Contacts of the helix formed by residues 34 - 44 (chain A) in PDB entry 3C5H
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 GLY 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLY 3.3 1.4 + - - -
33A ILE* 1.3 78.1 - - - +
35A LYS* 1.4 65.7 + - - +
37A CYS* 3.6 1.2 + - - +
38A LEU* 3.0 25.7 + - - +
200A THR* 4.5 10.3 - - - +
201A LYS* 4.1 1.1 - - - -
301A GNP 3.0 40.4 + - - -
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Residues in contact with LYS 35 (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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18A VAL* 4.1 23.3 - - + +
19A VAL 4.0 4.9 - - - -
20A GLY* 3.9 15.3 - - - +
21A LEU 3.2 9.9 + - - -
22A SER* 2.9 24.3 + - - +
33A ILE* 3.8 15.3 - - + +
34A GLY* 1.4 74.7 - - - +
36A SER* 1.3 58.9 + - - +
38A LEU* 3.2 6.0 + - - +
39A CYS* 3.0 33.2 + - - -
95A GLU* 3.5 26.0 - - + +
96A GLN 3.2 21.5 - - - +
97A THR* 3.7 5.6 - - - -
163A GLY* 6.0 0.4 - - - -
200A THR* 5.9 0.4 - - - -
301A GNP 2.8 46.2 + - - +
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Residues in contact with SER 36 (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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35A LYS* 1.3 73.8 - - - +
37A CYS* 1.3 58.6 + - - +
39A CYS 3.3 0.5 + - - -
40A ASN* 2.8 31.8 + - - +
54A HIS* 3.7 24.8 - - - +
74A LEU* 4.5 4.3 - - - +
76A TRP* 3.4 17.5 - - - -
95A GLU* 2.5 19.5 + - - -
301A GNP 2.9 14.8 + - - -
302A MG 2.1 29.4 - - - -
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Residues in contact with CYS 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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34A GLY 4.2 0.4 - - - +
36A SER* 1.3 72.9 - - - +
38A LEU* 1.3 62.6 + - - +
40A ASN* 4.2 3.1 - - - -
41A ARG* 3.1 17.8 + - - +
50A PHE* 3.4 15.2 - - + -
51A HIS 3.6 15.3 - - - -
52A LEU* 3.5 30.7 - - - -
54A HIS* 4.3 4.5 - - - -
230A ALA* 3.3 16.3 - - + +
301A GNP 2.8 55.0 + - - +
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Residues in contact with LEU 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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18A VAL* 4.4 16.8 - - + -
34A GLY 3.0 20.2 + - - +
35A LYS* 3.2 4.0 + - - +
37A CYS* 1.3 78.4 - - - +
39A CYS* 1.3 61.1 + - - +
41A ARG* 3.9 0.4 - - - -
42A PHE* 3.0 23.1 + - - +
161A LEU* 4.2 20.9 - - + -
163A GLY* 6.2 1.3 - - - -
198A VAL* 3.9 22.4 - - + -
200A THR* 4.6 8.7 - - + -
228A THR* 3.8 27.1 - - + +
230A ALA* 3.7 10.0 - - + +
236A VAL* 3.8 29.7 - - + +
239A ALA* 5.2 0.9 - - + -
240A PHE* 4.1 9.6 - - + -
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Residues in contact with CYS 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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18A VAL* 3.7 35.9 - - - -
35A LYS 3.0 17.9 + - - +
36A SER 3.6 0.2 - - - +
38A LEU* 1.3 75.5 - - - +
40A ASN* 1.3 56.6 + - - +
42A PHE* 3.2 6.2 + - - +
43A VAL* 2.9 35.0 + - - +
76A TRP* 3.5 40.4 - - + +
93A ILE* 3.7 15.3 - - + -
94A VAL 4.5 0.2 - - - -
95A GLU* 4.2 5.8 - - - -
240A PHE* 4.7 3.6 - - - -
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Residues in contact with ASN 40 (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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36A SER 2.8 22.0 + - - +
37A CYS* 3.8 6.5 - - - +
39A CYS* 1.3 72.2 - - - +
41A ARG* 1.3 57.8 + - - +
43A VAL* 5.1 0.7 - - - -
44A ARG* 2.8 40.5 + - - +
49A GLU 3.0 23.0 + - - -
50A PHE* 3.7 5.9 - - + +
51A HIS* 3.0 23.8 + - - +
54A HIS* 2.9 25.4 + - - +
76A TRP* 3.4 24.4 - - + -
134A PHE 5.2 0.7 - - - -
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Residues in contact with ARG 41 (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 CYS 3.1 18.8 + - - +
38A LEU 3.9 2.9 - - - +
40A ASN* 1.3 74.4 - - - +
42A PHE* 1.3 65.1 + - - +
44A ARG 4.3 0.2 - - - -
45A PRO* 2.9 57.7 + - - +
47A ALA* 4.4 8.7 - - - +
50A PHE* 3.5 42.7 - - + +
230A ALA* 2.9 21.5 + - + +
231A ARG 3.1 26.1 + - - -
233A ASN* 3.5 39.5 - - - +
236A VAL* 4.0 13.1 - - + +
237A ASP* 5.2 1.2 - - - +
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Residues in contact with PHE 42 (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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38A LEU 3.0 11.9 + - - +
39A CYS 3.7 3.4 - - - +
41A ARG* 1.3 78.6 - - - +
43A VAL* 1.3 62.0 + - + +
45A PRO* 4.1 2.3 - - - +
79A VAL* 3.4 28.5 - - + +
91A MET* 3.7 27.1 - - + -
93A ILE* 3.8 17.0 - - + -
236A VAL* 3.6 7.3 - - + +
237A ASP* 3.4 35.4 - - - +
240A PHE* 3.5 69.1 - + + -
308A UNX 3.2 29.4 - - - -
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Residues in contact with VAL 43 (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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39A CYS 2.9 19.5 + - - +
40A ASN 4.4 0.9 - - - +
42A PHE* 1.3 77.4 - - + +
44A ARG* 1.3 81.0 + - + +
45A PRO* 3.8 4.0 - - - +
76A TRP* 3.3 37.2 - - + +
77A GLY* 4.5 3.1 - - - +
78A GLU 4.4 8.9 - - - +
79A VAL* 3.8 18.5 - - + +
93A ILE* 3.9 28.7 - - + -
305A UNX 3.7 9.0 - - - -
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Residues in contact with ARG 44 (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 ASN* 2.8 32.4 + - - +
41A ARG* 4.3 0.7 - - - -
43A VAL* 1.3 87.8 - - - +
45A PRO* 1.3 63.5 - - - +
46A SER 3.4 10.1 + - - +
49A GLU* 3.6 46.7 + - + +
50A PHE* 4.1 1.4 + - - -
76A TRP* 3.2 46.0 + - - -
132A MET* 3.4 14.1 - - - +
133A TYR 2.9 24.4 + - - -
134A PHE* 3.7 27.8 + - - +
305A UNX 3.1 28.0 - - - -
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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