Contacts of the strand formed by residues 610 - 616 (chain A) in PDB entry 6Q6Q
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 610 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608A GLN 4.1 4.7 - - - +
609A GLU* 1.3 79.7 - - - +
611A PHE* 1.3 59.5 + - - +
639A VAL* 4.0 17.3 - - + -
679A LEU* 3.7 35.7 - - + -
680A ALA 3.5 13.5 - - - +
681A ASP* 3.4 31.0 - - - +
828A HIS* 4.8 5.4 - - + -
830A ARG* 3.6 42.2 - - + +
831A ALA 2.7 9.0 + - - +
832A VAL* 3.2 6.8 - - + -
833A ARG* 2.8 28.3 + - - +
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Residues in contact with PHE 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LYS* 5.6 1.8 - - - -
601A ASP* 5.7 0.2 - - - -
609A GLU* 5.9 0.4 - - - -
610A LEU* 1.3 74.1 - - - +
612A LEU* 1.3 86.1 + - - +
613A THR* 4.3 5.8 + - - -
678A VAL 3.8 0.5 - - - +
679A LEU* 3.4 5.7 - - - +
680A ALA 3.1 30.5 + - - -
681A ASP 4.5 1.2 + - - -
682A SER* 3.9 5.4 - - - +
683A GLU* 3.6 66.4 - - + +
686A ALA* 4.3 8.6 - - + +
687A LYS* 4.1 8.5 - - - -
833A ARG* 3.4 29.2 - - + -
835A VAL* 3.4 43.3 - - + -
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Residues in contact with LEU 612 (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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611A PHE* 1.3 87.0 - - - +
613A THR* 1.3 63.9 + - - +
614A PHE* 3.6 34.3 - - + -
642A MET* 4.1 13.5 - - + -
677A ALA* 3.8 17.9 - - + -
678A VAL 3.3 19.7 - - - +
679A LEU* 4.0 12.6 - - + -
820A VAL* 4.2 7.9 - - + +
821A THR* 3.6 24.7 - - - +
824A ALA* 4.6 5.2 - - + -
832A VAL* 3.7 14.8 - - + -
833A ARG 3.1 8.8 + - - +
834A CYS* 3.4 23.1 - - + +
835A VAL 5.3 0.2 - - - +
836A LEU* 5.6 0.3 - - - +
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Residues in contact with THR 613 (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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611A PHE* 4.2 9.1 - - - -
612A LEU* 1.3 75.0 - - - +
614A PHE* 1.3 71.9 + - - +
677A ALA* 3.5 3.3 - - - -
678A VAL* 2.7 45.7 + - + +
686A ALA* 3.5 42.1 - - + +
687A LYS* 3.9 16.8 - - - +
690A ALA* 4.0 10.7 - - + +
836A LEU* 5.9 1.8 - - - -
840A GLU* 3.3 16.8 + - - -
3006A MLI 5.3 1.2 + - - -
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Residues in contact with PHE 614 (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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612A LEU* 3.6 11.2 - - + -
613A THR* 1.3 86.5 + - - +
615A VAL* 1.3 68.5 + - - +
616A THR* 4.3 6.7 + - + +
663A LEU* 4.8 3.4 - - + -
674A LEU* 4.0 37.0 - - + -
676A CYS 3.5 14.8 - - - +
677A ALA* 4.1 11.4 - - + -
690A ALA* 4.6 0.5 - - - +
817A ILE* 3.7 23.8 - - + -
820A VAL* 3.5 34.1 - - + -
834A CYS* 3.4 26.0 - - - -
836A LEU* 4.2 17.3 - - + -
840A GLU* 3.8 11.8 + - - +
844A ILE* 4.9 4.7 - - + -
3006A MLI 3.8 13.3 - - - +
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Residues in contact with VAL 615 (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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613A THR 4.4 0.2 + - - -
614A PHE* 1.3 72.8 - - - +
616A THR* 1.3 61.2 + - - +
674A LEU* 4.1 1.4 - - - -
675A VAL* 3.1 20.5 + - + +
676A CYS* 3.2 35.9 + - + +
678A VAL* 4.1 11.7 - - + -
690A ALA* 3.6 42.0 - - + +
693A VAL* 4.4 9.2 - - + -
695A ILE* 4.0 25.1 - - + -
3006A MLI 3.7 13.7 - - + +
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Residues in contact with THR 616 (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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614A PHE* 4.6 5.6 - - + +
615A VAL* 1.3 81.9 - - - +
617A SER* 1.3 70.0 + - - +
618A SER* 3.6 3.1 + - - -
672A GLY* 3.6 28.6 - - - +
673A GLN 3.2 6.5 - - - +
674A LEU* 4.4 6.5 - - + -
675A VAL* 4.1 5.1 - - - +
695A ILE* 5.3 2.4 - - - +
697A TYR* 4.2 5.4 + - - -
840A GLU* 5.9 4.3 - - + +
843A LEU* 4.1 12.2 - - + +
844A ILE* 4.0 25.6 - - + -
3006A MLI 3.4 28.0 + - - +
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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