Contacts of the strand formed by residues 610 - 615 (chain M) in PDB entry 5D4C
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 ARG 610 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69K PRO* 6.0 0.8 - - - +
70K GLY* 5.2 1.6 - - - +
133K GLU* 3.0 37.8 + - - -
605M LYS* 3.4 25.7 - - - +
606M VAL 4.0 0.4 - - - +
607M ASP* 3.0 50.1 + - - +
608M GLY 3.7 0.8 - - - -
609M ASN* 1.3 86.6 - - + +
611M ILE* 1.3 66.2 + - - +
612M VAL* 4.1 8.5 - - + +
622M GLU* 3.5 31.8 + - + +
623M TYR 3.5 12.6 - - - +
624M PRO* 3.9 9.2 - - + -
625M LEU* 4.0 2.5 - - - -
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Residues in contact with ILE 611 (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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603M VAL* 4.2 9.0 - - + -
605M LYS 3.4 12.8 - - - +
606M VAL* 4.4 4.3 - - + -
607M ASP 4.4 0.9 - - - +
610M ARG* 1.3 78.8 - - - +
612M VAL* 1.3 64.1 + - - +
613M VAL* 4.0 9.0 - - + -
623M TYR* 2.9 45.4 + - + +
625M LEU* 3.8 16.8 - - + -
641M PRO* 3.6 34.1 - - + -
643M VAL* 4.3 7.9 - - + -
655M LEU* 3.6 41.7 - - + +
656M ALA* 4.0 8.3 - - + -
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Residues in contact with VAL 612 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603M VAL* 3.6 3.5 - - - +
604M ALA* 2.8 32.4 + - + -
605M LYS* 2.9 52.1 + - + +
610M ARG* 4.1 6.5 - - + -
611M ILE* 1.3 72.9 - - - +
613M VAL* 1.3 62.4 + - - +
620M LEU* 3.7 33.7 - - + -
621M VAL 3.6 9.9 - - - +
622M GLU* 3.7 32.8 - - + +
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Residues in contact with VAL 613 (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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597M ALA* 5.9 0.2 - - + -
602M GLU 3.8 14.6 - - - +
603M VAL* 4.7 6.1 - - + -
604M ALA 4.7 0.2 - - - -
611M ILE* 4.0 7.9 - - + -
612M VAL* 1.3 78.3 - - - +
614M ARG* 1.3 67.5 + - - +
615M TYR* 3.7 35.3 + - + +
619M ARG 3.9 1.0 - - - +
620M LEU* 3.8 4.9 - - - -
621M VAL* 2.9 40.4 + - - +
623M TYR* 4.1 7.6 - - + -
649M VAL* 4.7 11.2 - - + -
655M LEU* 3.7 36.6 - - + -
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Residues in contact with ARG 614 (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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601M GLY* 3.2 1.6 - - - -
602M GLU* 2.7 53.2 + - + +
604M ALA* 4.3 7.2 - - + +
613M VAL* 1.3 72.7 - - - +
615M TYR* 1.3 70.3 + - - +
618M GLY* 2.6 38.9 + - - +
619M ARG 3.7 4.5 - - - -
620M LEU* 3.4 31.9 - - + +
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Residues in contact with TYR 615 (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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597M ALA* 4.0 6.3 - - + -
598M GLU* 3.0 22.0 + - + -
599M GLU* 3.1 49.4 - - + -
600M ASP 3.2 14.6 - - - +
601M GLY* 4.3 0.9 - - - -
613M VAL* 3.7 24.0 - - + +
614M ARG* 1.3 83.9 - - - +
616M GLU* 1.3 68.5 + - - +
617M ASP* 3.1 13.7 - - + +
618M GLY* 3.1 11.0 + - - -
619M ARG* 3.6 18.2 + - + +
621M VAL* 3.5 37.5 - - + -
623M TYR* 2.3 38.0 + - - -
649M VAL* 5.5 0.2 - - + -
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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
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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