Contacts of the strand formed by residues 33 - 39 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31F ASN 4.0 0.2 - - - +
32F THR* 1.3 81.2 - - - +
34F HIS* 1.3 65.3 + - - +
35F LEU* 4.3 4.7 - - + -
62F ILE* 3.9 24.7 - - + -
102F ALA* 4.4 8.5 - - + -
103F ALA 3.4 17.0 - - - +
104F THR* 4.5 5.2 - - + -
249F THR* 3.7 34.8 - - + +
251F ARG* 3.2 46.9 - - - +
252F PRO 2.6 14.2 + - - +
253F CYS* 4.1 10.5 - - - -
254F LYS* 2.9 24.1 + - - +
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Residues in contact with HIS 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F CYS* 6.1 0.7 - - - -
32F THR* 3.8 18.2 + - + +
33F LEU* 1.3 81.1 + - - +
35F LEU* 1.3 63.4 + - - +
103F ALA 2.9 30.8 + - - -
104F THR 3.9 4.9 + - - -
105F SER* 3.5 25.4 - - - +
106F HIS* 3.5 34.0 + - + +
109F ALA* 3.2 8.0 - - - +
254F LYS* 3.2 42.7 + - + +
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Residues in contact with LEU 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F LEU 4.3 0.2 - - - -
34F HIS* 1.3 86.6 - - - +
36F ALA* 1.3 63.4 + - - +
100F LEU* 3.7 22.2 - - + -
101F VAL 3.0 7.0 - - - +
102F ALA* 3.7 23.3 - - + -
106F HIS* 4.6 13.8 + - - -
109F ALA* 3.8 4.5 - - - +
241F ALA* 3.8 3.6 - - + -
242F CYS* 3.7 31.9 - - - +
245F ALA* 3.7 17.3 - - + -
253F CYS* 4.1 17.3 - - - -
254F LYS 3.0 20.9 + - - +
255F MET* 3.6 25.6 - - + +
256F ARG 4.9 2.1 - - - +
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Residues in contact with ALA 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F LEU* 1.3 76.2 - - - +
37F PHE* 1.3 67.4 + - - +
100F LEU* 3.4 4.7 - - - +
101F VAL* 2.9 33.1 + - - +
109F ALA* 3.7 29.3 - - - +
110F ARG* 3.9 19.5 - - + +
113F ALA* 4.1 2.5 - - + -
255F MET* 3.6 10.8 - - - -
261F ASP* 5.4 2.9 - - - +
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Residues in contact with PHE 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F ALA* 1.3 76.4 - - - +
38F GLY* 1.3 58.5 + - - +
39F LEU* 3.5 24.4 + - + +
85F VAL* 4.3 13.2 - - + -
86F LEU* 3.9 17.0 - - + -
97F PRO* 3.5 29.6 - - + -
99F PHE 3.4 11.4 - - - -
100F LEU* 4.0 20.0 - - + -
113F ALA* 3.4 15.2 - - - +
237F HIS* 4.0 26.5 - - + -
241F ALA* 4.2 5.2 - - + -
255F MET* 3.6 19.5 - - + +
257F TYR* 3.3 28.0 - + - -
261F ASP* 5.4 5.8 + - - +
265F ILE* 4.1 11.7 - - + -
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Residues in contact with GLY 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F ALA 4.0 0.4 + - - -
37F PHE* 1.3 73.8 - - - +
39F LEU* 1.3 60.2 + - - -
97F PRO* 3.6 1.6 - - - +
98F ILE* 2.9 30.4 + - - +
99F PHE* 3.0 44.3 + - - -
113F ALA 3.9 9.4 - - - -
118F ILE* 6.1 0.4 - - - -
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Residues in contact with LEU 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F PHE* 3.5 34.1 + - + +
38F GLY* 1.3 75.6 - - - -
40F SER* 1.3 64.4 + - - +
41F THR* 3.5 10.7 + - + +
95F GLY* 3.1 31.4 - - - +
96F GLN 3.6 1.1 - - - -
97F PRO* 3.8 8.1 - - + -
98F ILE* 4.2 4.3 - - - +
113F ALA 5.2 0.4 + - - -
118F ILE* 5.0 5.4 - - - +
120F TYR* 4.3 2.9 + - - -
261F ASP* 3.9 22.4 - - - +
264F VAL* 4.1 15.5 - - + -
265F ILE* 3.8 22.4 - - + -
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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