE* 5.0 0.7 - - - -
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Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A VAL* 1.3 74.8 - - - +
97A ILE* 1.3 68.9 + - - +
98A THR* 5.2 0.4 - - - -
129A ASN* 2.8 24.4 + - - -
131A LYS* 2.8 25.7 + - - -
151A ALA* 3.5 3.1 - - - -
152A VAL* 3.1 46.4 + - + +
4C ILE 4.1 8.9 + - - +
6C HIS* 3.0 22.2 + - - +
51C GLY* 3.1 29.0 - - - +
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Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA* 4.1 19.1 - - + +
45A LEU* 3.8 38.6 - - + -
95A VAL* 5.0 4.5 - - + -
96A ASP* 1.3 79.6 + - - +
98A THR* 1.3 67.5 + - - +
99A ILE* 4.5 5.2 - - + -
117A ILE* 3.8 20.9 - - + -
128A VAL* 5.3 0.2 - - + -
129A ASN 2.9 14.1 + - - +
130A VAL* 3.5 12.2 - - + -
131A LYS* 2.9 32.1 + - - +
149A CYS* 3.4 26.5 - - - -
150A GLU 3.6 4.0 - - - +
151A ALA* 4.1 10.8 - - + -
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Residues in contact with THR 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ILE* 1.3 72.8 - - - +
99A ILE* 1.3 60.3 + - - +
100A ILE* 3.7 5.9 + - + +
131A LYS* 3.0 35.6 + - + -
133A THR* 4.1 23.8 - - + -
149A CYS* 3.4 4.8 - - - -
150A GLU* 2.8 37.1 + - - +
6C HIS* 3.0 39.3 + - + +
8C PHE* 4.2 12.6 - - + +
47C ASP* 6.1 0.2 - - - +
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Residues in contact with ILE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 4.8 7.9 - - + -
41A ALA* 4.4 12.3 - - + -
97A ILE* 4.5 1.1 - - + -
98A THR* 1.3 73.5 - - - +
100A ILE* 1.3 67.9 + - - +
101A ALA* 3.9 11.7 - - + -
106A MSE 4.4 22.4 - - + -
110A ILE* 4.6 3.8 - - + -
113A MSE 4.2 17.5 - - - -
130A VAL* 3.8 26.9 - - + -
131A LYS 2.8 16.2 + - - +
132A ALA* 3.3 6.9 - - + -
133A THR* 2.8 31.0 + - - +
147A ILE* 5.4 5.6 - - + -
148A ALA 3.9 10.3 - - - +
149A CYS* 4.0 13.0 - - - -
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Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 4.8 9.4 - - + -
98A THR* 3.9 11.9 - - + +
99A ILE* 1.3 75.4 - - - +
101A ALA* 1.3 62.9 + - - +
133A THR* 3.4 11.9 - - + +
135A THR* 3.7 30.5 - - + +
141A THR* 3.6 15.7 - - + +
148A ALA* 2.9 49.6 + - + +
149A CYS* 4.8 2.2 - - - +
150A GLU* 4.5 14.6 - - + +
170A ACY 4.4 7.4 - - + -
8C PHE* 3.7 35.4 - - + -
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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