Contacts of the helix formed by residues 31 - 38 (chain A) in PDB entry 1CHC
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 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A SER* 2.8 20.8 - - - -
30A TYR* 1.3 110.8 - - + +
32A CYS* 1.3 66.0 + - - +
33A ILE 3.5 0.7 - - - -
34A THR* 3.2 37.1 - - + +
35A ARG* 3.7 12.8 - - - +
53A VAL* 4.9 7.6 - - + -
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Residues in contact with CYS 32 (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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8A CYS* 4.0 1.8 - - - -
10A ILE* 3.0 29.8 - - + +
11A CYS* 3.9 11.0 - - - -
19A SER* 3.9 0.2 + - - -
29A CYS* 3.1 21.1 + - - +
30A TYR 2.7 10.2 + - - -
31A VAL* 1.3 72.8 - - - +
33A ILE* 1.3 67.3 + - - +
35A ARG* 2.9 22.3 + - - +
71A ZN 2.3 37.7 - - - -
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Residues in contact with ILE 33 (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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10A ILE* 3.6 10.2 - - + +
19A SER* 3.0 29.6 - - - +
21A ALA* 4.1 12.3 - - + -
28A PHE* 3.2 39.7 - - + -
32A CYS* 1.3 76.5 - - - +
34A THR* 1.3 76.4 + - - +
36A TRP* 2.8 16.9 + - + +
37A ILE* 2.9 27.7 + - + +
43A CYS* 5.2 0.7 - - - -
44A PRO* 3.2 42.6 - - + -
53A VAL* 4.6 7.0 - - + -
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Residues in contact with THR 34 (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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31A VAL* 3.2 38.6 - - + +
33A ILE* 1.3 77.3 - - - +
35A ARG* 1.3 67.6 + - - +
37A ILE* 2.9 31.9 - - + +
38A ARG* 3.1 36.9 + - + +
53A VAL* 3.5 27.7 - - + +
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Residues in contact with ARG 35 (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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10A ILE* 4.5 5.2 - - + -
31A VAL* 3.7 13.2 - - - +
32A CYS* 2.9 16.8 + - - +
34A THR* 1.3 82.7 - - - +
36A TRP* 1.3 66.6 + - - +
38A ARG* 3.5 19.4 + - - +
39A GLN* 3.8 7.4 + - - +
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Residues in contact with TRP 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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9A PRO 3.6 20.2 - - - -
10A ILE* 3.7 38.5 - - + +
32A CYS 3.6 0.8 + - - -
33A ILE* 2.8 20.2 + - + +
35A ARG* 1.3 76.6 - - - +
37A ILE* 1.3 60.6 + - - +
39A GLN* 3.1 3.6 + - - +
40A ASN* 2.8 72.7 + - + +
41A PRO 4.5 1.2 + - - -
42A THR 5.1 0.2 + - - -
44A PRO* 3.5 40.2 - - + +
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Residues in contact with ILE 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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33A ILE* 2.9 36.8 + - + +
34A THR* 2.9 38.1 - - + +
36A TRP* 1.3 78.1 - - + +
38A ARG* 1.3 69.8 + - + +
39A GLN 2.8 0.3 + - - -
40A ASN 3.2 10.1 - - - +
41A PRO* 2.7 38.6 - - + +
43A CYS* 4.5 2.2 - - - -
44A PRO* 4.4 5.2 - - + -
50A VAL* 3.6 46.4 - - + -
53A VAL* 5.2 4.9 - - + -
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Residues in contact with ARG 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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34A THR* 3.1 40.2 + - + +
35A ARG* 3.7 11.9 - - - +
36A TRP 3.3 0.4 + - - -
37A ILE* 1.3 79.4 - - + +
39A GLN* 1.3 58.7 + - + +
41A PRO* 4.7 3.7 - - - +
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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