Contacts of the strand formed by residues 36 - 42 (chain B) in PDB entry 2W5X
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 ASN 36 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B PRO* 3.7 3.8 - - - +
35B LYS* 1.3 90.4 - - - +
37B VAL* 1.3 67.9 + - - +
247B SER 4.1 1.2 - - - +
248B ALA* 3.2 12.6 - - - -
249B PHE* 3.0 58.3 + - + +
287B PHE* 4.7 0.6 - - - -
291B ASP* 3.4 15.8 + - - -
293B ASN* 3.1 4.8 + - - +
294B THR* 3.1 28.0 + - + +
295B LEU 2.9 24.8 + - - -
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Residues in contact with VAL 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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34B PRO* 4.8 1.6 - - + -
36B ASN* 1.3 79.9 - - - +
38B ILE* 1.3 72.3 + - - +
39B LEU* 4.1 0.7 - - + +
249B PHE* 3.1 8.5 + - - +
250B PHE* 3.3 29.2 - - + -
251B ILE 3.0 22.9 + - - +
295B LEU* 3.3 21.3 - - + +
297B ILE* 4.1 24.0 - - + -
367B ILE* 4.6 9.2 - - + -
371B THR* 3.7 30.3 - - + -
373B TRP* 4.4 8.9 - - + -
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Residues in contact with ILE 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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37B VAL* 1.3 80.5 - - - +
39B LEU* 1.3 60.2 + - - +
40B LEU* 3.8 28.2 + - + -
235B THR* 5.0 4.0 - - + -
239B ILE* 3.8 30.5 - - + -
249B PHE* 3.7 20.6 - - + -
251B ILE* 3.4 19.1 - - + +
284B ALA* 4.2 25.1 - - + +
287B PHE* 4.5 1.8 - - + -
294B THR* 4.0 16.4 - - + -
295B LEU 2.9 11.4 + - - +
296B VAL* 3.4 7.2 - - + +
297B ILE* 2.9 27.4 + - - +
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Residues in contact with LEU 39 (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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37B VAL* 4.1 2.1 - - + +
38B ILE* 1.3 71.6 - - - +
40B LEU* 1.3 65.8 + - - +
41B ILE* 4.1 15.0 - - + -
91B PHE* 4.5 11.7 - - + +
141B PHE* 3.7 33.9 - - + -
250B PHE* 4.4 15.7 - - + -
251B ILE 2.7 13.1 + - - +
252B MET* 3.2 7.3 - - + +
253B SER 3.0 24.4 + - - +
297B ILE* 3.4 37.5 - - + +
299B THR* 4.4 12.3 - - + -
363B ILE* 4.8 6.5 - - + -
367B ILE* 4.7 12.6 - - + -
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Residues in contact with LEU 40 (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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38B ILE* 3.9 19.5 - - + +
39B LEU* 1.3 73.9 - - - +
41B ILE* 1.3 63.9 + - - +
235B THR* 4.7 8.7 - - + +
253B SER* 3.3 31.4 - - - +
277B PHE* 3.7 17.9 - - + -
280B ALA* 4.1 8.3 - - + +
281B ILE* 3.7 34.3 - - + +
284B ALA* 3.8 17.7 - - + -
296B VAL* 4.3 2.2 - - + -
297B ILE 2.8 14.8 + - - +
298B VAL* 3.5 17.6 - - + -
299B THR 3.1 25.5 + - - +
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Residues in contact with ILE 41 (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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39B LEU* 4.1 15.3 - - + -
40B LEU* 1.3 76.6 - - - +
42B SER* 1.3 67.9 - - - +
43B ASP* 4.2 5.8 - - + +
88B ALA* 5.4 0.7 - - + -
91B PHE* 3.7 30.3 - - + -
137B THR* 3.9 24.5 - - + -
141B PHE* 4.0 9.4 - - + -
252B MET* 3.9 28.7 - - + -
253B SER 2.9 11.9 + - - +
254B GLU* 3.3 6.4 - - + +
255B GLY 2.8 26.0 + - - -
277B PHE* 3.5 2.9 - - - -
299B THR* 3.3 7.4 - - + +
300B SER* 4.5 0.4 - - - -
301B ASP* 4.3 18.2 - - + +
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Residues in contact with SER 42 (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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41B ILE* 1.3 69.9 - - - +
43B ASP* 1.3 65.6 + - - +
44B GLY 3.3 0.2 + - - -
45B ALA* 3.4 12.6 + - - +
50B ILE* 5.4 1.0 - - - +
63B TYR* 4.4 5.0 + - - -
255B GLY 4.0 0.2 - - - -
258B ILE* 3.6 22.2 - - - -
277B PHE* 3.5 29.2 - - - -
298B VAL* 5.1 1.4 - - - +
299B THR 3.0 10.2 + - - -
300B SER* 2.6 46.3 + - - -
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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