Contacts of the helix formed by residues 8 - 19 (chain B) in PDB entry 1VLM
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 PHE 8 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B ILE* 3.1 26.2 + - + +
5B PHE 3.8 2.7 - - - -
7B ARG* 1.3 94.7 - - + +
9B VAL* 1.3 64.7 + - - +
10B ASN* 3.3 2.9 - - - -
11B GLU* 3.0 31.6 + - + -
12B TYR 3.0 18.5 + - - -
146B VAL* 3.5 26.9 - - + -
147B PHE* 3.5 23.8 - - + -
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Residues in contact with VAL 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE 3.2 14.2 + - - +
6B GLU* 4.2 11.4 - - - +
7B ARG 5.5 0.4 - - - +
8B PHE* 1.3 77.4 - - - +
10B ASN* 1.3 74.2 + - - +
12B TYR* 3.3 2.8 + - - +
13B GLU* 2.9 31.8 + - + +
46B THR* 4.2 13.7 - - + -
64B ARG* 5.3 11.2 - - + +
65B MSE 3.6 36.1 - - + +
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Residues in contact with ASN 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PHE 3.3 1.0 - - - -
9B VAL* 1.3 89.7 - - - +
11B GLU* 1.3 57.1 + - - +
13B GLU* 3.4 7.3 + - - +
14B ARG* 2.9 29.1 + - - +
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Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 3.0 38.1 + - + +
10B ASN* 1.3 77.1 - - - +
12B TYR* 1.3 65.4 + - - +
14B ARG* 3.5 8.3 + - + +
15B TRP* 3.4 18.9 + - - +
146B VAL* 3.4 26.6 - - - +
147B PHE* 3.9 16.7 - - + -
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Residues in contact with TYR 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE* 3.6 30.3 - + - -
8B PHE 3.0 11.5 + - - +
9B VAL 3.4 7.6 - - - +
11B GLU* 1.3 77.0 - - - +
13B GLU* 1.3 69.7 + - + +
15B TRP* 3.3 15.1 - - + +
16B PHE* 3.2 44.7 - + - -
44B VAL 5.4 1.2 + - - -
45B GLY* 4.9 7.8 - - - -
46B THR* 3.5 24.7 + - + -
48B ARG* 5.0 2.9 - - - +
49B PHE* 5.4 5.5 - - - -
65B MSE 3.3 29.4 - - + -
98B THR* 6.5 1.3 - - + -
147B PHE* 4.0 16.7 - + + -
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Residues in contact with GLU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 2.9 23.9 + - + +
10B ASN* 3.7 7.9 - - - +
11B GLU 3.3 0.2 - - - -
12B TYR* 1.3 80.1 - - + +
14B ARG* 1.3 65.5 + - - +
16B PHE* 2.9 22.0 + - - +
17B LEU* 3.7 6.3 + - + +
46B THR* 2.6 39.5 + - + +
48B ARG* 3.0 26.6 + - - +
68B ILE* 5.4 1.6 - - - +
72B ARG* 3.0 34.0 + - - -
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Residues in contact with ARG 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASN 2.9 18.4 + - - +
11B GLU* 3.8 9.9 - - + +
12B TYR 3.3 0.4 - - - -
13B GLU* 1.3 75.1 - - - +
15B TRP* 1.3 62.5 + - - +
17B LEU* 3.1 18.3 + - + +
18B VAL* 2.9 53.9 + - + +
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Residues in contact with TRP 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLU 3.4 8.3 + - - +
12B TYR* 3.3 15.8 + - + +
13B GLU 3.0 0.4 + - - -
14B ARG* 1.3 78.3 - - - +
16B PHE* 1.3 89.6 + + + +
18B VAL* 4.7 0.9 - - - -
19B HIS* 2.8 81.5 + + + +
22B ALA* 4.3 7.9 - - + -
23B TYR* 3.9 26.0 - - + -
26B GLU* 3.8 30.1 - - - -
138B TYR* 5.2 7.8 + - - -
177B LEU* 6.1 0.7 - - + -
181B PRO* 5.4 6.8 - - + +
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Residues in contact with PHE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TYR* 3.2 66.4 - + - -
13B GLU* 2.9 12.5 + - - +
15B TRP* 1.3 100.7 - + - +
17B LEU* 1.3 64.3 + - - +
19B HIS 4.2 0.9 - - - -
20B ARG* 3.4 23.7 + - - +
23B TYR* 3.6 33.9 - + + -
48B ARG* 3.5 58.9 + - + +
49B PHE* 4.3 11.2 - + - -
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLU* 4.3 8.5 - - + +
14B ARG* 3.1 21.4 + - + +
16B PHE* 1.3 79.4 - - - +
18B VAL* 1.3 68.1 + - + +
19B HIS 3.4 0.3 + - - -
20B ARG* 3.6 14.3 + - - +
48B ARG* 4.8 15.3 - - - +
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ARG* 2.9 65.5 + - + +
15B TRP* 4.7 0.4 - - - -
17B LEU* 1.3 80.3 - - + +
19B HIS* 1.3 84.6 + - + +
20B ARG 3.8 1.2 + - - -
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Residues in contact with HIS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B TRP* 2.8 61.3 + + + +
16B PHE 4.1 0.9 - - - -
18B VAL* 1.3 99.3 + - + +
20B ARG* 1.3 62.9 + - - +
21B PHE 3.4 2.5 - - - -
22B ALA* 3.2 8.5 + - + +
23B TYR* 3.0 21.0 + - - +
180B HIS* 6.0 1.1 - + - -
181B PRO* 3.8 25.1 + - + +
182B SER* 4.2 23.7 - - - -
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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