Contacts of the helix formed by residues 24 - 35 (chain O) in PDB entry 1VQ7
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 ALA 24 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7090 G 3.6 21.4 + - - +
7100 G 3.1 30.1 + - - +
18O ALA* 5.5 0.4 - - - -
22O GLY 5.3 0.7 - - - +
23O GLY* 1.3 74.3 - - - +
25O VAL* 1.3 62.5 + - - +
26O TRP 3.4 1.7 - - - +
27O GLY* 3.7 5.2 + - - +
28O ASP* 3.0 27.0 + - - +
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Residues in contact with VAL 25 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7090 G 2.7 45.3 - - - +
7100 G 3.6 11.4 - - - -
24O ALA* 1.3 78.8 - - - +
26O TRP* 1.3 95.6 + - + +
28O ASP* 3.0 8.0 + - - +
29O VAL* 2.6 42.5 + - + +
59O VAL* 5.9 0.9 - - + -
108O GLY* 4.2 16.8 - - - +
111O VAL* 3.8 16.8 - - + -
113O VAL* 4.8 7.9 - - + -
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Residues in contact with TRP 26 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14O LEU* 3.5 44.6 - - + +
17O ALA* 3.8 19.3 - - + -
18O ALA* 3.8 8.5 - - + -
23O GLY* 5.0 3.6 - - - -
24O ALA 3.4 1.0 - - - +
25O VAL* 1.3 94.0 - - + +
27O GLY* 1.3 57.1 + - - +
29O VAL* 3.3 5.4 + - + +
30O ALA* 2.9 28.8 + - - +
57O THR* 6.2 0.4 - - + -
59O VAL* 4.0 33.7 - - + -
98O LEU* 5.0 8.5 - - + -
101O ALA* 4.0 31.6 - - + -
102O ILE* 4.2 9.0 - - + +
105O ASN* 3.2 24.8 + - + -
106O PRO* 3.1 30.9 + - - +
107O GLU 4.9 0.4 - - - -
108O GLY* 3.6 17.6 - - - +
111O VAL* 5.2 2.2 - - + -
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Residues in contact with GLY 27 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14O LEU 4.6 0.7 - - - -
15O LYS* 5.3 2.0 - - - -
18O ALA* 3.1 23.1 - - - +
24O ALA* 3.7 5.0 + - - -
26O TRP* 1.3 77.8 - - - +
28O ASP* 1.3 62.5 + - - +
30O ALA* 3.7 9.0 - - - +
31O GLU* 3.2 34.0 + - - +
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Residues in contact with ASP 28 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7080 A 2.6 31.5 + - - +
7090 G 3.6 14.8 + - - +
24O ALA 3.0 20.6 + - - +
25O VAL* 3.1 11.0 - - - +
27O GLY* 1.3 75.9 - - - +
29O VAL* 1.3 70.7 + - + +
31O GLU* 3.2 19.6 + - - +
32O ARG* 3.2 14.0 + - - +
113O VAL* 5.1 10.0 - - - +
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Residues in contact with VAL 29 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14O LEU* 4.0 21.1 - - + -
25O VAL* 2.6 26.5 + - + +
26O TRP* 3.7 7.4 - - + +
28O ASP* 1.3 75.1 - - - +
30O ALA* 1.3 60.8 + - - +
32O ARG* 3.1 4.1 + - - +
33O LEU* 2.9 41.1 + - + +
59O VAL* 3.9 26.7 - - + -
61O PRO* 4.0 27.8 - - + -
98O LEU* 4.3 11.0 - - + -
113O VAL* 5.2 5.2 - - + -
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Residues in contact with ALA 30 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11O ILE* 4.1 9.4 - - + +
14O LEU* 4.0 24.2 - - + +
15O LYS* 4.0 24.7 - - + -
26O TRP 2.9 18.3 + - - +
27O GLY* 3.7 9.2 - - - +
29O VAL* 1.3 76.1 - - - +
31O GLU* 1.3 63.1 + - + +
33O LEU* 3.4 5.2 + - - +
34O GLU* 3.1 29.6 + - - +
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Residues in contact with GLU 31 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27O GLY 3.2 18.0 + - - +
28O ASP* 3.2 12.8 + - - +
29O VAL 3.1 0.4 - - - -
30O ALA* 1.3 78.8 - - + +
32O ARG* 1.3 64.5 + - - +
34O GLU* 3.3 24.7 + - - +
35O LYS* 3.3 17.5 + - - +
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Residues in contact with ARG 32 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9360 C 3.1 25.9 + - - -
9370 C 5.5 3.2 + - - -
28O ASP* 3.2 9.4 + - - +
29O VAL* 3.1 7.6 + - - +
31O GLU* 1.3 75.6 - - - +
33O LEU* 1.3 66.2 + - - +
35O LYS* 3.1 37.1 + - - +
39O THR* 3.9 23.1 + - - -
40O HIS* 3.1 14.5 + - - +
61O PRO* 4.1 33.0 - - + +
115O ARG* 3.6 26.4 - - - +
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Residues in contact with LEU 33 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2O LYS* 3.1 13.3 - - - -
7O LEU* 4.2 8.4 - - + +
10O LEU* 4.0 19.7 - - + -
11O ILE* 3.8 24.7 - - + +
14O LEU* 3.9 26.7 - - + -
29O VAL* 2.9 23.3 + - + +
30O ALA 3.9 1.1 - - - +
31O GLU 3.3 0.2 - - - -
32O ARG* 1.3 77.2 - - - +
34O GLU* 1.3 57.4 + - - +
40O HIS* 2.8 36.8 + - + +
61O PRO* 3.7 25.8 - - + +
62O GLY* 4.7 0.2 - - - -
79O VAL* 3.7 22.2 - - + -
98O LEU* 4.8 0.7 - - + -
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Residues in contact with GLU 34 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6550 U 4.7 1.0 + - - -
12790 U 5.3 3.5 - - - +
2O LYS* 3.5 16.1 + - + +
11O ILE* 4.1 15.4 - - + +
15O LYS* 2.9 37.1 + - - -
30O ALA 3.1 19.7 + - - +
31O GLU* 3.4 22.4 - - - +
32O ARG 3.1 0.4 - - - -
33O LEU* 1.3 76.0 - - - +
35O LYS* 1.3 62.9 + - + +
36O PRO* 3.9 1.6 - - - +
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Residues in contact with LYS 35 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9350 G 4.7 9.0 - - - +
9360 C 2.7 40.3 + - - +
9370 C 5.4 3.2 + - - -
2O LYS* 2.8 10.4 + - - -
31O GLU* 3.3 13.2 + - - +
32O ARG* 3.1 39.1 + - - +
34O GLU* 1.3 80.1 - - + +
36O PRO* 1.3 65.2 - - + +
39O THR* 3.5 9.0 - - - +
40O HIS* 2.5 31.1 + - - -
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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