Contacts of the strand formed by residues 653 - 657 (chain M) in PDB entry 6M6A
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 LYS 653 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647M GLU* 2.9 17.5 - - - +
651M GLY 4.5 7.0 + - - -
652M GLY* 1.3 81.0 - - - +
654M VAL* 1.3 64.0 + - - +
699M PHE* 3.3 30.9 + - + +
700M ALA 4.7 4.6 + - - -
702M GLY* 3.9 22.7 - - - -
704M TYR 4.6 2.2 - - - +
705M ASP* 3.6 13.2 - - - +
707M LEU* 3.7 19.3 - - + -
719M VAL* 4.6 5.6 - - + -
721M GLU* 2.8 40.5 + - + +
722M ALA* 3.3 26.6 - - + +
723M ASN 3.3 2.3 + - - -
724M THR* 3.5 2.6 + - - +
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Residues in contact with VAL 654 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644M ILE* 4.1 21.8 - - + +
647M GLU* 3.8 21.8 - - + -
652M GLY 5.1 1.1 - - - +
653M LYS* 1.3 79.6 - - - +
655M PHE* 1.3 65.6 + - - +
656M TYR* 5.2 1.3 - - + -
705M ASP* 3.2 9.4 + - + +
706M VAL* 3.7 38.6 - - + -
707M LEU* 2.6 36.8 + - - +
724M THR* 3.7 5.8 - - + -
726M LEU* 3.9 23.1 - - + -
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Residues in contact with PHE 655 (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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654M VAL* 1.3 84.0 - - - +
656M TYR* 1.3 56.7 + - - +
657M VAL* 5.7 3.4 - - + -
707M LEU* 3.5 40.6 - - + -
709M ALA* 5.4 6.5 - - + -
715M ALA* 5.2 15.9 - - + -
717M LEU 4.6 11.4 - - - -
719M VAL* 5.0 6.7 - - + -
722M ALA* 3.7 20.9 - - + -
724M THR 3.2 20.7 + - - +
725M ILE* 3.3 29.0 - - + -
726M LEU* 2.6 37.2 + - - +
741M LEU* 6.1 0.9 - - + -
744M ARG* 3.5 28.7 - - + -
745M VAL* 4.3 5.6 - - + -
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Residues in contact with TYR 656 (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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654M VAL* 4.1 1.5 - - + -
655M PHE* 1.3 75.1 - - - +
657M VAL* 1.3 80.7 + - - +
658M HIS* 4.2 11.8 - - + -
667M ARG* 4.4 23.7 + - + -
671M LEU* 4.3 23.3 - - + -
706M VAL* 4.7 13.0 - - + +
707M LEU 3.1 8.6 + - - +
708M LEU* 3.4 29.2 - - + +
709M ALA* 3.1 24.0 + - - +
726M LEU* 3.2 37.0 - - + -
728M GLU* 3.3 34.8 + - + +
757M PHE* 5.5 2.7 - + - -
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Residues in contact with VAL 657 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655M PHE* 5.5 3.4 - - + -
656M TYR* 1.3 101.4 + - - +
658M HIS* 1.3 62.0 + - - +
659M ASP* 4.4 0.9 - - + -
709M ALA* 3.3 20.4 - - + +
710M THR* 4.9 7.4 - - - +
711M THR 5.2 3.6 - - - +
725M ILE* 5.6 3.8 - - + -
726M LEU 3.1 15.2 + - - +
727M ILE* 3.7 31.2 - - + -
728M GLU* 3.9 7.2 - - - +
729M ARG 5.6 0.7 - - - +
733M LEU* 6.2 1.3 - - + -
741M LEU* 4.6 22.4 - - + -
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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