Contacts of the strand formed by residues 36 - 42 (chain B) in PDB entry 2C1H
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 36 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 4.9 8.7 - - + -
32B THR 3.8 9.9 - - - +
33B VAL* 3.3 30.0 + - - +
34B ASN 3.3 2.2 + - - -
35B ASP* 1.3 83.4 - - - +
37B VAL* 1.3 66.4 + - - +
78B ILE* 3.7 20.6 - - + +
79B GLN* 4.4 3.3 + - - +
80B GLY 4.2 3.6 + - - +
304B LEU* 4.2 18.2 - - + -
315B ILE* 3.7 6.5 - - + +
317B THR* 3.8 24.0 - - + -
320B ALA* 3.8 29.4 - - + +
323B ALA* 4.0 12.6 - - + -
324B ALA* 4.1 9.2 - - + +
327B LEU* 4.4 6.1 - - + -
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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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35B ASP 4.1 0.2 + - - -
36B LEU* 1.3 77.1 - - - +
38B PHE* 1.3 62.2 + - - +
39B PRO* 3.4 1.4 - - - +
80B GLY* 3.4 26.9 - - - +
81B ILE 3.9 1.8 - - - +
82B ASP* 3.8 30.3 - - + +
121B MET* 4.9 10.8 - - + -
314B ILE* 3.7 23.1 - - + -
315B ILE 2.9 7.7 + - - +
316B PHE* 3.4 29.2 - - + -
317B THR 3.0 27.2 + - - +
320B ALA* 4.0 3.4 - - - +
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Residues in contact with PHE 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 LEU 4.3 0.2 - - - -
37B VAL* 1.3 71.6 - - - +
39B PRO* 1.4 82.4 - - + +
40B LEU* 4.1 18.6 - - + -
58B SER* 6.5 0.7 - - - -
61B PHE* 5.2 8.5 - + - -
69B GLU* 4.5 16.4 - - + -
73B LEU* 3.6 41.3 - - + -
78B ILE* 4.4 5.1 - - + +
80B GLY 3.3 5.4 + - - +
81B ILE* 3.3 11.3 - - + +
82B ASP 3.1 18.6 + - - -
317B THR 4.3 4.0 - - - -
318B TYR* 4.1 17.5 - + - -
320B ALA* 3.8 24.2 - - + +
321B LYS* 4.0 18.8 - - + -
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Residues in contact with PRO 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 3.4 4.9 - - - +
38B PHE* 1.4 101.4 - - + +
40B LEU* 1.3 58.8 + - - +
41B PHE* 4.4 3.6 + - + -
82B ASP* 3.3 14.6 - - + +
84B PHE* 4.1 8.7 - - + -
276B TYR* 3.6 31.4 - - + +
316B PHE* 4.5 7.0 - - + -
317B THR 3.2 28.9 - - - +
318B TYR* 3.6 30.1 - - + +
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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 PHE* 3.7 15.2 + - + +
39B PRO* 1.3 73.2 - - - +
41B PHE* 1.3 79.2 + - - +
42B VAL* 3.9 13.1 + - + -
61B PHE* 3.6 26.7 - - + -
66B ALA* 4.0 13.0 - - + +
69B GLU* 4.5 4.9 - - + -
70B CYS* 3.7 29.2 - - - -
73B LEU* 4.4 15.5 - - + -
81B ILE* 4.6 5.4 - - + -
82B ASP 2.9 10.1 + - - +
83B LEU* 3.5 20.3 - - + +
84B PHE* 2.9 27.8 + - - +
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Residues in contact with PHE 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 PRO* 4.8 3.4 - - + -
40B LEU* 1.3 76.9 - - - +
42B VAL* 1.3 60.5 + - - +
52B VAL* 4.7 6.1 - - + -
55B MET* 3.9 18.8 - - + -
58B SER* 4.8 4.3 - - - -
59B PHE 4.0 22.7 + - - +
60B ARG* 3.9 5.3 - - + -
61B PHE* 2.9 32.4 + - - +
84B PHE* 3.6 24.9 - + + +
86B ILE* 4.4 15.9 - - + -
209B PHE* 3.6 23.6 - + - -
212B ALA* 4.1 20.2 - - + -
213B LEU* 3.6 23.8 - - + -
318B TYR* 3.5 29.8 - + - -
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Residues in contact with VAL 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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40B LEU* 3.9 9.4 - - + -
41B PHE* 1.3 78.3 - - - +
43B MET* 1.3 62.2 + - - +
61B PHE 3.2 9.4 - - - +
63B ILE* 3.8 29.2 - - + +
66B ALA* 4.3 7.9 - - + -
83B LEU* 3.8 28.5 - - + -
84B PHE 2.8 16.4 + - - +
85B GLY* 3.6 2.0 - - - -
86B ILE* 2.8 31.0 + - - +
103B ILE* 3.7 24.0 - - + +
104B LEU* 5.4 2.0 - - + -
107B ALA* 4.1 11.9 - - + -
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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