Contacts of the strand formed by residues 600 - 605 (chain A) in PDB entry 5M64
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 600 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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588A LEU* 3.6 42.2 - - + -
589A MET 3.8 8.1 - - - +
590A ASN* 3.9 5.2 - - - +
597A LYS 3.8 1.5 + - - +
598A ALA 3.2 1.6 - - - -
599A SER* 1.3 81.2 - - - +
601A MET* 1.3 59.7 + - - +
651A ALA* 5.6 0.3 - - - +
1075B GLU* 3.3 33.9 - - - +
1078B ALA* 3.9 35.4 - - + +
1079B LEU* 3.6 24.5 - - + -
1082B HIS* 2.3 45.4 + - + +
1087B LEU* 4.6 4.7 - - + -
1091B ARG* 4.7 2.5 - - - +
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Residues in contact with MET 601 (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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588A LEU* 3.7 5.6 - - - -
589A MET* 2.8 34.2 + - - +
598A ALA* 3.3 30.3 - - - +
600A MET* 1.3 79.2 - - - +
602A GLY* 1.3 58.6 + - - +
603A HIS* 3.5 21.7 - - + +
620A ASN* 3.6 20.0 - - - +
623A ALA* 4.3 11.9 - - + -
624A TYR* 3.3 14.6 + - - +
651A ALA* 4.2 6.5 - - - +
653A THR* 3.5 34.5 - - - +
656A GLN* 4.6 14.6 - - + +
1082B HIS* 4.8 6.7 - - + -
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Residues in contact with GLY 602 (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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586A VAL* 4.8 0.7 - - - -
587A VAL 3.5 11.2 - - - -
588A LEU* 3.9 12.3 - - - +
601A MET* 1.3 73.6 - - - +
603A HIS* 1.3 72.2 + - - -
647A ALA* 4.0 14.0 - - - +
651A ALA* 3.3 24.9 + - - +
652A ASN* 3.8 10.9 - - - +
653A THR 4.1 0.2 + - - -
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Residues in contact with HIS 603 (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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492A THR 4.1 5.1 + - - -
493A ASN* 3.1 22.7 - - - +
495A ILE* 3.7 28.7 - - + -
586A VAL* 3.3 9.6 - - - +
587A VAL* 2.8 37.2 + - - +
589A MET* 4.8 1.6 - - + -
601A MET* 3.5 33.3 - - + +
602A GLY* 1.3 84.0 + - - -
604A LYS* 1.3 58.7 + - - +
620A ASN* 3.7 24.0 + - + -
624A TYR* 4.1 2.0 + - - -
652A ASN* 5.0 4.5 - - - -
653A THR* 3.5 37.4 - - - +
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Residues in contact with LYS 604 (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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491A GLU* 4.9 1.9 + - - -
493A ASN* 2.9 71.9 + - + +
494A GLU* 3.2 13.9 - - + +
495A ILE* 2.9 15.1 + - - +
583A ASN 5.1 8.7 - - - +
584A ARG 5.1 3.1 - - - +
585A ASP 3.7 18.4 - - - +
586A VAL* 4.6 3.1 - - + +
603A HIS* 1.3 77.4 - - - +
605A VAL* 1.3 66.5 + - - +
648A LEU* 5.6 13.2 - - + +
652A ASN* 4.4 15.8 + - - +
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Residues in contact with VAL 605 (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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494A GLU* 5.2 0.2 - - - -
495A ILE* 3.2 29.8 - - + +
497A VAL* 3.8 22.4 - - + -
581A ILE* 3.7 25.1 - - + -
582A LYS 3.7 13.2 - - - +
583A ASN* 3.6 23.7 - - - +
585A ASP* 3.9 7.3 + - - +
587A VAL* 3.6 35.9 - - + -
604A LYS* 1.3 79.5 - - - +
606A ARG* 1.3 61.1 + - - +
607A VAL* 4.2 1.3 - - + -
635A MET* 4.8 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