Contacts of the strand formed by residues 36 - 42 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LEU* 4.3 17.9 - - + -
32A THR 3.8 8.3 - - - +
33A VAL* 3.2 31.1 + - + +
34A ASN 3.4 1.6 - - - -
35A ASP* 1.3 84.3 - - - +
37A VAL* 1.3 66.4 + - - +
78A ILE* 3.6 20.9 - - + +
79A GLN* 4.3 2.9 + - - +
80A GLY 4.2 3.8 + - - +
304A LEU* 4.3 10.3 - - + -
315A ILE* 3.7 3.1 - - + +
317A THR* 3.9 22.4 - - + -
320A ALA* 3.8 29.8 - - + +
323A ALA* 3.9 17.9 - - + -
324A ALA* 4.2 7.2 - - + +
327A LEU* 4.2 6.3 - - + -
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 1.3 76.4 - - - +
38A PHE* 1.3 60.5 - - - +
39A PRO* 3.4 2.1 - - - +
80A GLY* 3.4 24.7 - - - +
81A ILE 4.0 2.2 - - - -
82A ASP* 3.9 20.4 - - + +
121A MET* 4.7 10.3 - - + -
314A ILE* 3.6 23.6 - - + -
315A ILE 3.0 6.8 + - - +
316A PHE* 3.7 39.0 - - + -
317A THR 3.0 27.9 + - - +
320A ALA* 4.0 3.5 - - - +
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Residues in contact with PHE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 1.3 69.8 - - - +
39A PRO* 1.3 89.0 - - + +
40A LEU* 3.7 21.0 - - + +
61A PHE* 4.9 7.4 - + - -
69A GLU* 4.4 13.2 - - + -
73A LEU* 3.6 38.8 - - + -
78A ILE* 4.3 5.7 - - + +
80A GLY 3.2 7.8 + - - +
81A ILE* 3.2 18.4 - - + +
82A ASP 3.0 17.6 + - - -
317A THR 4.3 3.8 - - - -
318A TYR* 4.2 18.8 - + - -
320A ALA* 3.8 23.3 - - + +
321A LYS* 4.0 19.7 - - + -
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Residues in contact with PRO 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL 3.4 4.5 - - - +
38A PHE* 1.3 103.3 - - + +
40A LEU* 1.3 58.3 + - - +
41A PHE* 4.3 3.6 + - + -
82A ASP* 3.3 12.3 - - + +
84A PHE* 4.0 12.1 - - + -
276A TYR* 3.8 19.7 - - + +
316A PHE* 4.5 5.2 - - + -
317A THR 3.2 31.0 - - - +
318A TYR* 3.5 39.4 - - + -
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A PHE* 3.7 16.8 + - + +
39A PRO* 1.3 71.4 - - - +
41A PHE* 1.3 60.7 + - - +
42A VAL* 3.8 1.0 + - + -
61A PHE* 3.4 42.6 - - + -
66A ALA* 4.5 9.6 - - + +
69A GLU* 4.3 7.4 - - + -
70A CYS* 3.6 31.2 - - - -
73A LEU* 3.9 14.6 - - + -
81A ILE* 3.9 18.2 - - + -
82A ASP 2.8 10.0 + - - +
83A LEU* 3.5 20.9 - - + +
84A PHE* 2.8 31.4 + - - +
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Residues in contact with PHE 41 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A PRO* 4.8 3.6 - - + -
40A LEU* 1.3 75.0 - - - +
42A VAL* 1.3 61.7 + - - +
43A MET 4.0 0.2 - - - -
52A VAL* 4.6 6.3 - - + -
55A MET* 4.2 13.5 - - + -
58A SER* 4.9 4.3 - - - -
59A PHE 3.7 24.3 + - - +
60A ARG* 3.9 4.4 - - + -
61A PHE* 2.8 32.8 + - - +
84A PHE* 3.5 24.7 - + + +
86A ILE* 4.2 17.9 - - + -
209A PHE* 3.6 30.3 - + - -
212A ALA* 4.1 23.1 - - + -
213A LEU* 3.6 15.0 - - + -
318A TYR* 3.5 33.0 - + - -
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 4.5 2.2 - - + +
41A PHE* 1.3 75.8 - - - +
43A MET* 1.3 63.6 + - - +
61A PHE* 3.1 13.9 - - + +
63A ILE* 3.8 24.0 - - + +
66A ALA* 4.2 15.9 - - + -
83A LEU* 4.0 26.9 - - + -
84A PHE 2.8 14.7 + - - +
85A GLY* 3.9 1.3 - - - -
86A ILE* 3.1 26.7 + - - +
103A ILE* 3.4 25.9 - - + +
104A LEU* 5.3 2.2 - - + -
107A ALA* 4.0 15.5 - - + -
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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