Contacts of the helix formed by residues 21 - 30 (chain B) in PDB entry 1C7G
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 ARG 21 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B SER* 1.3 73.8 - - - +
22B ASP* 1.3 64.5 + - - +
24B ARG* 3.3 33.5 + - - +
25B VAL* 3.0 54.9 + - + +
372B MET* 3.4 13.0 + - - +
373B GLU* 2.6 45.9 + - - +
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Residues in contact with ASP 22 (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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20B SER* 3.1 9.1 + - - +
21B ARG* 1.3 89.2 + - - +
23B GLU* 1.3 62.4 + - + +
25B VAL* 3.4 8.0 + - - +
26B LYS* 3.1 35.6 + - + +
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Residues in contact with GLU 23 (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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19B ILE* 3.7 30.1 - - + +
20B SER* 3.1 35.0 + - - +
22B ASP* 1.3 74.9 - - + +
24B ARG* 1.3 61.3 + - - +
26B LYS* 3.1 22.9 + - - +
27B LYS* 2.8 43.7 + - + +
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Residues in contact with ARG 24 (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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19B ILE* 3.2 40.3 + - + -
20B SER* 3.1 11.8 + - - +
21B ARG* 3.3 32.6 - - - +
22B ASP 3.3 0.2 - - - -
23B GLU* 1.3 75.5 - - - +
25B VAL* 1.3 58.6 + - - +
27B LYS* 4.3 0.4 - - - -
28B MET* 2.9 31.5 + - - +
42B ASP 5.4 0.2 - - - -
371B TYR* 3.5 31.2 + - + +
372B MET* 3.0 29.1 + - - +
373B GLU 3.3 19.7 + - - -
374B THR 4.3 7.4 + - - -
375B GLY* 3.6 26.6 - - - -
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Residues in contact with VAL 25 (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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21B ARG* 3.0 49.9 + - + +
22B ASP* 3.6 10.1 - - - +
24B ARG* 1.3 77.0 - - - +
26B LYS* 1.3 64.1 + - + +
28B MET* 3.4 2.1 + - - +
29B GLN* 3.0 36.4 + - + +
33B TYR* 5.7 1.6 - - - +
372B MET* 4.2 31.3 - - + +
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Residues in contact with LYS 26 (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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22B ASP* 3.1 25.2 + - + +
23B GLU* 3.1 26.4 + - - +
25B VAL* 1.3 78.2 - - + +
27B LYS* 1.3 60.9 + - + +
29B GLN* 3.3 18.3 - - - +
30B GLU* 2.9 35.4 + - - +
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Residues in contact with LYS 27 (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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19B ILE* 3.8 20.9 - - + -
23B GLU* 2.8 36.8 + - + +
24B ARG 3.7 4.0 - - - +
26B LYS* 1.3 73.0 - - + +
28B MET* 1.3 64.6 + - - +
30B GLU* 3.3 21.8 + - - +
31B ALA* 3.0 23.4 + - - +
38B LEU* 4.0 8.4 - - + +
39B ASN* 5.4 2.2 - - - +
41B LYS* 5.3 5.1 - - - +
42B ASP* 3.4 37.8 + - + +
371B TYR* 4.1 11.4 - - - +
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Residues in contact with MET 28 (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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24B ARG 2.9 18.1 + - - +
25B VAL 3.8 2.7 - - - +
27B LYS* 1.3 73.4 - - - +
29B GLN* 1.3 66.0 + - - +
31B ALA* 3.1 6.5 + - - +
33B TYR* 2.9 64.1 + - + -
34B ASN 4.2 4.3 - - - -
35B THR* 4.0 10.8 - - + -
38B LEU* 4.1 16.8 - - + +
368B ALA* 3.2 23.1 - - + +
371B TYR* 3.2 43.7 - - + -
372B MET* 3.6 19.7 - - + -
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Residues in contact with GLN 29 (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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25B VAL* 3.0 28.6 + - + +
26B LYS* 3.3 23.0 - - - +
28B MET* 1.3 76.3 - - - +
30B GLU* 1.3 54.8 + - + +
32B GLY* 2.7 27.0 + - - -
33B TYR* 3.3 36.0 + - + +
452B ARG* 3.8 5.2 + - - -
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Residues in contact with GLU 30 (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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26B LYS* 2.9 21.8 + - - +
27B LYS* 3.6 27.9 + - - +
29B GLN* 1.3 77.1 - - + +
31B ALA* 1.3 51.6 + - - +
32B GLY 3.1 0.4 - - - -
452B ARG* 2.7 29.7 + - - +
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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