Contacts of the strand formed by residues 694 - 698 (chain B) in PDB entry 5MJA
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 694 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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616B VAL* 3.9 23.3 - - + +
619B VAL* 4.1 23.6 - - + +
621B ILE* 3.8 25.8 - - + -
650B ILE* 3.9 26.9 - - + -
651B LYS 3.4 5.2 - - - -
652B THR* 4.5 6.5 - - + -
665B PHE* 4.3 1.6 - - - -
666B LEU* 5.0 1.6 - - - +
686B VAL* 3.4 7.3 - - - +
687B VAL* 3.0 39.6 + - + +
692B PRO* 3.4 31.9 - - + +
693B VAL* 1.3 74.4 - - - +
695B ILE* 1.3 64.4 + - - +
696B ILE* 4.1 7.9 - - + -
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Residues in contact with ILE 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649B ALA 3.8 0.5 - - - +
650B ILE* 3.5 3.1 - - - -
651B LYS* 2.8 43.2 + - + +
665B PHE* 3.2 52.7 - - + +
666B LEU* 4.6 3.4 - - + -
668B GLU* 4.6 10.3 - - + +
669B ALA* 3.7 26.0 - - + +
672B MET* 4.2 17.0 - - - -
683B LEU* 3.8 21.5 - - + -
685B GLY 4.1 2.2 - - - -
686B VAL* 4.5 0.9 - - + -
694B MET* 1.3 76.1 - - - +
696B ILE* 1.3 60.7 + - - +
697B THR* 4.1 7.7 + - + -
901B 7O3 4.4 8.6 - - + +
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Residues in contact with ILE 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614B ILE* 3.7 31.4 - - + -
619B VAL* 4.0 16.2 - - + -
638B LEU* 4.6 5.6 - - + -
648B VAL* 3.6 38.6 - - + -
649B ALA 3.5 3.6 - - - +
650B ILE* 4.1 19.7 - - + -
683B LEU* 3.6 5.0 - - - +
684B GLU* 2.7 35.4 + - + -
685B GLY 2.9 28.4 + - - +
686B VAL 4.4 0.2 - - - +
687B VAL* 4.4 2.9 - - + -
694B MET* 4.2 14.1 - - + -
695B ILE* 1.3 74.5 - - - +
697B THR* 1.3 57.7 + - - +
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Residues in contact with THR 697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648B VAL* 3.3 8.8 - - - +
649B ALA* 2.9 28.5 + - - +
672B MET* 3.2 34.1 - - + -
681B ILE* 4.2 8.5 - - + -
682B ARG 3.1 10.3 - - - +
684B GLU* 3.7 6.1 - - - -
695B ILE* 4.2 5.6 - - + -
696B ILE* 1.3 78.6 - - - +
698B GLU* 1.3 61.6 + - - +
901B 7O3 3.3 52.0 + - + +
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Residues in contact with GLU 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646B ILE* 5.7 0.7 - - - -
647B PTR 4.8 3.8 - - - -
680B ILE 3.8 1.6 - - - +
681B ILE* 3.5 7.1 - - + -
682B ARG* 2.8 65.7 + - - +
684B GLU* 3.6 13.2 - - - +
697B THR* 1.3 75.2 + - - +
699B PHE* 1.3 63.2 + - - +
700B MET* 3.6 13.8 + - - +
753B ASN* 4.8 3.3 + - - -
759B LYS* 2.7 46.4 + - - +
901B 7O3 3.3 17.3 - - - -
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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