Contacts of the strand formed by residues 40 - 45 (chain B) in PDB entry 3OFN
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 ILE 40 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ALA 4.2 0.2 - - - +
36B VAL* 3.2 3.7 - - - +
37B GLY 2.9 35.5 + - - +
38B ASP* 3.1 23.5 - - + +
39B GLY* 1.3 83.3 - - - +
41B ALA* 1.3 65.8 + - - +
42B ARG* 4.1 6.9 + - + +
67B ILE* 5.4 1.1 - - + -
74B GLY* 4.8 6.1 - - - -
75B ILE 3.4 23.1 - - - +
76B VAL* 4.1 11.7 - - + -
283B LEU* 4.9 2.7 - - + +
286B LEU* 4.3 14.4 - - + +
287B LEU* 3.8 40.4 - - + +
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 4.8 1.6 - - + -
35B ALA 3.3 7.4 - - - +
36B VAL* 3.8 13.9 - - + +
39B GLY 4.3 0.2 - - - -
40B ILE* 1.3 76.7 - - - +
42B ARG* 1.3 64.4 + - - +
43B VAL* 3.6 4.7 - - + +
57B PHE* 4.2 17.5 - - + -
73B VAL 3.6 0.9 - - - +
75B ILE* 2.8 36.6 + - - +
77B LEU* 3.8 23.6 - - + -
84B VAL* 4.3 3.1 - - + -
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Residues in contact with ARG 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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33B VAL* 3.7 0.9 - - - -
34B LEU* 2.7 42.4 + - + +
35B ALA* 2.8 40.7 + - - +
40B ILE* 4.1 8.2 - - + -
41B ALA* 1.3 72.7 - - - +
43B VAL* 1.3 56.7 - - - +
72B GLN* 3.1 41.3 + - - +
73B VAL 3.5 5.4 - - - +
74B GLY* 4.5 8.5 - - - -
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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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31B GLY* 3.7 6.1 - - - -
32B ARG 3.3 13.5 - - - +
33B VAL* 4.4 6.1 - - + -
34B LEU* 4.7 0.2 - - - +
41B ALA 3.6 7.6 - - - +
42B ARG* 1.3 80.1 - - - +
44B PHE* 1.3 72.3 + - - +
45B GLY 4.0 0.2 + - - -
46B LEU* 4.4 7.4 - - + -
57B PHE* 4.6 7.4 - - + -
72B GLN* 3.2 5.5 - - - +
73B VAL* 2.6 43.5 + - + +
75B ILE* 3.6 28.7 - - + -
90B VAL* 3.5 35.4 - - + -
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Residues in contact with PHE 44 (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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27B LEU* 3.7 33.4 - - + +
31B GLY* 3.2 5.4 - - - -
32B ARG* 2.8 43.2 + - + +
34B LEU* 3.7 27.7 - - + +
43B VAL* 1.3 71.8 - - - +
45B GLY* 1.3 77.6 + - - +
71B GLY* 3.3 28.7 - - - -
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Residues in contact with GLY 45 (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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27B LEU* 3.6 18.8 - - - -
30B THR 4.0 2.7 - - - -
43B VAL 4.0 0.4 + - - +
44B PHE* 1.3 89.2 - - - +
46B LEU* 1.3 74.6 + - - +
47B ASN* 3.3 12.9 + - - +
71B GLY 4.6 4.1 + - - -
72B GLN* 5.2 1.1 - - - +
73B VAL* 4.1 11.6 - - - +
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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