Contacts of the helix formed by residues 920 - 930 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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917F GLN 4.6 0.6 + - - -
918F ARG 3.6 4.9 + - - -
919F SER* 1.3 72.4 - - - +
921F CYS* 1.3 65.2 + - - +
923F LEU* 4.4 1.1 - - - +
924F PHE* 2.9 33.4 + - - +
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Residues in contact with CYS 921 (chain F).
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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919F SER* 3.4 1.5 - - - +
920F GLU* 1.3 79.8 - - - +
922F GLN* 1.3 63.6 + - + +
923F LEU 3.2 0.2 + - - -
924F PHE* 3.3 4.7 + - - +
925F GLU* 2.9 28.7 + - - +
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Residues in contact with GLN 922 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901F ALA* 4.8 6.4 - - - +
908F GLN* 3.9 29.7 + - - +
909F ARG* 4.0 12.8 - - - +
918F ARG* 3.8 18.3 + - - +
919F SER* 3.8 15.7 - - - -
921F CYS* 1.3 78.6 - - + +
923F LEU* 1.3 65.1 + - + +
925F GLU* 3.2 7.6 - - - +
926F HIS* 2.9 44.4 + - + +
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Residues in contact with LEU 923 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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916F PHE* 3.0 49.6 - - + +
917F GLN* 4.6 3.6 - - - +
918F ARG* 5.6 0.2 - - - +
919F SER* 3.1 29.9 + - - +
920F GLU* 4.4 0.7 - - - +
921F CYS 3.1 0.6 - - - -
922F GLN* 1.3 82.6 - - + +
924F PHE* 1.3 61.2 + - - +
926F HIS* 3.6 24.4 + - + +
927F TRP* 2.9 26.9 + - - +
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Residues in contact with PHE 924 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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920F GLU 2.9 22.0 + - - +
921F CYS* 3.8 4.0 - - - +
923F LEU* 1.3 75.5 - - - +
925F GLU* 1.3 54.2 + - - +
927F TRP* 3.0 10.3 + - + +
928F LYS* 2.7 32.9 + - - +
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Residues in contact with GLU 925 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714F GLN* 5.8 1.8 - - - +
890F LEU* 5.3 1.8 - - + +
921F CYS 2.9 14.0 + - - +
922F GLN* 3.2 13.7 - - - +
924F PHE* 1.3 76.3 - - - +
926F HIS* 1.3 66.1 + - + +
928F LYS* 3.0 32.4 + - - +
929F THR 4.3 1.2 + - - -
1513F MET* 5.5 5.9 - - - +
1514F ALA* 3.2 36.0 + - + +
1517F ASN* 5.3 1.2 - - - +
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Residues in contact with HIS 926 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712F VAL* 4.7 17.9 - - + +
890F LEU* 3.4 43.2 - - + +
893F LEU* 5.3 11.4 - - + +
899F ILE* 6.2 2.0 - - + -
922F GLN* 2.9 33.7 + - + +
923F LEU* 3.6 26.5 - - + +
925F GLU* 1.3 81.6 - - + +
927F TRP* 1.3 57.5 + - - +
928F LYS 3.4 0.2 - - - -
929F THR* 4.1 6.2 + - - -
930F LEU* 3.8 11.1 + - - -
1513F MET* 6.2 0.2 - - - -
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Residues in contact with TRP 927 (chain F).
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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923F LEU 2.9 18.4 + - - +
924F PHE* 3.0 13.4 + - + +
926F HIS* 1.3 73.8 - - - +
928F LYS* 1.3 66.1 + - - +
929F THR 3.1 2.7 + - - -
930F LEU* 3.2 23.6 + - + +
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Residues in contact with LYS 928 (chain F).
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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924F PHE 2.7 13.7 + - - +
925F GLU* 3.0 23.9 + - - +
927F TRP* 1.3 75.5 - - - +
929F THR* 1.3 58.9 + - - +
930F LEU* 5.1 0.3 - - - +
1513F MET* 6.6 0.2 - - + -
1517F ASN* 4.9 13.9 - - - +
1540F HIS* 4.2 11.6 + - - -
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Residues in contact with THR 929 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891F GLN* 6.2 3.4 - - - -
925F GLU 4.3 0.8 + - - -
926F HIS 4.1 5.4 + - - -
927F TRP 3.1 0.2 - - - -
928F LYS* 1.3 80.3 - - - +
930F LEU* 1.3 71.4 + - - +
1513F MET* 3.9 36.1 - - - -
1540F HIS* 4.3 25.8 + - - -
1581F LYS 3.8 10.8 - - - +
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Residues in contact with LEU 930 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891F GLN* 6.2 2.9 - - - -
926F HIS 3.8 6.0 + - - -
927F TRP* 3.2 26.4 + - + +
928F LYS 5.1 0.2 - - - +
929F THR* 1.3 86.2 - - - +
1581F LYS* 3.1 30.2 - - - +
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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