Contacts of the strand formed by residues 815 - 818 (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 MET 815 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610W THR* 3.3 11.9 - - + -
707W LEU* 4.1 21.8 - - + -
712W HIS* 4.0 22.9 - - + +
784W ASP* 3.2 6.5 + - + +
785W THR* 3.4 20.9 - - + +
786W VAL* 3.0 26.0 + - - +
812W ASN 6.0 1.3 - - - +
813W HIS* 5.9 7.0 - - + -
814W VAL* 1.3 88.1 - - - +
816W VAL* 1.3 64.0 + - - +
817W TYR* 3.7 25.8 - - + +
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Residues in contact with VAL 816 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609W LYS* 4.8 5.8 - - - -
610W THR* 2.7 23.0 + - - +
611W GLU* 2.7 33.4 - - + +
612W ARG* 2.1 40.6 + - - +
786W VAL* 3.0 33.2 - - + +
788W ILE* 4.0 18.2 - - + -
802W MET* 4.6 18.2 - - + -
814W VAL* 4.3 9.4 - - + -
815W MET* 1.3 73.7 - - - +
817W TYR* 1.3 63.1 + - - +
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Residues in contact with TYR 817 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611W GLU* 4.0 0.7 - - - -
612W ARG* 2.8 51.4 + - + +
614W LEU* 4.3 15.7 - - + -
703W LEU* 3.6 30.9 - - + +
707W LEU* 4.5 12.4 - - + +
785W THR* 3.4 25.1 - - + -
786W VAL 3.0 5.3 + - - -
787W VAL* 3.2 30.4 - - + +
788W ILE* 2.5 37.5 + - - +
815W MET* 3.7 32.2 - - + +
816W VAL* 1.3 78.7 - - - +
818W ARG* 1.4 54.8 + - - +
819W LEU* 4.2 2.2 - - + -
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Residues in contact with ARG 818 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611W GLU* 2.8 47.4 + - - +
612W ARG 2.6 9.2 + - - +
613W ILE* 3.0 11.6 - - + +
614W LEU* 2.4 36.8 + - - -
788W ILE* 3.6 36.1 - - + +
791W SER* 4.8 16.5 + - - +
798W ASP* 4.1 22.8 + - - -
802W MET* 5.1 6.3 - - - +
816W VAL* 5.0 0.4 - - - +
817W TYR* 1.4 70.5 - - - +
819W LEU* 1.3 57.0 + - - +
820W VAL* 3.1 17.4 + - + +
826W GLU* 6.2 0.2 - - - +
830W LEU* 5.1 12.2 - - + +
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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
------------------------------------------------------------
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