Contacts of the strand formed by residues 33 - 39 (chain B) in PDB entry 2W3S
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 LEU 33 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B ASN 3.8 0.2 - - - +
32B THR* 1.3 77.9 - - - +
34B HIS* 1.3 71.6 + - - +
35B LEU* 4.6 0.7 - - + -
62B ILE* 4.0 29.8 - - + -
102B ALA* 4.1 12.1 - - + -
103B ALA 3.7 11.4 - - - +
104B THR* 4.5 4.9 - - + -
249B THR* 3.3 40.2 - - + +
251B ARG* 3.4 44.2 - - - +
252B PRO 2.9 14.6 + - - +
253B CYS* 4.3 8.5 - - - -
254B LYS 2.9 23.2 + - - -
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Residues in contact with HIS 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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32B THR* 3.6 19.6 + - + +
33B LEU* 1.3 81.8 + - - +
35B LEU* 1.3 63.3 + - - +
101B VAL 3.4 1.4 - - - +
102B ALA* 3.3 4.0 - - - -
103B ALA 2.8 30.1 + - - +
104B THR 4.0 4.6 + - - -
105B SER* 3.5 40.1 - - - +
106B HIS* 3.5 22.6 + - + +
109B ALA* 3.7 5.6 - - - +
254B LYS* 3.2 38.8 + - - +
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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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34B HIS* 1.3 87.8 - - - +
36B ALA* 1.3 61.3 + - - +
100B LEU* 3.8 17.9 - - + -
101B VAL 3.1 4.5 - - - +
102B ALA* 3.7 24.5 - - + +
106B HIS* 4.7 10.6 - - - +
109B ALA* 4.2 2.2 - - - -
241B ALA* 3.3 38.4 - - + +
242B CYS* 3.8 9.4 - - - +
245B ALA* 3.9 7.6 - - + -
253B CYS* 4.1 16.4 - - + -
254B LYS 2.9 17.6 + - - +
255B MET* 3.3 32.5 - - + +
256B ARG 4.7 2.1 + - - +
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Residues in contact with ALA 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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35B LEU* 1.3 75.1 - - - +
37B PHE* 1.3 63.1 + - - +
100B LEU* 3.7 0.9 - - - +
101B VAL* 2.8 34.5 + - - +
106B HIS* 6.0 0.4 - - + -
109B ALA* 3.6 36.3 - - + +
110B ARG* 3.7 16.2 - - + +
113B ALA* 4.2 5.8 - - + -
255B MET* 3.7 6.7 - - - -
261B ASP* 5.5 4.7 - - - +
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Residues in contact with PHE 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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36B ALA* 1.3 73.4 - - - +
38B GLY* 1.3 58.4 + - - +
39B LEU* 3.7 23.4 + - + +
85B VAL* 4.2 13.0 - - + -
86B LEU* 3.8 19.3 - - + -
97B PRO* 3.5 28.3 - - + -
99B PHE 3.4 9.9 - - - -
100B LEU* 4.0 19.3 - - + -
113B ALA* 3.3 15.2 - - - +
237B HIS* 3.8 25.6 - - + -
241B ALA* 4.1 5.6 - - + -
255B MET* 3.6 24.4 - - + +
257B TYR* 3.4 34.7 - + - -
261B ASP* 4.9 9.5 + - - +
265B ILE* 4.4 4.7 - - + -
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Residues in contact with GLY 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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36B ALA 3.9 0.8 + - - -
37B PHE* 1.3 71.7 - - - +
39B LEU* 1.3 54.4 + - - -
97B PRO* 3.3 3.3 - - - +
98B ILE* 2.7 33.8 + - - -
99B PHE* 2.7 50.3 + - - -
113B ALA* 4.1 9.2 - - - +
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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 PHE* 3.7 23.1 + - + +
38B GLY* 1.3 72.0 - - - -
40B SER* 1.3 67.5 + - - +
41B THR* 3.6 8.1 + - - +
95B GLY* 2.9 37.2 - - - +
96B GLN 3.3 1.3 - - - -
97B PRO* 3.6 22.2 - - + -
98B ILE* 4.3 4.2 - - - +
118B ILE* 4.9 6.1 - - - +
120B TYR* 4.3 2.8 + - - -
261B ASP* 4.8 12.8 - - - +
264B VAL* 4.1 12.1 - - + -
265B ILE* 3.6 24.7 - - + -
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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