Contacts of the helix formed by residues 19 - 28 (chain N) 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 ASP 19 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23680 A 3.8 35.6 - - - +
23690 A 4.7 3.2 + - - -
17N ARG 4.2 1.2 + - - -
18N THR* 1.3 72.6 - - - +
20N TYR* 1.3 54.9 + - - +
21N HIS* 3.0 12.1 + - - +
22N GLN* 2.9 36.9 + - + +
23N ARG* 2.9 23.0 + - - +
25N ARG* 5.7 0.7 + - - -
105N GLY* 5.6 3.7 - - - +
106N LEU* 3.9 23.0 - - + +
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Residues in contact with TYR 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23680 A 4.8 2.4 + - - -
30079 G 4.7 0.2 - - - -
30089 G 2.5 40.4 + - - -
30109 C 3.5 18.6 + - - -
10N MET* 3.4 30.7 - - + -
12N ARG* 3.5 29.9 + - + +
13N ARG* 4.4 9.6 - - + +
18N THR* 3.2 37.6 + - + -
19N ASP* 1.3 69.7 + - - +
21N HIS* 1.3 66.6 + - + +
23N ARG* 3.6 10.0 - - + +
24N LEU* 3.3 17.7 + - - +
23Q THR* 5.7 6.9 - - + +
24Q SER 5.9 0.2 - - - +
26Q PRO* 3.5 33.4 - - + +
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Residues in contact with HIS 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23670 A 5.0 1.0 + - - -
23680 A 4.8 10.1 - + + -
23690 A 3.6 51.5 + - - +
23700 A 4.9 14.8 + - - -
19N ASP* 3.0 8.3 + - - +
20N TYR* 1.3 81.2 - - + +
22N GLN* 1.3 62.9 + - - +
24N LEU* 3.7 7.4 + - - +
25N ARG* 3.2 40.8 + - - +
23Q THR* 3.2 39.8 + - + +
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Residues in contact with GLN 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24130 A 3.8 24.7 + - - +
24140 A 4.0 7.8 + - - -
24150 A 3.8 11.5 - - + -
19N ASP* 2.9 27.8 + - - +
21N HIS* 1.3 77.5 - - - +
23N ARG* 1.3 65.9 + - - +
25N ARG* 3.3 25.7 + - - +
26N LEU* 2.8 41.2 + - + +
103N ASP* 4.6 0.3 - - - +
104N ILE* 4.8 5.1 + - - +
105N GLY* 3.5 31.6 + - - +
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Residues in contact with ARG 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30079 G 2.8 42.7 + - - -
30089 G 2.6 31.7 + - - -
18N THR* 4.3 7.4 - - + -
19N ASP 2.9 16.3 + - - +
20N TYR* 3.6 15.7 - - + +
21N HIS 3.3 0.2 - - - -
22N GLN* 1.3 76.9 - - - +
24N LEU* 1.3 53.1 + - - +
26N LEU* 3.1 11.1 + - - +
27N LEU* 2.7 57.7 + - + +
33N ARG* 3.9 17.1 - - - +
50N LEU* 3.6 14.6 - - - +
55N ASP* 2.8 34.4 + - - -
103N ASP* 5.3 1.3 - - - -
26Q PRO* 4.4 8.9 - - + +
27Q GLN* 5.3 2.0 + - - +
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Residues in contact with LEU 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20N TYR 3.3 10.5 + - - +
21N HIS* 3.8 11.7 - - - +
22N GLN 3.2 0.6 - - - -
23N ARG* 1.3 76.3 - - - +
25N ARG* 1.3 68.1 + - + +
27N LEU* 3.1 3.8 + - - -
28N LYS* 3.1 49.3 + - + +
24Q SER 6.1 0.4 - - - +
26Q PRO* 3.9 26.4 - - + +
29Q ALA* 4.3 17.0 - - + +
30Q VAL* 4.0 19.3 - - + -
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Residues in contact with ARG 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23260 U 5.8 0.8 + - - -
23270 A 5.6 3.4 + - - -
23690 A 5.0 4.4 + - - -
24140 A 4.9 2.6 + - - +
24150 A 3.0 60.4 + - + +
24160 G 3.1 29.9 - - - +
24170 C 5.4 2.5 - - - -
19N ASP* 5.7 0.4 + - - -
21N HIS* 3.2 42.2 + - - +
22N GLN* 3.3 23.5 + - - +
24N LEU* 1.3 78.5 - - + +
26N LEU* 1.3 64.1 + - - +
28N LYS* 3.2 25.5 + - + +
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Residues in contact with LEU 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24140 A 4.8 2.2 - - + -
24150 A 2.9 34.9 + - + +
22N GLN* 2.8 35.2 + - + +
23N ARG* 3.2 12.6 - - - +
25N ARG* 1.3 76.0 - - - +
27N LEU* 1.3 58.6 + - - +
28N LYS 3.0 3.5 + - - -
29N SER* 3.2 11.1 + - - -
31N LYS 5.3 0.5 - - - +
33N ARG* 4.0 23.0 - - + +
101N VAL* 4.0 22.7 - - + +
102N LEU 3.8 19.3 - - - +
103N ASP* 3.5 35.9 - - + +
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Residues in contact with LEU 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23N ARG* 2.7 52.9 + - + +
24N LEU 3.1 5.8 + - - +
26N LEU* 1.3 72.7 - - + +
28N LYS* 1.3 61.3 + - - +
29N SER* 3.2 1.6 + - - -
30N GLY* 3.4 12.5 + - - -
31N LYS 5.6 4.4 - - - +
33N ARG* 4.2 25.1 - - + +
50N LEU* 3.7 38.8 - - + +
26Q PRO* 4.3 10.8 - - + -
27Q GLN* 5.3 2.2 - - - +
30Q VAL* 3.8 36.2 - - + +
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Residues in contact with LYS 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24160 G 3.5 34.9 + - - +
24170 C 2.7 30.5 + - - +
24N LEU* 3.1 43.9 + - + +
25N ARG* 3.3 17.2 - - - +
26N LEU 3.0 2.0 + - - -
27N LEU* 1.3 76.7 - - - +
29N SER* 1.3 64.6 + - - +
30N GLY* 3.2 1.4 + - - -
30Q VAL* 5.2 6.1 - - + -
69Q ASP* 5.5 9.6 - - - +
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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