Contacts of the strand formed by residues 33 - 38 (chain D) in PDB entry 1WNT
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 ARG 33 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D GLY* 3.6 29.3 + - - -
8D ARG 2.6 12.3 + - - +
9D ARG* 3.0 52.4 - - + +
10D VAL* 2.6 35.9 + - - +
31D GLY 5.3 0.4 - - - +
32D ALA* 1.3 71.2 - - - +
34D VAL* 1.3 54.0 + - - +
53D GLY 5.2 5.6 - - - +
55D GLU* 5.5 4.9 - - - +
76D PRO* 4.2 8.5 + - - +
78D ASP* 5.3 1.4 + - - -
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Residues in contact with VAL 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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10D VAL* 3.3 12.6 - - + +
12D VAL* 4.8 7.9 - - + -
24D VAL* 4.2 30.5 - - + +
27D LEU* 4.1 27.8 - - + -
28D HIS* 4.4 5.1 - - - +
32D ALA 3.6 14.3 + - - +
33D ARG* 1.3 77.8 - - - +
35D VAL* 1.3 75.7 + - - +
36D ALA* 4.1 3.4 - - + +
53D GLY 4.3 7.1 + - - +
54D ILE* 3.4 19.8 - - + +
55D GLU* 3.0 29.5 + - - +
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Residues in contact with VAL 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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9D ARG* 3.0 44.0 - - + +
10D VAL 2.7 13.4 + - - +
11D LEU* 3.4 19.0 - - + +
12D VAL 2.9 26.0 + - - -
34D VAL* 1.3 73.6 - - - +
36D ALA* 1.3 61.3 + - - +
37D VAL* 3.6 11.7 + - + -
55D GLU* 3.4 17.9 - - + +
57D VAL* 4.1 9.9 - - + -
74D VAL* 3.8 25.1 - - + -
77D VAL* 5.4 1.3 - - + -
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Residues in contact with ALA 36 (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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12D VAL 3.8 0.7 - - - -
15D ALA* 3.3 23.6 - - + -
24D VAL* 3.9 12.6 - - + -
34D VAL* 3.9 6.2 + - + -
35D VAL* 1.3 71.3 - - - +
37D VAL* 1.3 60.3 + - - +
44D LEU* 2.8 40.2 - - + +
47D LEU* 4.6 6.1 - - + -
54D ILE* 4.7 8.7 - - + -
55D GLU 3.2 7.2 + - - +
56D PRO* 3.4 0.4 - - + +
57D VAL 2.9 15.7 + - - -
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Residues in contact with VAL 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LEU* 3.3 38.4 - - + -
12D VAL 3.0 4.9 + - - -
13D THR* 3.8 9.9 - - + -
14D GLY 2.6 32.9 + - - -
15D ALA 3.0 5.1 + - - -
35D VAL* 4.0 10.3 - - + -
36D ALA* 1.3 72.8 - - - +
38D SER* 1.3 60.1 + - - +
57D VAL* 3.4 16.6 - - + +
59D VAL* 3.9 26.5 - - + -
61D LEU* 4.1 20.6 - - + -
71D LEU* 4.5 8.7 - - + -
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Residues in contact with SER 38 (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 GLY* 4.0 1.4 - - - +
15D ALA 3.8 2.3 + - - -
16D GLY* 2.8 38.1 + - - -
37D VAL* 1.3 76.0 - - - +
39D ARG* 1.3 61.6 + - - +
40D THR 3.5 6.1 - - - -
43D ASP* 4.4 0.5 + - - -
44D LEU* 4.0 15.6 - - - +
57D VAL 2.9 6.7 + - - -
58D CYS* 3.2 9.1 - - - -
59D VAL 3.1 26.8 + - - +
3245D NAP 3.6 22.1 + - - -
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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