Contacts of the helix formed by residues 22 - 31 (chain A) in PDB entry 2C7O
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 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ASP* 3.7 7.2 - - - -
19A ALA 2.8 14.5 + - - -
20A GLY 3.2 0.8 + - - -
21A LEU* 1.3 80.1 - - - +
23A GLY* 1.3 65.9 + - - +
24A PHE 3.2 2.7 - - - -
25A ARG* 2.9 15.3 + - - +
26A LEU* 3.0 17.7 + - - +
49A TYR* 3.5 20.0 - - - -
53A PHE* 3.9 4.3 - - - -
285A TYR* 4.4 0.2 - - - -
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Residues in contact with GLY 23 (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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22A GLY* 1.3 77.6 - - - +
24A PHE* 1.3 60.5 + - - +
26A LEU* 3.3 1.7 + - - -
27A ALA* 3.0 21.8 + - - +
285A TYR* 3.3 22.1 + - - -
306A VAL* 3.8 7.6 - - - -
308A ILE* 3.5 22.9 - - - +
311A LEU* 4.3 0.4 - - - +
1328A SAH 3.1 14.3 + - - -
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Residues in contact with PHE 24 (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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14A PHE* 4.5 1.8 - - - -
16A ASP* 3.9 17.0 + - - +
17A LEU 5.7 1.3 - - - -
22A GLY 3.2 0.6 - - - -
23A GLY* 1.3 76.5 - - - +
25A ARG* 1.3 57.0 + - - +
27A ALA* 3.4 0.8 + - - -
28A LEU* 2.9 38.0 + - + +
76A CYS* 3.6 31.6 - - + -
77A ALA 4.4 0.4 - - - -
78A GLY* 3.8 25.4 - - - -
117A PHE* 3.7 48.7 - + - -
118A MET 4.6 0.7 - - - -
119A GLU* 3.8 22.7 - - + -
306A VAL* 3.9 14.1 - - + -
311A LEU* 3.6 26.7 - - + -
1328A SAH 3.9 13.2 - - - -
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Residues in contact with ARG 25 (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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14A PHE* 3.7 15.3 - - + -
16A ASP* 3.4 13.3 + - - +
22A GLY 2.9 11.4 + - - +
24A PHE* 1.3 76.4 - - - +
26A LEU* 1.3 65.3 + - - +
29A GLU* 2.9 61.6 + - + +
35A CYS* 3.7 23.2 + - - +
49A TYR* 3.0 27.0 + - - -
53A PHE* 3.3 41.3 + - + +
55A GLU* 2.7 42.6 + - - +
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Residues in contact with LEU 26 (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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1A MET* 3.8 15.4 - - + +
22A GLY 3.0 14.2 + - - +
23A GLY 3.7 5.2 - - - +
25A ARG* 1.3 76.4 - - - +
27A ALA* 1.3 63.4 + - - +
29A GLU* 4.0 5.6 - - - +
30A SER* 3.1 25.8 + - - -
53A PHE* 3.8 24.7 - - + -
285A TYR* 3.6 37.9 - - + -
286A PRO* 4.1 17.9 - - + -
289A TYR* 4.0 13.5 - - + -
308A ILE* 3.9 16.4 - - + -
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Residues in contact with ALA 27 (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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23A GLY 3.0 14.0 + - - +
24A PHE 3.7 3.8 - - - +
26A LEU* 1.3 77.1 - - - +
28A LEU* 1.3 67.3 + - + +
30A SER* 2.7 24.3 + - - -
31A CYS* 3.5 10.7 + - - -
308A ILE* 4.1 5.9 - - + +
311A LEU* 3.6 33.0 - - + -
312A GLN* 4.0 21.0 - - + +
315A ALA* 4.9 1.3 - - - -
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Residues in contact with LEU 28 (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 LEU* 3.9 17.7 - - + -
14A PHE* 3.6 36.1 - - + -
24A PHE* 2.9 27.7 + - + +
27A ALA* 1.3 76.2 - - + +
29A GLU* 1.3 65.0 + - - +
31A CYS* 3.1 11.9 + - - +
32A GLY 3.3 0.2 + - - -
33A ALA* 3.0 24.3 + - + +
74A ILE* 4.1 20.0 - - + -
76A CYS* 3.4 32.3 - - - -
117A PHE* 4.4 14.6 - - + -
315A ALA* 4.2 13.7 - - + -
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Residues in contact with GLU 29 (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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7A LYS* 5.1 1.4 + - - -
14A PHE* 4.0 7.0 - - + -
25A ARG* 2.9 64.4 + - + +
26A LEU* 4.1 5.1 - - - +
28A LEU* 1.3 75.5 - - - +
30A SER* 1.3 58.1 + - - +
31A CYS 3.0 0.2 - - - -
32A GLY* 2.9 19.4 + - - -
33A ALA 3.6 21.0 - - - +
35A CYS* 4.1 8.5 + - - +
53A PHE* 4.1 11.1 - - - -
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Residues in contact with SER 30 (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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1A MET* 3.7 10.3 - - - -
2A ILE 5.0 1.3 - - - -
4A ILE* 3.4 16.1 - - - +
7A LYS* 2.8 29.7 + - - +
26A LEU 3.1 16.4 + - - -
27A ALA 2.7 18.0 + - - -
29A GLU* 1.3 77.1 - - - +
31A CYS* 1.3 58.1 + - - +
32A GLY 3.3 0.7 - - - -
312A GLN* 2.9 32.1 + - - +
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Residues in contact with CYS 31 (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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4A ILE* 4.3 19.3 - - - -
7A LYS* 3.1 19.5 - - - -
8A GLN* 4.7 2.9 - - + +
9A LEU* 2.9 44.6 + - + +
27A ALA 3.5 11.0 + - - +
28A LEU 3.1 9.5 + - - +
29A GLU 3.0 1.0 - - - -
30A SER* 1.3 85.0 + - - +
32A GLY* 1.3 55.6 + - - +
33A ALA 3.6 0.9 - - - -
312A GLN 4.0 7.4 - - - -
315A ALA* 4.0 7.4 - - - -
316A TYR* 4.0 30.5 - - - -
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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