Contacts of the strand formed by residues 19 - 28 (chain A) in PDB entry 2QVH
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 ILE 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A LEU* 3.8 15.1 - - + +
15A ARG* 3.3 6.0 - - - +
16A PHE* 3.1 37.2 + - + +
17A ARG* 3.8 17.9 - - + +
18A GLY* 1.3 81.9 - - - +
20A THR* 1.3 65.2 + - - +
21A VAL 3.8 21.1 - - - +
22A ARG* 3.9 14.8 - - - -
39A PHE* 3.7 32.1 - - + -
230A VAL* 6.0 2.0 - - + -
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Residues in contact with THR 20 (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 PRO* 3.4 3.6 - - - +
12A LEU* 2.9 34.4 + - - +
14A THR 5.9 0.2 - - - -
15A ARG* 3.8 42.4 - - + +
19A ILE* 1.3 78.4 - - - +
21A VAL* 1.3 75.1 + - - +
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Residues in contact with VAL 21 (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 ALA* 4.2 16.4 - - + -
10A ILE 3.5 23.3 - - - +
11A PRO* 4.3 10.1 - - + -
12A LEU* 3.5 5.0 - - - +
19A ILE* 3.8 16.5 - - - +
20A THR* 1.3 97.3 + - - +
22A ARG* 1.3 65.2 + - - +
23A GLU* 3.8 12.8 + - + +
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Residues in contact with ARG 22 (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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8A PHE* 3.5 18.3 - - + -
9A ALA* 3.5 0.2 - - - -
10A ILE* 2.7 42.8 + - + +
12A LEU* 3.4 9.6 - - + +
19A ILE* 3.9 18.6 - - - +
21A VAL* 1.3 71.6 - - - +
23A GLU* 1.3 82.1 + - - +
35A GLU* 5.1 0.2 - - - -
37A SER* 2.9 44.4 + - - -
38A PRO 4.8 1.2 + - - -
39A PHE* 3.4 26.9 - - - +
50A TRP* 4.4 0.8 - - - -
229A ALA* 2.8 28.4 + - - +
230A VAL* 2.8 34.8 + - - +
231A GLU* 4.4 2.6 - - - +
232A THR* 6.1 0.2 - - + -
261A LEU* 3.9 12.6 - - + -
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Residues in contact with GLU 23 (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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8A PHE* 3.3 18.6 - - - +
9A ALA* 3.7 17.3 - - + +
21A VAL* 3.8 13.0 + - + +
22A ARG* 1.3 96.6 + - - +
24A GLY* 1.3 58.7 + - - +
37A SER* 3.5 3.8 - - - -
38A PRO 4.7 0.3 - - - +
294A ILE* 3.8 14.1 - - - +
299A TRP* 2.9 37.1 + - + +
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Residues in contact with GLY 24 (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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7A ALA* 3.2 6.2 - - - +
8A PHE* 2.9 46.0 + - - +
23A GLU* 1.3 78.4 - - - +
25A MSE 1.3 60.0 + - - -
36A PHE 3.4 11.9 - - - -
37A SER* 3.7 1.8 - - - -
299A TRP* 3.6 15.5 - - - -
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Residues in contact with MSE 25 (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 GLY* 3.5 26.7 - - - +
6A ARG 3.2 21.8 - - - +
7A ALA* 4.1 1.8 - - - +
8A PHE* 3.6 1.0 - - - -
24A GLY* 1.3 75.1 - - - +
26A LEU* 1.3 68.5 + - - +
27A VAL* 3.7 7.9 + - + +
35A GLU* 3.5 2.4 - - - +
36A PHE* 2.8 46.4 + - + +
296A PRO* 5.0 2.2 - - - +
299A TRP* 4.0 16.2 - - + +
300A GLN* 3.0 51.1 - - - +
303A LEU* 3.4 28.7 - - + -
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Residues in contact with LEU 26 (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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4A THR 3.5 2.4 - - - +
5A GLY* 3.2 5.0 - - - -
6A ARG 2.8 33.9 + - - +
8A PHE* 3.9 14.1 - - + -
25A MSE 1.3 74.2 - - - +
27A VAL* 1.3 60.0 + - - +
33A TRP* 4.0 16.8 - - + -
34A GLY 3.3 1.6 - - - -
35A GLU* 3.8 22.7 - - + -
232A THR* 4.1 3.1 - - - +
234A VAL* 3.8 33.7 - - + -
265A VAL* 3.8 28.7 - - + -
284A VAL* 4.6 7.2 - - + -
289A LEU* 4.1 29.6 - - + -
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Residues in contact with VAL 27 (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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4A THR* 3.8 7.0 - - - +
5A GLY* 4.4 2.9 - - - -
25A MSE 3.7 27.4 - - + +
26A LEU* 1.3 80.2 - - - +
28A ARG* 1.3 69.7 + - - +
33A TRP* 3.5 5.5 - - - -
34A GLY 2.9 31.9 + - - -
51A TRP* 4.8 10.1 - - + -
54A CYS* 4.1 20.0 - - - -
58A ALA* 3.5 13.8 - - + +
303A LEU* 3.8 15.5 - - + -
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Residues in contact with ARG 28 (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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4A THR* 3.5 27.0 + - + +
27A VAL* 1.3 81.7 - - - +
29A GLY* 1.3 79.0 + - - +
30A ALA* 4.7 4.2 + - - +
31A ALA 4.9 0.4 - - - -
32A GLY* 3.8 20.6 - - - +
33A TRP* 3.2 49.7 - - + +
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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