Contacts of the helix formed by residues 796 - 802 (chain W) in PDB entry 6G0L
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 GLN 796 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544W PRO* 2.9 32.3 - - + +
547W ASN* 5.1 9.4 - - - +
795W PRO* 1.3 81.9 - - - +
797W ALA* 1.3 61.3 + - - -
798W ASP* 3.0 18.0 + - - -
799W LEU* 3.1 26.7 + - + +
800W GLN* 3.3 13.2 + - - +
836W LYS 5.9 0.7 - - - -
837W MET* 3.6 38.3 - - - +
840W GLU* 2.7 36.5 + - - +
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Residues in contact with ALA 797 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771W THR* 3.9 23.6 + - + +
772W ARG* 5.7 6.1 - - + +
792W ASP* 3.9 19.5 - - + +
794W ASN* 4.2 10.4 + - + +
795W PRO 3.1 7.3 + - - -
796W GLN* 1.3 72.5 - - - +
798W ASP* 1.3 58.3 + - - +
800W GLN* 3.5 18.0 + - - +
801W ALA* 3.0 26.6 + - - +
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Residues in contact with ASP 798 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788W ILE* 4.6 23.1 - - + +
791W SER* 4.4 12.1 + - - +
792W ASP* 4.6 14.0 + - + +
794W ASN 4.7 6.5 - - - +
795W PRO* 5.2 1.2 - - - +
796W GLN* 3.0 23.0 + - - -
797W ALA* 1.3 73.0 - - - +
799W LEU* 1.3 74.4 + - - +
801W ALA* 3.3 10.3 - - + +
802W MET* 2.8 40.0 + - + +
818W ARG* 4.1 24.3 + - - -
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Residues in contact with LEU 799 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402W GLU* 5.9 2.7 - - - +
403W MET* 6.1 3.1 - - + -
609W LYS* 6.1 0.7 - - - +
796W GLN* 3.1 31.1 + - + +
798W ASP* 1.3 81.6 + - - +
800W GLN* 1.3 60.0 + - - +
802W MET* 3.0 40.2 - - + +
803W ALA* 3.2 7.4 + - + +
837W MET* 4.9 11.7 - - + -
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Residues in contact with GLN 800 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403W MET* 5.4 4.3 - - + -
516W HIS* 5.2 11.2 + - - -
771W THR 4.4 7.7 + - - -
772W ARG* 5.4 3.8 - - - +
775W GLY* 3.7 34.2 + - - +
796W GLN 3.3 9.0 + - - +
797W ALA* 3.5 18.1 + - - +
799W LEU* 1.3 80.6 - - - +
801W ALA* 1.3 64.3 + - - +
803W ALA* 2.4 38.4 + - + +
804W ARG* 3.2 18.8 + - - +
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Residues in contact with ALA 801 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717W PHE* 3.5 48.1 - - + -
770W SER 5.4 0.2 - - - +
771W THR* 5.1 8.3 - - - +
775W GLY* 4.9 8.3 - - - -
788W ILE* 6.3 2.7 - - + -
792W ASP* 5.1 5.6 - - - +
797W ALA 3.0 18.5 + - - +
798W ASP* 2.9 16.5 + - + +
800W GLN* 1.3 78.1 - - - +
802W MET* 1.3 59.3 + - - +
803W ALA 3.5 0.2 + - - -
804W ARG* 3.7 8.8 + - - +
805W ALA 4.5 0.7 + - - -
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Residues in contact with MET 802 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609W LYS* 3.1 38.4 - - - +
611W GLU* 5.4 4.3 - - + -
717W PHE* 5.3 0.4 - - - -
786W VAL* 4.5 24.7 - - + -
788W ILE* 5.4 2.9 - - + -
798W ASP* 2.8 26.9 + - + +
799W LEU* 3.0 34.5 - - + +
801W ALA* 1.3 71.4 - - - +
803W ALA* 1.3 54.2 + - - +
804W ARG 3.2 2.7 - - - -
805W ALA* 3.3 3.4 + - - +
806W HIS* 2.6 38.7 + - + +
814W VAL* 6.4 0.2 - - + -
816W VAL* 4.6 17.3 - - + -
818W ARG* 5.1 9.6 - - - +
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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