Contacts of the strand formed by residues 38 - 43 (chain B) in PDB entry 2F5Y
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 VAL 38 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ILE* 3.5 35.4 - - + -
33B CYS 4.0 1.3 - - - +
34B CYS 3.5 19.7 - - - +
37B PRO* 1.3 76.2 - - - +
39B ARG* 1.3 61.8 + - - +
59B THR* 3.7 2.9 - - - +
60B VAL* 2.9 32.4 + - + +
68B VAL* 5.1 3.0 + - + +
71B TRP* 3.4 24.7 - - + +
72B LYS 3.7 4.0 - - - +
73B CYS* 3.5 16.2 - - - +
76B LEU* 3.7 29.4 - - + -
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Residues in contact with ARG 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A CYS* 3.5 25.8 - - - +
35A ASP 3.0 18.6 + - - -
36A SER 4.1 1.4 + - - -
37A PRO* 2.9 40.2 + - - +
38A VAL 4.7 0.2 - - - -
39A ARG* 4.3 30.8 - - - +
59A THR* 4.9 3.8 + - - +
32B ILE* 3.2 9.4 - - - +
33B CYS* 2.8 39.7 + - - +
37B PRO 3.9 0.2 + - - -
38B VAL* 1.3 73.4 - - - +
40B VAL* 1.3 76.2 + - - +
41B GLN* 3.8 8.3 - - - +
57B LEU* 3.5 42.0 - - - +
58B ASP 3.6 10.3 - - - +
59B THR* 4.1 9.4 - - - +
60B VAL* 5.1 0.9 - - - -
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Residues in contact with VAL 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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30B PHE* 4.5 7.2 - - + -
31B THR 3.6 6.5 - - - +
32B ILE* 4.5 0.7 - - + -
39B ARG* 1.3 76.5 + - - +
41B GLN* 1.3 60.8 + - - +
42B ALA 3.8 20.6 - - - +
43B VAL* 3.8 15.3 - - + -
54B LEU* 3.6 35.4 - - + -
55B GLN 3.4 23.3 - - - +
57B LEU* 3.0 26.7 + - - -
58B ASP* 2.8 22.9 + - + +
60B VAL* 4.4 14.4 - - + -
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Residues in contact with GLN 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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34A CYS* 3.8 0.2 - - - -
35A ASP* 2.8 58.9 + - - +
36A SER* 4.9 2.4 + - - -
31B THR* 2.9 35.8 + - + +
32B ILE 4.1 2.5 - - - -
33B CYS* 3.4 27.5 - - + +
39B ARG* 3.3 8.3 + - - +
40B VAL* 1.3 75.1 - - - +
42B ALA* 1.3 65.4 + - + +
56B GLN* 3.9 13.8 - - - +
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Residues in contact with ALA 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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30B PHE* 3.3 5.8 - - - +
31B THR* 2.9 36.3 + - + +
40B VAL* 3.6 2.9 - - - +
41B GLN* 1.3 85.9 - - + +
43B VAL* 1.3 69.5 + - - +
56B GLN* 4.8 6.1 - - - -
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Residues in contact with VAL 43 (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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29B GLY 3.7 8.3 - - - +
30B PHE* 4.1 7.2 - - + -
40B VAL* 3.8 18.4 - - + -
42B ALA* 1.3 83.4 - - - +
44B ASP* 1.3 66.1 + - - +
45B SER* 3.6 3.5 + - - -
49B ALA 3.8 0.9 - - - -
50B GLU* 3.2 49.3 - - + +
54B LEU* 3.7 24.2 - - + +
55B GLN* 3.9 9.6 - - - -
56B GLN 4.4 1.1 - - - +
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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