Contacts of the strand formed by residues 25 - 30 (chain A) in PDB entry 1W6J
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 TRP 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A THR* 2.9 24.7 + - - -
21A ASP 3.9 6.3 - - - -
22A LEU* 3.3 17.6 + - + +
24A ARG* 1.3 76.8 - - - +
26A ARG* 1.3 64.6 + - - +
36A TRP* 3.9 20.6 - + + -
37A THR 3.4 20.9 - - - -
38A TYR* 3.3 34.8 - + + -
48A GLN* 3.0 22.5 + - - +
52A GLU* 4.3 2.1 - - - -
56A LEU* 3.9 17.6 - - + +
122A GLY* 3.7 30.1 - - - -
123A TYR* 3.8 35.2 - + - -
126A GLU* 3.8 9.6 - - + -
371A MET* 3.8 31.4 - - + +
376A MET* 4.0 10.5 - - + -
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Residues in contact with ARG 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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23A GLY 2.9 27.9 + - - -
24A ARG* 3.5 7.7 - - - +
25A TRP* 1.3 87.8 + - - +
27A LEU* 1.3 59.2 - - - +
28A ASN* 4.0 14.2 + - - +
35A THR 3.8 0.3 - - - +
36A TRP* 3.3 10.7 - - - -
37A THR* 2.8 42.9 + - - +
39A LEU* 3.5 39.8 - - + +
42A GLU* 5.6 2.6 + - - +
46A ARG* 3.1 58.7 + - + +
47A GLU* 4.5 0.6 - - - +
48A GLN* 3.6 21.6 - - - +
52A GLU* 3.3 8.5 - - - +
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Residues in contact with LEU 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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26A ARG* 1.3 72.5 - - - +
28A ASN* 1.3 68.4 + - - +
29A CYS* 3.9 11.3 + - - -
34A GLN* 4.1 14.4 - - + -
35A THR 3.7 21.3 - - - +
36A TRP* 3.8 38.9 - - + +
46A ARG* 3.2 19.2 + - - -
51A LEU* 4.6 15.7 - - + -
52A GLU* 2.8 18.7 + - + +
55A ALA* 5.7 0.9 - - + -
90A GLU* 5.4 2.1 - - - +
95A THR* 4.0 22.4 - - + +
370A TRP* 4.0 21.5 - - + -
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Residues in contact with ASN 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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26A ARG* 4.2 16.0 + - - +
27A LEU* 1.3 80.0 - - - +
29A CYS* 1.3 62.2 + - - +
33A ARG 3.2 4.2 - - - +
34A GLN* 3.6 2.4 - - - -
35A THR* 3.0 44.1 + - - +
37A THR* 4.0 19.4 + - - -
46A ARG* 4.0 12.4 + - - -
90A GLU* 5.3 1.1 - - - -
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Residues in contact with CYS 29 (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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27A LEU* 3.9 26.9 - - - -
28A ASN* 1.3 80.8 - - - +
30A GLU* 1.3 62.7 + - - +
33A ARG 3.1 5.6 - - - +
34A GLN* 4.2 7.9 - - - -
51A LEU* 5.9 0.4 - - - -
89A ALA* 4.0 14.4 - - + -
90A GLU* 2.8 42.6 + - - +
91A ASP* 3.9 9.4 - - - +
93A HIS* 3.9 19.5 - - - +
95A THR* 4.1 3.6 - - - -
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Residues in contact with GLU 30 (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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28A ASN 4.3 0.2 - - - -
29A CYS* 1.3 75.0 - - - +
31A ARG* 1.3 85.9 + - + +
32A GLY 3.1 0.4 - - - -
33A ARG* 3.1 30.6 + - + +
91A ASP* 3.8 2.6 + - - -
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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