Contacts of the strand formed by residues 465 - 467 (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 ASP 465 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417M ARG* 4.0 17.7 + - - +
457M ASP* 4.4 3.8 + - - -
463M PRO 3.2 9.9 + - - +
464M MET* 1.3 73.5 - - - +
466M ARG* 1.3 60.4 + - - +
588M LYS* 5.4 1.2 + - - -
593M THR* 4.5 5.2 + - - -
595M TYR* 5.0 2.6 - - - -
609M LEU* 5.6 0.3 - - - +
612M LEU* 3.7 22.2 - - - +
613M LYS* 3.3 42.2 + - - +
614M ASP* 2.9 33.0 + - - +
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Residues in contact with ARG 466 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453M GLU* 2.4 64.5 + - - +
454M VAL* 3.4 28.3 - - + +
456M ARG* 3.0 21.1 - - - +
457M ASP* 2.8 18.8 + - - +
464M MET* 3.6 31.0 + - + -
465M ASP* 1.3 73.7 - - - +
467M LEU* 1.3 58.7 + - - +
468M VAL* 5.4 1.6 - - + -
593M THR 4.7 1.0 + - - -
594M LEU* 4.8 6.4 - - + +
595M TYR* 3.1 20.5 + - - +
613M LYS* 2.8 22.3 + - - +
614M ASP* 3.2 32.9 - - - +
616M SER* 4.1 8.3 + - - +
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Residues in contact with LEU 467 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466M ARG* 1.3 73.7 - - - +
468M VAL* 1.3 64.4 + - - +
469M SER* 5.7 2.9 - - - +
595M TYR* 3.3 9.2 - - + +
597M SER* 4.7 17.9 - - - +
600M PRO* 5.8 0.7 - - + -
606M TYR* 4.4 15.3 - - + +
609M LEU* 3.8 22.2 - - + -
613M LYS* 3.6 26.6 - - + +
614M ASP 3.2 13.8 + - - +
615M LEU* 3.7 30.7 - - + -
616M SER* 2.7 37.3 + - - +
617M SER* 5.1 6.5 - - - +
784M LEU* 6.1 2.9 - - + -
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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
------------------------------------------------------------
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