Contacts of the strand formed by residues 687 - 692 (chain A) in PDB entry 6NFJ
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 LEU 687 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596A HIS* 3.5 36.6 - - + +
636A SER* 5.4 3.1 - - - -
637A ALA 4.2 10.9 + - - +
638A MET* 3.5 32.0 - - + -
639A VAL 3.4 13.0 + - - -
685A VAL* 3.2 17.6 - - - +
686A LYS* 1.3 88.4 - - + +
688A TRP* 1.3 62.0 + - - +
737A ALA* 3.3 20.0 - - + -
820A PHE* 4.5 9.0 - - + -
886A TYR* 4.8 14.6 - - + +
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Residues in contact with TRP 688 (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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601A LEU* 5.5 0.2 - - + -
639A VAL* 3.7 36.1 - - + -
641A LEU* 5.4 9.6 - - + -
677A CYS* 3.7 24.2 - - + -
678A PHE* 3.7 23.1 - + + -
681A LEU* 3.6 38.6 - - + -
682A GLY* 4.0 4.5 - - - -
685A VAL* 3.5 39.1 + - + +
686A LYS 4.5 0.4 - - - -
687A LEU* 1.3 79.5 - - - +
689A ILE* 1.3 70.3 + - - +
726A TYR* 4.1 19.8 - + - -
737A ALA 2.7 15.4 + - - +
738A VAL* 3.3 29.4 - - + -
739A SER 2.9 25.3 + - - -
820A PHE* 4.2 5.5 - - - -
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Residues in contact with ILE 689 (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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598A ARG* 3.8 10.3 - - - +
638A MET* 3.5 37.5 - - + -
639A VAL 2.9 6.5 + - - +
640A THR* 3.1 22.9 - - + +
641A LEU* 3.1 18.9 + - - +
688A TRP* 1.3 80.2 - - - +
690A THR* 1.3 66.2 + - - +
691A ILE 3.5 12.3 - - - +
739A SER 3.2 2.9 - - - +
740A LEU* 3.7 2.7 - - - -
741A SER* 3.1 47.1 - - - +
820A PHE* 4.6 6.5 - - + -
822A ALA* 4.4 6.7 - - + -
888A THR* 3.9 6.5 - - + -
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Residues in contact with THR 690 (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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641A LEU* 3.5 5.5 + - - +
642A TYR* 3.0 28.9 + - - +
670A PHE* 4.3 14.8 - - + -
678A PHE* 5.7 2.5 - - + -
689A ILE* 1.3 75.3 - - - +
691A ILE* 1.3 74.8 + - - +
719A HIS* 2.6 38.5 + - + +
722A ALA* 4.2 22.2 - - + -
723A TRP 5.3 0.2 - - - +
738A VAL* 4.0 16.8 - - + -
739A SER 2.8 14.7 + - - +
740A LEU* 3.2 9.4 - - - +
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Residues in contact with ILE 691 (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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640A THR* 4.2 2.2 - - - -
642A TYR* 3.7 31.2 - - + -
644A PRO* 4.3 9.0 - - + -
661A TRP* 5.3 3.8 - - + -
670A PHE* 4.9 6.7 - - + -
689A ILE* 3.5 3.8 - - - +
690A THR* 1.3 93.8 + - - +
692A ASN* 1.3 62.2 + - - +
693A GLU 3.9 0.4 - - - -
694A PRO* 3.6 34.5 - - + +
715A LEU* 3.5 49.1 - - + +
718A ALA* 5.4 2.2 - - + -
719A HIS* 5.0 6.7 - - + +
740A LEU* 3.8 5.3 - - + +
741A SER 3.3 25.5 + - - +
772A PHE* 5.7 0.2 - - + -
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Residues in contact with ASN 692 (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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598A ARG* 3.7 24.9 - - - +
640A THR* 3.7 10.1 - - + +
642A TYR 3.2 13.5 + - - +
643A TYR* 3.4 33.3 - - + -
644A PRO* 3.8 15.8 - - - +
691A ILE* 1.3 72.5 - - - +
693A GLU* 1.3 72.9 + - - +
741A SER 4.1 1.1 - - - -
824A ASN* 5.0 0.9 - - - +
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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