Contacts of the strand formed by residues 29 - 35 (chain D) in PDB entry 4WNP
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 VAL 29 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D ARG* 5.5 1.6 - - - +
21D LEU* 3.1 31.6 - - + -
23D GLY 3.7 3.4 - - - +
24D HIS* 4.3 14.6 - - + +
28D ALA* 1.3 78.5 - - - +
30D VAL* 1.3 60.6 + - - +
31D PHE* 3.3 23.0 - - + -
45D VAL 3.6 1.6 - - - +
47D CYS* 2.8 39.2 + - + +
48D ILE 4.2 4.9 - - - +
49D ASN* 3.9 31.2 - - + +
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Residues in contact with VAL 30 (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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21D LEU* 3.6 5.4 - - - +
22D ILE* 2.7 39.9 + - + -
23D GLY* 2.8 25.5 + - - +
28D ALA* 4.8 3.4 - - + -
29D VAL* 1.3 80.7 - - - +
31D PHE* 1.3 60.8 + - - +
44D ALA* 4.0 16.2 - - + -
45D VAL 3.3 9.2 - - - +
46D LYS* 3.6 26.9 - - + -
401D 3RJ 3.9 40.4 - - + -
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Residues in contact with PHE 31 (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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16D PHE* 3.8 26.7 - + + -
17D SER 3.8 11.9 - - - +
18D ARG* 3.3 73.8 - - + -
20D ASP 3.2 5.6 - - - +
21D LEU* 3.7 25.6 - - + -
22D ILE* 3.6 4.9 - - - +
29D VAL* 3.3 27.1 - - + -
30D VAL* 1.3 73.9 - - - +
32D LYS* 1.3 63.3 + - - +
44D ALA* 3.4 3.5 - - - -
45D VAL* 2.8 36.9 + - - +
47D CYS* 3.8 18.4 - - - -
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Residues in contact with LYS 32 (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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16D PHE* 3.4 14.5 - - - +
17D SER 4.2 0.2 + - - -
20D ASP* 2.9 37.9 + - + +
22D ILE* 3.3 19.2 - - + +
31D PHE* 1.3 75.3 - - - +
33D GLY* 1.3 65.9 + - - +
42D GLU* 2.5 36.4 + - + -
43D VAL 3.6 8.3 - - - +
94D TYR* 3.4 36.0 + - + +
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Residues in contact with GLY 33 (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 GLU 3.0 14.4 - - - -
16D PHE* 3.8 7.4 - - - -
31D PHE 3.8 1.0 + - - -
32D LYS* 1.3 79.4 - - - +
34D ARG* 1.3 63.8 + - - +
42D GLU* 3.6 5.9 - - - +
43D VAL* 2.8 35.4 + - - +
45D VAL* 5.0 0.2 - - - -
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Residues in contact with ARG 34 (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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14D PHE* 3.4 8.1 - - - -
15D GLU* 2.7 65.9 + - + +
33D GLY* 1.3 74.9 - - - +
35D HIS* 1.3 68.9 + - - +
39D HIS* 3.2 59.4 + - - +
41D LEU 3.3 14.1 - - - +
42D GLU* 4.8 1.6 - - + -
43D VAL* 3.6 4.1 - - - +
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Residues in contact with HIS 35 (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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13D LYS* 3.6 35.3 - - + +
14D PHE* 3.7 32.5 - + + -
34D ARG* 1.3 72.9 - - - +
36D ARG* 1.3 64.9 + - + +
37D ALA* 3.1 38.0 + - + -
38D ALA* 3.2 31.8 + - + +
39D HIS* 3.2 17.8 + - - -
41D LEU* 3.0 29.2 + - + -
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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