Contacts of the strand formed by residues 686 - 692 (chain B) in PDB entry 1QAS
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 686 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633B VAL 3.6 1.4 - - - +
634B ARG* 3.4 2.0 - - - -
635B ILE* 2.8 34.3 + - - +
671B GLN 4.6 2.2 - - - +
672B THR* 3.8 16.4 - - + -
673B ALA* 3.7 34.1 - - + +
684B TRP* 4.0 17.7 - - + +
685B ASP* 1.3 77.0 - - - +
687B GLU* 1.3 69.1 + - - +
688B PHE* 4.0 21.9 - - + -
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Residues in contact with GLU 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632B ARG* 3.3 37.3 + - + +
633B VAL 3.1 12.6 - - - +
634B ARG* 3.5 32.4 - - + +
685B ASP 4.2 0.6 + - - -
686B MET* 1.3 79.0 - - - +
688B PHE* 1.3 78.3 + - - +
689B GLU* 4.3 4.3 - - - +
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Residues in contact with PHE 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631B LEU 4.4 0.2 - - - -
632B ARG* 3.2 6.2 - - - -
633B VAL* 2.7 39.1 + - + +
635B ILE* 3.5 28.9 - - + -
658B VAL* 4.1 18.4 - - + -
670B ARG* 3.3 33.2 - - + +
671B GLN* 3.3 27.1 - - - -
672B THR* 3.1 27.4 - - + -
686B MET* 4.0 20.2 - - + -
687B GLU* 1.3 81.6 - - - +
689B GLU* 1.3 63.8 + - - +
690B PHE* 4.0 10.1 - - + -
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Residues in contact with GLU 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630B ARG* 3.3 43.7 + - + +
631B LEU 3.2 4.0 - - - +
632B ARG* 2.7 35.6 + - + -
670B ARG* 2.9 22.7 + - - +
687B GLU* 4.3 5.1 - - - +
688B PHE* 1.3 78.6 - - - +
690B PHE* 1.3 61.4 + - - +
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Residues in contact with PHE 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630B ARG* 3.5 5.9 - - - +
631B LEU* 2.9 53.6 + - + +
633B VAL* 4.6 7.0 - - + -
658B VAL* 3.5 43.3 - - + -
660B ILE* 3.6 31.0 - - + -
666B ASP 5.8 0.2 - - - -
668B GLY* 4.5 4.5 - - - -
669B SER* 4.1 7.9 - - - -
670B ARG* 3.2 52.9 - - + +
688B PHE* 4.0 15.3 - - + -
689B GLU* 1.3 78.1 - - - +
691B GLU* 1.3 62.3 + - - +
692B VAL* 3.9 7.9 + - + -
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Residues in contact with GLU 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628B PRO* 3.2 23.8 - - - +
629B GLU 2.8 24.8 + - - +
630B ARG* 3.2 33.2 + - - +
665B ARG 5.3 0.9 - - - +
666B ASP* 4.0 13.7 - - - +
670B ARG* 5.0 1.4 - - - +
690B PHE* 1.3 74.1 - - - +
692B VAL* 1.3 64.7 + - - +
693B THR* 3.3 25.1 - - - +
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Residues in contact with VAL 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B PRO* 3.1 1.9 - - - +
629B GLU 3.0 30.6 + - - +
660B ILE* 4.3 16.6 - - + -
666B ASP* 3.2 21.5 - - + +
690B PHE* 4.4 15.5 - - + +
691B GLU* 1.3 78.8 + - - +
693B THR* 1.3 59.4 + - - +
695B PRO* 3.6 29.9 - - + +
698B ALA* 4.0 12.8 - - + -
723B TRP* 3.4 35.0 - - + -
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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