Contacts of the helix formed by residues 677 - 682 (chain A) in PDB entry 6RQT
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 677 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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673A HIS 3.5 3.7 + - - -
674A ILE* 3.3 13.7 + - - -
676A ALA* 1.3 78.3 - - - +
678A VAL* 1.3 63.8 + - - +
679A TRP 3.4 0.2 - - - -
680A LEU* 3.5 7.1 + - - +
681A THR* 3.5 22.9 + - - +
781A LEU* 4.0 17.2 - - - +
817A PHE* 3.6 22.7 - - - -
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Residues in contact with VAL 678 (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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674A ILE 4.0 8.1 - - - +
675A SER 3.9 10.3 - - - +
676A ALA 3.3 0.8 - - - -
677A GLY* 1.3 79.8 - - - +
679A TRP* 1.3 68.8 + - + +
680A LEU 3.2 3.7 + - - -
682A SER* 3.5 24.6 + - - -
755A ILE* 5.5 2.9 - - + -
760A TRP* 4.7 15.3 - - + -
780A ILE* 4.1 12.1 - - + +
781A LEU 4.4 3.1 - - - +
782A ASP* 4.0 29.6 - - - +
920A PHE* 4.6 20.0 - - + -
921A PRO* 6.4 1.6 - - + -
927A ALA* 4.4 16.4 - - + +
931A SER* 4.4 2.7 - - - -
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Residues in contact with TRP 679 (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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675A SER 3.8 16.8 - - - -
676A ALA* 3.9 9.9 + - - +
677A GLY 3.4 0.2 - - - -
678A VAL* 1.3 84.1 - - + +
680A LEU* 1.3 53.9 + - - +
682A SER* 5.0 1.6 - - - -
684A ASP* 5.2 13.2 - - + -
685A SER* 3.4 13.3 - - - -
820A TYR* 2.4 31.3 + - + +
826A PHE* 4.0 21.1 - + + -
921A PRO* 3.1 37.0 - - + -
922A CYS* 3.9 8.7 - - - -
923A ASN 3.6 19.2 + - - -
927A ALA* 4.0 18.7 - - + +
1023B ARG* 3.3 44.7 + - + +
21H ASN* 5.1 9.0 - - - -
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Residues in contact with LEU 680 (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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676A ALA 3.5 17.0 + - - +
677A GLY 3.5 4.9 + - - +
678A VAL 3.2 1.2 - - - -
679A TRP* 1.3 79.2 - - - +
681A THR* 1.3 68.7 + - - +
682A SER 3.4 0.7 - - - -
685A SER* 3.3 19.6 + - - -
687A PHE* 3.6 19.7 - - + -
695A TYR* 5.2 1.8 - - + -
728A GLY* 3.3 25.1 - - - +
731A ILE* 3.8 27.8 - - + -
732A ILE* 5.1 4.5 - - + +
816A LEU* 4.3 11.0 - - + -
817A PHE* 4.0 17.0 - - + -
820A TYR* 3.6 33.7 - - + -
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Residues in contact with THR 681 (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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677A GLY 3.5 15.2 + - - +
680A LEU* 1.3 80.4 - - - +
682A SER* 1.3 60.9 + - - +
727A THR* 4.9 0.2 - - - +
728A GLY* 3.2 23.8 + - - -
729A LYS* 2.5 50.4 + - - +
732A ILE* 4.6 4.6 - - - +
776A LEU* 3.3 23.8 - - + +
779A GLY 4.8 0.2 - - - +
780A ILE* 3.8 20.4 - - + -
781A LEU* 4.0 10.3 - - + +
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Residues in contact with SER 682 (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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678A VAL 3.5 17.6 + - - -
679A TRP* 5.4 2.0 - - - -
680A LEU 3.4 1.2 - - - -
681A THR* 1.3 84.8 - - - +
683A LYS* 1.3 66.1 + - - +
684A ASP* 3.2 12.5 + - - +
685A SER* 3.2 26.4 + - - +
686A PHE* 4.8 0.3 - - - -
727A THR* 5.3 0.6 - - - +
728A GLY 4.7 1.4 + - - -
729A LYS* 3.5 7.9 - - - +
760A TRP* 3.4 27.8 - - - -
780A ILE* 3.7 18.0 - - - +
20H TYR* 3.9 5.7 - - - -
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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