Contacts of the helix formed by residues 21 - 30 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C SER* 1.3 72.9 - - - +
22C ASP* 1.3 69.5 + - - +
24C ARG* 3.3 27.2 + - - +
25C VAL* 2.9 54.9 + - - +
372C MET* 4.0 10.4 + - - +
373C GLU* 2.8 41.0 + - - -
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Residues in contact with ASP 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C SER* 3.7 9.6 + - - +
21C ARG* 1.3 91.2 + - - +
23C GLU* 1.3 61.7 + - + +
25C VAL* 3.4 8.2 + - - +
26C LYS* 3.1 33.2 + - - +
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Residues in contact with GLU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 3.4 34.0 - - + +
20C SER* 3.0 33.2 + - - +
21C ARG 3.2 0.4 - - - -
22C ASP* 1.3 78.6 - - + +
24C ARG* 1.3 54.5 + - - +
26C LYS* 3.1 23.5 + - - +
27C LYS* 2.8 47.3 + - + +
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Residues in contact with ARG 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 3.5 40.1 + - + -
20C SER* 3.0 18.7 + - - +
21C ARG* 3.5 25.1 - - - +
23C GLU* 1.3 72.5 - - - +
25C VAL* 1.3 61.5 + - - +
27C LYS* 3.3 0.6 + - - -
28C MET* 2.8 26.9 + - - +
42C ASP 5.4 0.7 - - - -
371C TYR* 3.3 42.2 + - + +
372C MET* 2.9 28.2 + - - +
373C GLU* 3.1 21.5 + - - +
374C THR 4.1 8.7 + - - -
375C GLY* 3.5 19.0 - - - -
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Residues in contact with VAL 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ARG* 2.9 50.4 + - + +
22C ASP* 3.6 8.3 - - - +
23C GLU 3.2 0.2 - - - -
24C ARG* 1.3 76.1 - - - +
26C LYS* 1.3 63.7 + - + +
28C MET* 3.5 2.1 + - - +
29C GLN* 3.0 34.6 + - + +
33C TYR* 5.6 1.6 - - - +
372C MET* 4.1 32.2 - - + +
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Residues in contact with LYS 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ASP* 3.1 23.0 + - - +
23C GLU* 3.1 24.6 + - - +
25C VAL* 1.3 76.4 - - + +
27C LYS* 1.3 65.8 + - + +
29C GLN* 3.2 16.5 + - - +
30C GLU* 3.0 34.5 + - + +
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Residues in contact with LYS 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 3.8 22.9 - - + -
23C GLU* 2.8 29.6 + - + +
24C ARG 3.6 4.7 - - - +
26C LYS* 1.3 79.3 - - + +
28C MET* 1.3 61.7 + - - +
30C GLU* 3.2 22.9 + - - +
31C ALA* 3.0 22.2 + - - +
38C LEU* 4.1 8.3 - - + +
39C ASN* 5.6 2.0 - - - +
41C LYS* 5.6 3.0 - - - +
42C ASP* 3.4 40.4 + - + +
371C TYR* 3.9 12.3 - - - +
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Residues in contact with MET 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ARG 2.8 18.3 + - - +
25C VAL 3.7 2.9 - - - +
27C LYS* 1.3 76.0 - - - +
29C GLN* 1.3 63.0 + - - +
31C ALA* 3.1 7.3 + - - +
33C TYR* 2.9 57.7 + - + -
34C ASN 4.5 2.7 - - - +
35C THR* 3.8 12.3 - - + -
38C LEU* 4.2 16.3 - - + +
368C ALA* 3.1 37.7 - - + +
371C TYR* 3.2 32.1 - - + -
372C MET* 3.6 23.3 - - + -
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Residues in contact with GLN 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C VAL* 3.0 23.5 + - + +
26C LYS* 3.3 21.9 - - - +
27C LYS 3.2 0.2 - - - -
28C MET* 1.3 76.9 - - - +
30C GLU* 1.3 60.1 + - + +
32C GLY* 3.0 21.1 + - - -
33C TYR* 3.1 35.1 + - + +
452C ARG* 4.6 3.1 + - - -
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Residues in contact with GLU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LYS* 3.0 19.7 + - + +
27C LYS* 3.5 23.9 + - - +
29C GLN* 1.3 81.7 - - + +
31C ALA* 1.3 52.0 + - - +
32C GLY 3.2 0.9 - - - -
452C ARG* 2.4 26.6 + - - +
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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