Contacts of the helix formed by residues 10 - 25 (chain V) in PDB entry 1V7M
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 ARG 10 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8V ASP* 3.1 29.4 - - + +
9V LEU* 1.3 76.0 - - - +
11V VAL* 1.3 62.6 + - - +
12V LEU 3.0 2.5 - - - +
13V SER* 3.4 19.4 - - - +
14V LYS* 2.9 65.2 + - - +
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Residues in contact with VAL 11 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7V CYS* 4.0 20.4 - - + -
8V ASP* 3.3 30.0 - - + +
10V ARG* 1.3 81.3 - - - +
12V LEU* 1.3 51.5 + - - +
14V LYS* 4.8 2.0 - - - +
15V LEU* 2.7 49.0 + - + +
100V LEU* 5.9 2.2 - - + -
103V ALA* 5.1 7.9 - - + -
143V MET* 4.0 18.4 - - + -
151V CYS* 4.0 18.2 - - - +
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Residues in contact with LEU 12 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9V LEU 4.6 5.6 - - - +
10V ARG 3.0 0.8 - - - +
11V VAL* 1.3 83.5 - - - +
13V SER* 1.3 58.0 + - - +
15V LEU* 3.6 4.6 - - + +
16V LEU* 2.8 34.5 + - + +
100V LEU* 6.1 0.2 - - + -
135V LEU* 3.2 50.3 - - + +
139V VAL* 3.8 24.9 - - + -
140V ARG* 3.8 40.8 - - - +
143V MET* 3.6 28.2 - - + +
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Residues in contact with SER 13 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9V LEU 5.2 2.1 + - - -
10V ARG* 3.2 25.1 + - - +
12V LEU* 1.3 75.7 - - - +
14V LYS* 1.3 61.3 + - - +
15V LEU 3.1 1.1 - - - -
16V LEU* 3.0 6.9 + - - +
17V ARG* 2.8 29.7 + - - +
140V ARG* 4.7 13.5 + - - -
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Residues in contact with LYS 14 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10V ARG* 2.9 56.8 + - - +
11V VAL* 4.8 2.0 - - - +
13V SER* 1.3 73.6 - - - +
15V LEU* 1.3 57.1 + - - +
17V ARG* 3.5 41.2 - - + +
18V ASP* 3.1 51.4 + - - +
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Residues in contact with LEU 15 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11V VAL* 2.7 31.7 + - + +
12V LEU* 3.6 8.7 - - + +
14V LYS* 1.3 75.8 - - - +
16V LEU* 1.3 65.1 + - - +
18V ASP* 3.9 2.9 + - - +
19V SER* 3.4 21.0 + - - -
96V GLN* 4.0 23.6 - - - +
99V LEU* 3.8 33.9 - - + -
100V LEU* 4.0 34.8 - - + -
131V PHE* 4.6 6.3 - - + -
135V LEU* 4.0 22.3 - - + +
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Residues in contact with LEU 16 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12V LEU* 2.8 25.7 + - + +
13V SER* 3.0 6.2 + - - +
15V LEU* 1.3 68.6 - - - +
17V ARG* 1.3 61.1 + - - +
19V SER* 2.1 30.4 + - - +
20V HIS* 2.9 44.2 + - + +
132V GLN* 4.4 9.4 - - + +
135V LEU* 3.6 43.7 - - + +
136V ARG* 3.4 38.4 - - + +
140V ARG* 5.8 2.0 - - - +
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Residues in contact with ARG 17 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13V SER 2.8 17.0 + - - +
14V LYS* 3.5 43.4 - - + +
16V LEU* 1.3 73.7 - - - +
18V ASP* 1.3 55.0 + - - +
19V SER 2.6 17.1 + - - -
20V HIS* 3.1 25.0 + - + +
21V VAL* 3.6 29.2 - - - +
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Residues in contact with ASP 18 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14V LYS* 3.1 39.8 + - - +
15V LEU 4.0 1.6 - - - +
17V ARG* 1.3 77.0 + - - +
19V SER* 1.3 56.1 + - - +
21V VAL* 4.0 9.7 + - - +
22V LEU* 3.3 33.6 + - - +
96V GLN* 2.6 33.8 + - - +
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Residues in contact with SER 19 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15V LEU 3.4 11.4 + - - -
16V LEU* 2.1 33.9 + - - -
17V ARG 2.6 8.5 + - - -
18V ASP* 1.3 72.7 - - - +
20V HIS* 1.3 65.2 + - - +
21V VAL 3.2 0.7 - - - -
22V LEU* 3.7 6.0 + - - +
23V HIS* 3.4 19.1 + - - +
93V LEU* 5.4 5.2 - - - +
96V GLN* 5.1 4.0 - - - -
128V PHE* 4.9 3.3 - - - -
131V PHE* 4.4 21.5 - - - -
132V GLN* 3.7 24.1 - - - +
135V LEU* 4.7 1.0 - - - +
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Residues in contact with HIS 20 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16V LEU* 2.9 52.9 + - + +
17V ARG* 3.1 21.9 - - - +
19V SER* 1.3 74.5 + - - +
21V VAL* 1.3 55.2 + - + +
23V HIS* 3.0 9.4 + - - +
24V SER* 2.8 36.3 + - - -
132V GLN* 3.1 25.2 + - - +
136V ARG* 4.5 10.8 - - - -
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Residues in contact with VAL 21 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17V ARG* 3.6 43.3 - - - +
18V ASP* 4.0 11.2 - - - +
19V SER 3.2 1.0 - - - -
20V HIS* 1.3 76.4 - - + +
22V LEU* 1.3 61.7 + - + +
24V SER* 2.3 26.4 + - - +
25V ARG* 2.9 25.2 - - - +
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Residues in contact with LEU 22 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18V ASP* 3.3 23.8 + - + +
19V SER* 3.7 4.9 + - - +
20V HIS 3.3 0.6 - - - -
21V VAL* 1.3 81.2 - - + +
23V HIS* 1.3 61.9 + - - +
25V ARG* 2.8 44.3 + - - +
26V LEU 3.7 0.2 + - - -
89V LEU* 3.3 17.0 - - + +
92V GLN* 3.8 50.5 - - + +
93V LEU* 3.9 11.0 - - + +
96V GLN* 4.4 8.5 - - + -
128V PHE* 4.0 12.5 - - + -
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Residues in contact with HIS 23 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19V SER 3.4 10.2 + - - +
20V HIS* 3.0 9.3 + - - +
22V LEU* 1.3 77.0 - - - +
24V SER* 1.3 65.1 + - - +
26V LEU* 3.1 32.3 + - + +
125V ASN* 3.1 26.9 + - + -
128V PHE* 3.6 37.7 - + + +
129V LEU* 4.0 24.0 - - + +
132V GLN* 3.8 17.8 + - - +
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Residues in contact with SER 24 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V HIS 2.8 16.8 + - - -
21V VAL* 2.3 32.5 + - - +
23V HIS* 1.3 74.3 - - - +
25V ARG* 1.3 62.0 + - - +
26V LEU 3.1 5.5 + - - -
27V SER* 3.4 18.0 + - - -
28V GLN* 4.4 1.5 + - - +
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Residues in contact with ARG 25 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21V VAL* 2.9 30.9 + - - +
22V LEU* 2.8 24.1 + - - +
24V SER* 1.3 79.7 + - - +
26V LEU* 1.3 53.9 + - - -
27V SER 3.0 12.2 + - - -
28V GLN* 3.2 41.7 + - + +
29V CYS* 4.3 4.9 + - - -
89V LEU* 3.5 43.8 - - + +
92V GLN* 5.6 4.6 + - - +
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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