Contacts of the helix formed by residues 11 - 22 (chain S) in PDB entry 1VQ4
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 THR 11 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14440 G 3.6 37.0 - - - +
14450 G 2.9 15.8 + - - -
9S HIS* 3.3 26.9 + - + -
10S VAL* 1.3 82.7 - - - +
12S GLU* 1.3 64.6 + - - +
13S LYS 3.7 1.0 + - - -
14S ALA* 2.8 21.1 + - - +
15S MET* 2.8 32.5 + - - +
25S GLN* 4.4 0.2 + - - -
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Residues in contact with GLU 12 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14430 G 5.5 2.5 + - - -
14440 G 3.7 30.8 + - - +
15010 A 3.2 31.0 + - - +
11S THR* 1.3 71.7 - - - +
13S LYS* 1.3 64.9 + - - +
15S MET* 3.1 13.2 + - - +
16S ASN* 3.0 29.2 + - - +
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Residues in contact with LYS 13 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14440 G 5.3 0.2 - - - +
14450 G 3.1 39.8 + - - +
14460 U 2.8 27.0 + - - +
14470 U 3.1 19.0 + - - -
15020 A 4.1 26.2 + - + +
15030 U 3.1 25.9 + - - +
11S THR* 3.2 1.2 + - - -
12S GLU* 1.3 79.2 + - - +
14S ALA* 1.3 64.3 + - - +
16S ASN* 3.2 15.0 + - + +
17S ASP* 3.2 27.4 + - - +
25S GLN* 3.8 10.0 + - - +
63S LYS* 5.6 2.5 - - - +
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Residues in contact with ALA 14 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S HIS 3.0 29.2 - - - +
10S VAL* 4.1 1.6 - - - -
11S THR* 2.8 28.3 + - - +
13S LYS* 1.3 79.4 - - - +
15S MET* 1.3 61.8 + - - +
17S ASP* 3.4 4.7 + - - +
18S MET* 3.2 19.8 + - - +
23S LYS 4.4 2.1 - - - +
25S GLN* 3.4 26.6 + - + +
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Residues in contact with MET 15 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10S VAL* 4.2 22.4 - - + -
11S THR 2.8 26.2 + - - +
12S GLU* 3.1 10.5 + - - +
14S ALA* 1.3 74.3 - - - +
16S ASN* 1.3 52.7 + - - +
18S MET* 2.6 54.5 + - + +
19S ASP* 2.7 32.7 + - - +
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Residues in contact with ASN 16 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15020 A 6.1 0.2 - - - +
12S GLU* 3.0 24.0 + - - +
13S LYS* 3.5 16.4 - - + +
15S MET* 1.3 77.1 - - - +
17S ASP* 1.3 61.2 + - - +
19S ASP* 4.5 2.5 - - - +
20S PHE* 2.7 60.5 + - + +
21S GLN* 5.5 0.2 - - - -
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Residues in contact with ASP 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14470 U 4.6 13.4 + - - +
15070 C 5.5 0.2 + - - -
13S LYS* 3.2 13.4 + - - +
14S ALA 3.7 8.3 - - - +
15S MET 3.2 0.6 - - - -
16S ASN* 1.3 78.6 - - - +
18S MET* 1.3 56.5 + - - +
21S GLN* 3.0 37.8 + - - +
22S ASN 3.0 0.2 + - - -
23S LYS* 2.8 50.7 + - + +
25S GLN* 3.5 22.8 + - - +
65S VAL* 3.6 9.5 - - - +
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Residues in contact with MET 18 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S ALA 3.2 10.4 + - - +
15S MET* 2.6 49.0 + - + +
17S ASP* 1.3 70.5 - - - +
19S ASP* 1.3 85.6 + - - +
20S PHE 3.4 0.3 + - - -
22S ASN* 3.5 17.0 + - - +
23S LYS 3.2 15.7 + - - +
24S LEU* 4.3 4.5 - - + -
74S ALA* 3.9 8.6 - - + +
75S GLN* 3.7 36.4 - - + +
78S ALA* 3.8 28.0 - - + -
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Residues in contact with ASP 19 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S MET* 2.7 35.3 + - - +
16S ASN* 4.4 2.4 - - - +
18S MET* 1.3 85.9 - - - +
20S PHE* 1.3 79.6 + - + +
75S GLN* 2.8 45.4 + - - +
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Residues in contact with PHE 20 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16S ASN* 2.7 43.4 + - + +
19S ASP* 1.3 96.8 - - + +
21S GLN* 1.3 66.2 + - + +
22S ASN 3.7 1.3 - - - -
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Residues in contact with GLN 21 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15070 C 3.0 10.1 + - - +
15080 C 3.1 39.7 + - - -
16S ASN 5.5 0.2 - - - -
17S ASP* 3.0 28.2 + - - +
20S PHE* 1.3 87.4 - - + +
22S ASN* 1.3 73.8 + - - +
23S LYS* 2.7 44.2 + - + +
67S ARG* 3.6 11.5 - - - +
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Residues in contact with ASN 22 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17S ASP 3.0 2.2 + - - -
18S MET 3.5 13.0 + - - +
19S ASP 5.1 0.2 - - - -
20S PHE 3.7 1.2 - - - -
21S GLN* 1.3 81.4 - - - +
23S LYS* 1.3 57.5 + - - +
67S ARG* 3.5 1.4 - - + +
68S LEU* 2.9 57.9 + - - +
69S SER 3.1 18.6 + - - -
70S GLU* 4.5 3.1 - - - +
72S ASP 3.3 7.7 + - - +
73S ASP* 3.3 9.9 - - - +
74S ALA* 2.9 33.0 + - - +
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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