Contacts of the strand formed by residues 2 - 12 (chain C) 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 ILE 2 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ILE* 3.3 16.2 - - + -
93A GLY 5.4 2.8 - - - -
94A ASN* 4.2 0.7 - - - +
154A LEU* 3.5 19.1 - - + +
156A ILE* 4.4 18.1 - - + +
2B ILE* 3.3 39.5 - - + -
0C SER* 3.6 3.9 - - - -
1C LEU* 1.3 83.0 - - + +
3C ARG* 1.3 75.3 + - - +
90C TYR* 5.5 0.2 - - - -
154C LEU* 3.6 30.3 - - + -
155C LEU 3.3 8.5 - - - +
156C ILE* 4.8 5.4 - - + -
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Residues in contact with ARG 3 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A GLY 4.5 0.8 + - - -
94A ASN* 3.3 34.0 - - - +
126A GLU* 2.9 49.6 + - - +
127A GLN* 3.8 10.5 - - - +
154A LEU* 4.4 0.9 - - - -
0C SER* 3.1 24.7 + - - +
2C ILE* 1.3 82.1 - - - +
4C ILE* 1.3 59.3 + - - +
52C ALA* 2.6 44.2 + - + +
53C ALA* 4.0 9.3 - - - -
54C ALA* 4.2 2.4 - - - +
88C LYS* 6.0 0.2 - - - -
90C TYR* 3.6 26.0 - - + +
153C ALA 3.6 0.5 - - - +
154C LEU* 3.3 9.4 - - - +
155C LEU* 2.7 52.9 + - + +
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Residues in contact with ILE 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 3.2 42.4 - - + -
94A ASN* 3.0 42.9 + - - +
95A VAL* 5.0 0.7 - - - -
96A ASP* 4.1 4.3 - - - +
152A VAL* 3.9 31.9 - - + +
153A ALA* 4.1 5.4 - - - +
154A LEU* 3.9 24.6 - - + +
4B ILE* 3.4 19.3 - - + -
3C ARG* 1.3 73.9 - - - +
5C GLY* 1.3 62.5 + - - +
52C ALA* 3.3 8.5 - - - -
152C VAL* 5.7 0.2 - - + -
153C ALA 3.4 2.2 - - - -
154C LEU* 4.6 2.5 - - + -
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Residues in contact with GLY 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ASP* 3.6 9.2 - - - -
152A VAL* 4.2 4.3 - - - +
4C ILE* 1.3 77.9 - - - +
6C HIS* 1.3 59.5 + - - +
48C ALA* 3.4 24.2 - - - -
52C ALA* 3.7 2.9 - - - +
152C VAL* 3.0 9.7 - - - +
153C ALA 2.8 36.8 + - - -
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Residues in contact with HIS 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A HIS* 5.4 1.3 - + - -
96A ASP* 3.0 13.3 + - - +
98A THR* 3.0 29.6 + - - +
131A LYS* 2.8 28.9 + - - -
150A GLU* 3.3 28.7 + - + +
152A VAL* 3.8 31.4 - - + -
6B HIS* 5.5 1.6 - + - -
5C GLY* 1.3 75.0 - - - +
7C GLY* 1.3 76.3 + - - +
8C PHE* 3.9 6.3 - - + -
48C ALA* 3.6 10.4 - - - +
150C GLU* 2.5 32.0 + - + -
151C ALA 3.3 11.4 - - - -
152C VAL* 4.5 7.4 - - + -
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Residues in contact with GLY 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A THR* 4.7 1.1 - - - -
131A LYS* 5.3 0.2 - - - -
6C HIS* 1.3 84.9 + - - +
8C PHE* 1.3 60.5 + - - -
44C ALA* 3.3 25.6 - - - -
47C ASP* 3.9 8.3 - - - -
48C ALA* 3.6 1.2 - - - +
150C GLU* 3.5 3.1 - - - -
151C ALA 2.7 40.4 + - - +
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Residues in contact with PHE 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A THR* 4.2 12.7 - - + +
100A ILE* 3.7 33.4 - - + -
133A THR* 3.8 26.4 + - + +
134A THR 5.2 0.4 - - - -
135A THR* 4.1 14.1 - - + -
150A GLU* 5.0 2.2 - - - -
170A ACY 5.1 7.9 - - + -
6C HIS* 3.9 14.9 + - + -
7C GLY* 1.3 73.9 - - - +
9C ASP* 1.3 64.1 + - - +
10C VAL* 3.6 29.8 - - + -
44C ALA* 4.2 2.3 - - - +
47C ASP* 4.0 10.6 + - - +
100C ILE* 4.9 6.5 - - + -
140C PHE* 5.2 3.1 - + - -
148C ALA* 4.2 16.6 - - + -
149C CYS 3.3 20.0 - - - -
150C GLU* 4.2 19.1 - - - -
170C ACY 5.9 2.5 - - + -
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Residues in contact with ASP 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A THR* 4.5 5.4 + - - -
134A THR 5.5 0.2 - - - -
8C PHE* 1.3 79.6 - - - +
10C VAL* 1.3 69.3 + - - +
11C HIS* 5.4 0.2 - - - +
38C GLY 5.3 0.3 - - - -
40C VAL* 3.2 45.5 - - - +
43C HIS* 3.2 28.9 - - + +
44C ALA* 3.9 8.1 - - + +
47C ASP* 5.5 2.1 - - - +
148C ALA* 3.2 3.6 - - - +
149C CYS 2.9 33.5 + - - -
169C MN 2.8 26.6 + - - -
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Residues in contact with VAL 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A THR 4.2 3.8 + - - +
135A THR* 3.6 43.3 - - + +
136A GLU* 3.3 16.0 - - - +
138A LEU* 4.2 3.4 - - + -
8C PHE* 3.6 30.1 - - + -
9C ASP* 1.3 84.4 + - - +
11C HIS* 1.3 71.1 + - - +
40C VAL* 3.7 3.4 - - - -
140C PHE* 3.7 20.9 - - + -
147C ILE 3.3 12.6 - - - +
148C ALA* 4.1 6.3 - - + -
169C MN 3.4 12.6 + - - -
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Residues in contact with HIS 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A GLU* 3.2 7.8 + - - -
10C VAL* 1.3 76.7 - - - +
12C ALA* 1.3 77.0 + - - +
13C PHE* 4.0 24.6 - + - -
14C GLY 5.2 2.1 + - - -
32C PHE* 6.0 0.9 - + - -
34C ALA* 4.7 18.8 - - + +
37C ASP 5.1 3.0 + - - -
38C GLY* 3.6 34.5 - - - +
40C VAL* 3.5 18.6 - - + +
146C GLY* 3.2 4.2 - - - -
147C ILE* 2.9 37.3 + - + -
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Residues in contact with ALA 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A GLU* 2.6 37.8 + - + +
138A LEU* 3.7 24.7 - - + -
11C HIS* 1.3 89.0 - - - +
13C PHE* 1.3 68.0 + - - +
14C GLY* 3.7 0.7 + - - -
32C PHE* 3.8 22.1 - - + +
145C GLU 3.8 6.1 - - - +
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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