Contacts of the strand formed by residues 46 - 53 (chain D) in PDB entry 2ZVW
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 46 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU* 4.3 9.9 - - + -
40D MET* 3.1 8.7 - - - +
41D ASP* 2.8 30.1 + - - +
44D HIS 3.4 0.2 - - - -
45D VAL* 1.3 81.4 - - - +
47D LEU* 1.3 62.6 + - - +
211D TYR* 3.8 25.4 - - + -
215D PHE* 4.1 17.7 - - + -
250D TYR 3.2 11.7 - - - +
251D LEU* 4.2 1.3 - - + -
147L MET* 3.9 3.4 - - - -
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Residues in contact with LEU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU* 4.8 3.1 - - - +
38D GLN* 3.7 30.5 - - + +
39D ALA* 3.4 11.4 - - - +
40D MET* 3.9 11.9 - - + -
46D ALA* 1.3 78.0 - - - +
48D VAL* 1.3 73.7 + - - +
49D SER* 4.0 1.3 - - - +
126D LEU* 3.7 30.7 - - + -
128D ILE* 3.8 16.2 - - + -
249D TYR* 3.4 5.0 - - - +
250D TYR* 2.7 57.3 + - + +
147L MET* 4.1 15.3 - - + -
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Residues in contact with VAL 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D VAL* 4.0 17.9 - - + -
22D LEU* 4.0 14.6 - - + -
23D VAL* 3.8 22.9 - - + -
37D LEU* 3.7 12.8 - - + +
38D GLN* 3.3 5.4 - - - +
39D ALA 2.8 43.9 + - - +
47D LEU* 1.3 78.2 - - - +
49D SER* 1.3 64.7 + - - +
50D LEU* 4.8 3.1 - - + +
247D ILE* 3.8 26.9 - - + -
248D ARG 3.3 3.8 - - - +
249D TYR* 3.9 13.0 - - + -
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Residues in contact with SER 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU 3.5 5.1 + - - -
38D GLN* 4.5 10.3 + - - +
47D LEU* 4.0 6.2 - - - +
48D VAL* 1.3 73.9 - - - +
50D LEU* 1.3 60.7 + - - +
128D ILE* 5.4 1.3 - - - -
246D TYR* 3.8 16.8 + - - -
247D ILE* 3.6 1.0 - - - -
248D ARG* 2.7 48.9 + - - +
250D TYR* 4.0 20.6 + - - -
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Residues in contact with LEU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D VAL* 3.5 30.1 - - + -
19D VAL* 5.2 6.7 - - + -
28D PHE* 3.9 27.1 - - + -
35D PHE* 5.1 2.2 - - + +
36D SER* 3.3 7.6 - - - -
37D LEU* 2.8 47.6 + - + +
48D VAL* 4.0 3.8 - - + -
49D SER* 1.3 77.3 + - - +
51D LEU* 1.3 66.5 + - - +
52D LEU* 4.2 21.3 - - + -
246D TYR* 3.3 17.9 - - - +
247D ILE* 3.6 24.9 - - + +
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Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D THR* 4.7 14.1 - - + -
34D GLY* 4.6 9.6 - - - -
35D PHE 3.8 3.6 - - - +
36D SER* 4.1 16.6 - - - -
50D LEU* 1.3 77.2 - - - +
52D LEU* 1.3 81.4 + - - +
53D ARG* 3.9 32.3 - - + +
245D GLY* 3.1 4.2 - - - -
246D TYR* 2.9 75.7 + - + +
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Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 5.2 5.2 - - + -
11D LEU* 6.2 1.3 - - + -
12D LEU* 4.4 18.8 - - + -
15D VAL* 4.6 11.0 - - + -
34D GLY* 3.3 0.2 - - - -
35D PHE* 2.8 57.4 + - + +
50D LEU* 4.2 19.1 - - + -
51D LEU* 1.3 84.5 - - - +
53D ARG* 1.3 66.8 + - - +
57D PHE* 3.5 13.4 - - + -
241D VAL* 3.8 32.1 - - + -
244D MET* 3.5 27.1 - - + -
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Residues in contact with ARG 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D THR* 3.5 12.1 - - + +
34D GLY* 4.2 0.4 - - - -
51D LEU* 3.9 26.6 - - + +
52D LEU* 1.3 75.0 - - - +
54D SER* 1.3 65.5 + - - +
55D GLU* 3.1 29.6 - - + +
56D GLY* 3.0 14.6 + - - -
57D PHE* 3.4 8.0 - - - -
243D GLU 4.6 6.2 + - - -
244D MET* 2.7 22.0 + - - +
245D GLY* 3.9 21.2 + - - +
246D TYR* 3.8 23.7 - - - -
248D ARG* 5.3 2.2 - - - +
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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