Contacts of the helix formed by residues 8 - 19 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ILE* 3.1 43.7 + - + +
5A PHE 3.8 3.6 - - - -
6A GLU 3.3 0.2 - - - -
7A ARG* 1.3 93.6 - - + +
9A VAL* 1.3 58.9 + - - +
10A ASN 3.3 2.7 - - - -
11A GLU* 3.2 17.8 + - + -
12A TYR* 2.9 27.9 + - - +
146A VAL* 3.8 29.2 - - + -
147A PHE* 3.6 15.8 - - + -
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Residues in contact with VAL 9 (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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5A PHE 3.3 15.1 + - - +
6A GLU 3.9 4.3 - - - +
7A ARG 3.7 0.6 - - - -
8A PHE* 1.3 75.9 - - - +
10A ASN* 1.3 75.8 + - - +
12A TYR* 3.3 3.1 + - - +
13A GLU* 3.0 23.8 + - + +
46A THR* 4.1 5.4 - - + -
64A ARG* 3.6 35.2 - - + +
65A MSE 3.9 29.6 - - + -
68A ILE* 3.9 28.0 - - + -
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Residues in contact with ASN 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE 3.3 0.4 - - - -
9A VAL* 1.3 88.9 - - - +
11A GLU* 1.3 57.6 + - - +
13A GLU* 3.3 8.0 + - - +
14A ARG* 2.9 28.1 + - - +
64A ARG* 6.1 0.6 - - - +
68A ILE* 5.8 1.9 - - - +
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Residues in contact with GLU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 3.2 30.7 + - + +
10A ASN* 1.3 77.7 - - - +
12A TYR* 1.3 62.2 + - - +
14A ARG* 3.3 27.1 - - - +
15A TRP* 3.4 8.3 + - - +
146A VAL* 5.4 4.7 - - + -
147A PHE* 4.4 15.3 - - + -
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Residues in contact with TYR 12 (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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5A PHE* 3.8 31.0 - + - -
8A PHE 2.9 12.2 + - - +
9A VAL 3.3 9.0 - - - +
11A GLU* 1.3 73.3 - - - +
13A GLU* 1.3 70.7 + - + +
15A TRP* 3.4 11.7 + - + +
16A PHE* 3.2 49.8 - + - -
44A VAL 5.3 1.4 + - - -
45A GLY* 4.9 5.1 - - - -
46A THR* 3.6 28.7 + - + -
48A ARG* 4.5 6.6 - - + +
49A PHE* 5.6 3.5 - - - -
65A MSE 3.2 29.2 - - + -
98A THR* 5.8 2.1 + - - -
147A PHE* 3.7 19.2 - + + -
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Residues in contact with GLU 13 (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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9A VAL* 3.0 21.6 + - + +
10A ASN* 3.3 8.3 + - - +
12A TYR* 1.3 76.0 - - + +
14A ARG* 1.3 66.9 + - - +
16A PHE* 2.9 18.9 + - - +
17A LEU* 3.2 18.5 - - + +
46A THR* 2.4 40.9 + - + +
48A ARG* 2.9 30.8 + - - +
68A ILE* 5.1 4.9 - - + -
72A ARG* 2.8 28.4 + - - -
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Residues in contact with ARG 14 (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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10A ASN 2.9 14.0 + - - +
11A GLU* 3.3 25.4 - - - +
13A GLU* 1.3 75.9 - - - +
15A TRP* 1.3 62.9 + - - +
17A LEU* 2.9 11.9 + - + +
18A VAL* 2.9 39.4 + - + +
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Residues in contact with TRP 15 (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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11A GLU 3.4 7.9 + - - +
12A TYR* 3.4 14.1 - - + +
13A GLU 3.1 0.8 - - - -
14A ARG* 1.3 78.1 - - - +
16A PHE* 1.3 96.9 + + + +
18A VAL* 4.7 2.0 - - - -
19A HIS* 2.9 70.5 + + + +
22A ALA* 4.3 8.1 - - + -
23A TYR* 4.0 24.7 - - + -
26A GLU* 3.9 28.3 - - - -
138A TYR* 4.8 13.3 + - - -
147A PHE* 6.3 1.6 - - + -
177A LEU* 6.3 0.4 - - + -
181A PRO* 5.1 6.0 - - + +
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Residues in contact with PHE 16 (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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12A TYR* 3.2 66.2 - + - -
13A GLU* 2.9 11.2 + - - +
15A TRP* 1.3 104.1 - + + +
17A LEU* 1.3 61.0 + - - +
19A HIS 4.1 0.2 - - - -
20A ARG* 3.4 23.9 + - - +
23A TYR* 3.5 42.0 - + + -
26A GLU* 5.3 0.4 - - - -
48A ARG* 3.4 48.1 + - + +
49A PHE* 4.3 12.1 - + - -
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Residues in contact with LEU 17 (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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13A GLU* 3.2 32.3 - - + +
14A ARG* 2.9 8.8 + - + +
16A PHE* 1.3 80.0 - - - +
18A VAL* 1.3 67.1 + - + +
19A HIS 3.3 0.2 - - - -
20A ARG* 4.0 11.5 + - - +
48A ARG* 3.7 20.9 - - - +
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Residues in contact with VAL 18 (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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14A ARG* 2.9 35.1 + - + +
15A TRP* 4.1 2.7 - - - +
17A LEU* 1.3 81.6 - - + +
19A HIS* 1.3 84.1 + - + +
20A ARG 3.6 1.6 + - - -
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Residues in contact with HIS 19 (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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15A TRP* 2.9 66.0 + + + +
16A PHE 3.9 3.8 - - - -
18A VAL* 1.3 99.3 - - + +
20A ARG* 1.3 57.6 + - - +
21A PHE 3.4 2.5 - - - -
22A ALA* 3.4 8.4 + - + -
23A TYR* 3.0 26.3 + - - +
180A HIS* 6.1 1.0 - - - -
181A PRO* 4.0 33.1 - - + +
182A SER* 4.1 13.3 + - - -
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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