Contacts of the helix formed by residues 920 - 930 (chain G) in PDB entry 6C3P
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 GLU 920 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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917G GLN 4.6 0.4 + - - -
918G ARG 3.6 5.7 + - - -
919G SER* 1.3 70.6 - - - +
921G CYS* 1.3 64.1 + - - +
923G LEU* 4.9 0.9 - - - -
924G PHE* 2.9 32.9 + - - +
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Residues in contact with CYS 921 (chain G).
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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919G SER* 3.4 1.7 - - - +
920G GLU* 1.3 79.1 - - - +
922G GLN* 1.3 63.0 + - + +
924G PHE* 3.3 4.8 + - - +
925G GLU* 2.9 29.2 + - - +
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Residues in contact with GLN 922 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901G ALA* 4.8 6.6 - - - +
908G GLN* 3.9 29.6 + - - +
909G ARG* 4.0 13.7 - - - +
918G ARG* 3.8 18.1 + - - +
919G SER* 3.8 16.6 - - - -
921G CYS* 1.3 78.3 - - + +
923G LEU* 1.3 66.9 + - + +
925G GLU* 3.2 6.5 - - - +
926G HIS* 2.9 44.7 + - + +
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Residues in contact with LEU 923 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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916G PHE* 3.0 50.3 - - + +
917G GLN* 4.6 3.1 - - - +
919G SER* 3.1 29.3 + - - +
920G GLU* 4.4 0.9 - - - +
921G CYS 3.1 0.6 - - - -
922G GLN* 1.3 85.6 - - + +
924G PHE* 1.3 59.9 + - - +
926G HIS* 3.6 23.0 + - + +
927G TRP* 2.9 26.6 + - - +
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Residues in contact with PHE 924 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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920G GLU 2.9 21.6 + - - +
921G CYS* 3.8 4.7 - - - +
923G LEU* 1.3 75.3 - - - +
925G GLU* 1.3 54.7 + - - +
927G TRP* 3.0 10.3 + - + +
928G LYS* 2.7 32.7 + - - +
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Residues in contact with GLU 925 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714G GLN* 5.8 2.2 - - - +
890G LEU* 5.3 1.7 - - + +
921G CYS 2.9 14.2 + - - +
922G GLN* 3.2 13.7 - - - +
924G PHE* 1.3 76.5 - - - +
926G HIS* 1.3 64.8 + - + +
928G LYS* 3.0 32.6 + - - +
929G THR* 4.3 1.2 + - - -
1513G MET* 5.0 5.4 - - - +
1514G ALA* 3.2 34.6 + - + +
1517G ASN* 5.3 1.4 - - - +
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Residues in contact with HIS 926 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712G VAL* 4.8 17.5 - - + +
890G LEU* 3.4 43.5 - - + +
893G LEU* 5.3 11.4 - - + +
899G ILE* 6.2 2.0 - - + -
922G GLN* 2.9 33.8 + - + +
923G LEU* 3.6 25.8 - - + +
925G GLU* 1.3 82.5 - - + +
927G TRP* 1.3 57.3 + - - +
928G LYS 3.4 0.4 + - - -
929G THR* 4.1 5.4 + - - -
930G LEU* 3.8 11.4 + - - -
1513G MET* 6.0 0.4 - - - -
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Residues in contact with TRP 927 (chain G).
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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923G LEU 2.9 19.3 + - - +
924G PHE* 3.0 12.9 + - - +
926G HIS* 1.3 73.7 - - - +
928G LYS* 1.3 64.2 + - - +
929G THR 3.1 3.8 + - - -
930G LEU* 3.2 23.6 + - + +
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Residues in contact with LYS 928 (chain G).
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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924G PHE 2.7 12.8 + - - +
925G GLU* 3.0 24.8 + - - +
927G TRP* 1.3 75.4 - - - +
929G THR* 1.3 58.7 + - - +
930G LEU* 5.1 0.3 - - - +
1513G MET* 6.6 0.2 - - + -
1517G ASN* 4.9 13.2 - - - +
1540G HIS* 4.2 12.5 + - - -
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Residues in contact with THR 929 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891G GLN* 6.2 2.9 - - - -
925G GLU 4.3 1.0 + - - -
926G HIS 4.1 5.1 + - - -
927G TRP 3.1 0.4 - - - -
928G LYS* 1.3 79.6 - - - +
930G LEU* 1.3 71.3 + - - +
1513G MET* 3.9 35.4 - - - -
1540G HIS* 4.3 25.3 + - - -
1581G LYS 3.8 11.7 - - - +
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Residues in contact with LEU 930 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891G GLN* 6.2 3.1 - - - -
926G HIS 3.8 6.6 + - - -
927G TRP* 3.2 24.7 + - + +
928G LYS 5.1 0.2 - - - +
929G THR* 1.3 86.2 - - - +
1581G LYS* 3.1 29.8 - - - +
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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