Contacts of the strand formed by residues 31 - 38 (chain B) in PDB entry 1WKJ
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 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PRO* 5.0 12.9 - - - +
29B GLY 3.8 1.7 + - - +
30B PHE* 1.3 73.2 - - - +
32B ILE* 1.3 73.1 + - - +
33B ALA* 3.4 10.7 + - - +
75B LEU* 3.3 7.4 - - - -
76B GLU* 2.8 67.0 + - + +
137B LEU* 2.7 45.9 + - - +
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Residues in contact with ILE 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A VAL* 5.9 7.0 - - + +
18A VAL* 4.6 15.3 - - + -
37A LEU* 3.3 25.1 - - + +
69A PRO* 5.8 1.7 - - - +
71A VAL* 5.9 1.6 - - + -
22B LEU* 4.0 22.0 - - + -
25B PHE* 6.1 0.7 - - + -
26B GLU* 4.1 31.0 - - + +
30B PHE 4.0 2.9 + - - +
31B ARG* 1.3 84.8 + - - +
33B ALA* 1.3 56.9 - - - +
34B ALA 3.4 24.0 - - - +
35B LEU* 4.0 19.7 - - + -
73B MET* 5.1 0.9 - - + -
74B VAL 3.6 5.2 - - - +
75B LEU* 4.2 15.9 - - + -
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.6 6.6 - - - +
3B ARG* 6.2 0.2 - - - -
31B ARG* 3.4 24.3 + - - +
32B ILE* 1.3 74.3 - - - +
34B ALA* 1.3 60.9 + - - +
74B VAL* 2.8 22.3 + - + +
76B GLU* 3.8 24.2 - - + +
135B GLU 3.9 0.2 - - - +
136B LEU* 3.7 5.7 - - + -
137B LEU* 2.7 37.5 + - - +
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.7 6.0 - - - +
32B ILE* 3.4 8.3 - - - +
33B ALA* 1.3 80.7 - - - +
35B LEU* 1.3 66.1 + - - +
73B MET* 3.3 5.9 - - - +
74B VAL* 3.1 36.8 + - + -
131B PHE* 3.7 21.5 - - + -
135B GLU 3.5 19.3 - - - +
136B LEU* 3.9 7.0 - - + -
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 4.8 1.8 - - + -
35A LEU* 4.2 24.2 - - + -
36A LYS* 3.0 4.2 - - - +
37A LEU* 2.9 37.8 + - + +
71A VAL* 4.4 25.4 - - + -
22B LEU* 4.2 24.7 - - + -
32B ILE* 4.0 11.7 - - + -
34B ALA* 1.3 77.0 - - - +
36B LYS* 1.3 66.9 + - - +
71B VAL* 3.6 28.3 - - + -
72B ALA 3.3 5.6 - - - +
73B MET* 3.7 24.0 - - + -
131B PHE* 3.9 3.4 - - - -
135B GLU 4.9 0.8 + - - -
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Residues in contact with LYS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 3.0 15.9 - - - +
36A LYS* 4.2 6.5 - - + -
35B LEU* 1.3 80.1 - - - +
37B LEU* 1.3 66.0 + - - +
38B MET* 3.7 28.0 + - + +
71B VAL* 3.5 6.1 - - - -
72B ALA* 2.9 35.2 + - + +
130B PHE 2.7 29.5 + - - -
131B PHE* 3.6 24.6 - - + +
132B ARG* 4.6 2.8 - - - +
135B GLU* 2.9 34.1 + - - +
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG* 6.0 0.2 - - - +
32A ILE* 3.3 33.0 - - + +
33A ALA* 3.6 23.8 - - - +
34A ALA* 3.7 4.0 - - - +
35A LEU* 2.9 29.2 + - + +
135A GLU* 4.9 7.4 - - - +
137A LEU* 4.0 21.5 - - + +
13B VAL* 4.5 9.6 - - + -
36B LYS* 1.3 77.2 - - - +
38B MET* 1.3 62.1 + - - +
69B PRO* 3.8 20.4 - - + -
70B VAL 3.4 16.6 - - - +
71B VAL* 3.9 18.2 - - + +
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Residues in contact with MET 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU* 3.6 10.3 - - - -
36B LYS* 3.7 30.7 - - + +
37B LEU* 1.3 76.9 - - - +
39B GLN* 1.3 68.3 + - - +
40B ILE* 4.6 2.5 - - + -
44B LEU* 4.2 16.2 - - + -
69B PRO* 3.3 2.6 - - - +
70B VAL* 2.9 51.5 + - + +
72B ALA* 4.0 17.3 - - - -
130B PHE* 3.8 40.6 - - + +
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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