Contacts of the strand formed by residues 815 - 821 (chain M) 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 MET 815 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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610M THR* 3.8 28.7 - - + +
612M ARG* 5.3 4.7 - - - -
707M LEU* 6.0 4.5 - - + -
784M ASP* 3.4 5.1 + - - +
785M THR* 3.3 20.3 - - + +
786M VAL 3.1 22.5 + - - -
814M VAL* 1.3 73.8 - - - +
816M VAL* 1.3 66.1 + - - +
817M TYR* 3.5 46.0 - - + +
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Residues in contact with VAL 816 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610M THR 4.0 11.8 + - - +
611M GLU* 3.7 22.1 - - + +
612M ARG 3.0 26.3 + - - -
786M VAL* 3.3 22.4 - - + +
788M ILE* 5.0 7.4 - - + -
802M MET* 3.6 35.2 - - + -
814M VAL* 3.8 20.9 - - + -
815M MET* 1.3 80.9 - - - +
817M TYR* 1.3 75.3 + - - +
818M ARG* 4.2 3.4 - - + +
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Residues in contact with TYR 817 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612M ARG* 3.3 48.2 + - + +
614M LEU* 5.9 2.9 - - + -
703M LEU* 3.8 34.3 - - + -
706M ARG* 4.6 14.6 + - - -
707M LEU* 5.2 17.3 - - + +
785M THR* 5.3 3.4 - - + -
786M VAL 3.2 7.1 + - - +
787M VAL* 3.6 24.7 - - + +
788M ILE* 3.1 27.0 + - - +
815M MET* 3.5 40.0 + - + +
816M VAL* 1.3 84.4 - - - +
818M ARG* 1.3 60.7 + - - +
819M LEU* 4.0 6.7 + - + -
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Residues in contact with ARG 818 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611M GLU* 2.5 47.1 + - - +
612M ARG 3.2 7.7 + - - -
613M ILE* 3.4 14.6 - - + +
614M LEU* 2.8 31.6 + - - -
788M ILE* 3.9 22.4 - - + +
790M ASP* 5.7 2.5 - - - -
791M SER* 4.3 17.1 + - - +
798M ASP* 3.9 28.9 + - - +
799M LEU* 6.3 0.8 - - - +
802M MET* 5.6 7.1 - - - +
816M VAL* 5.6 2.4 - - + +
817M TYR* 1.3 71.9 - - - +
819M LEU* 1.3 60.3 + - - +
820M VAL* 3.0 25.6 + - + +
830M LEU* 4.5 12.5 - - - +
834M ARG* 3.9 25.7 - - - +
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Residues in contact with LEU 819 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614M LEU* 3.5 31.9 - - + -
616M VAL* 4.4 5.4 - - + -
696M LYS* 3.4 43.4 + - + +
699M LEU* 5.5 3.6 - - + -
700M LEU* 5.0 5.8 - - + +
703M LEU* 5.3 4.7 - - + -
787M VAL* 4.4 15.5 - - + -
788M ILE 3.1 12.4 + - - +
789M PHE* 2.8 60.0 - - + +
790M ASP* 4.6 2.5 - - - +
817M TYR* 5.1 7.9 - - + -
818M ARG* 1.3 72.9 - - - +
820M VAL* 1.3 64.8 + - - +
821M SER 3.4 2.6 + - - -
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Residues in contact with VAL 820 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613M ILE* 4.1 19.7 - - + -
614M LEU 2.8 14.5 + - - +
615M ARG* 3.2 26.9 - - + +
616M VAL* 2.7 33.1 + - - -
696M LYS* 5.0 0.2 - - - -
790M ASP* 6.2 0.2 - - - +
818M ARG* 3.0 34.3 + - + +
819M LEU* 1.3 70.4 - - - +
821M SER* 1.3 67.7 + - - +
826M GLU* 6.0 0.9 - - + -
827M GLU* 4.9 11.7 - - + +
830M LEU* 4.4 19.1 - - + -
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Residues in contact with SER 821 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616M VAL 3.8 6.1 - - - -
618M LEU* 5.4 2.0 - - - -
659M SER 4.5 3.0 + - - -
660M ASN* 4.3 7.4 - - - +
696M LYS* 3.1 30.5 + - - +
790M ASP* 5.3 0.7 - - - +
819M LEU 3.4 1.4 + - - -
820M VAL* 1.3 76.9 - - - +
822M LYS* 1.3 60.6 + - - +
824M THR* 2.9 38.7 + - - -
826M GLU* 3.7 21.2 + - - +
827M GLU* 3.0 14.0 + - - +
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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