Contacts of the strand formed by residues 679 - 684 (chain A) in PDB entry 4E5Z
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 679 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A ILE* 5.9 3.1 - - + -
410A LEU* 5.5 3.2 - - - +
637A VAL* 5.5 1.2 - - - +
639A ARG* 2.8 53.0 - - - +
650A PHE* 5.1 2.7 - - + -
652A CYS* 4.8 3.8 - - - -
656A PRO* 6.2 1.6 - - + -
673A LEU* 4.7 13.2 - - + -
676A VAL* 4.0 23.6 - - + -
678A TYR* 1.3 78.6 - - - +
680A CYS* 1.3 69.0 + - - +
691A LEU* 3.5 32.3 - - + -
692A ALA 3.3 8.5 - - - +
693A LEU* 3.3 38.4 - - + +
694A ALA* 4.4 1.6 - - - +
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Residues in contact with CYS 680 (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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410A LEU* 3.0 39.0 - - + +
411A TRP* 4.9 6.1 - - - -
412A PRO* 4.4 11.0 - - + -
639A ARG* 3.0 10.1 - - - +
679A MET* 1.3 81.5 - - - +
681A PRO* 1.4 76.1 - - + +
682A LEU* 3.1 16.8 - - + +
691A LEU* 3.1 2.0 - - - +
692A ALA 2.8 35.3 + - - -
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Residues in contact with PRO 681 (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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412A PRO* 3.9 15.3 - - + +
422A ASP* 5.5 2.3 - - - +
639A ARG* 2.9 16.2 - - + +
640A THR 5.3 1.3 - - - +
641A PHE* 3.4 42.6 - - + -
680A CYS* 1.4 92.8 - - + +
682A LEU* 1.3 66.2 + - - +
683A ASN* 4.1 6.4 + - - +
690A SER 4.5 2.7 - - - +
691A LEU* 4.1 6.3 - - + -
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Residues in contact with LEU 682 (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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410A LEU* 5.1 4.9 - - + -
412A PRO* 4.0 23.3 - - + -
422A ASP* 5.1 8.5 - - - +
423A ASP 6.0 1.6 - - - +
425A LEU* 5.0 23.1 - - + -
438A LEU* 5.4 11.7 - - + -
680A CYS* 3.1 35.7 + - + +
681A PRO* 1.3 78.2 - - - +
683A ASN* 1.3 63.7 + - - +
684A SER* 3.6 9.0 + - - +
687A TYR* 4.8 2.3 - - - +
690A SER* 3.0 32.9 + - - -
691A LEU* 3.4 8.4 + - - +
692A ALA* 3.6 22.7 - - + -
701A ILE* 5.5 2.7 - - + -
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Residues in contact with ASN 683 (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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414A ARG* 3.9 1.2 + - - -
421A THR* 2.6 25.9 + - - -
422A ASP* 4.0 13.7 + - - +
642A ARG* 6.0 1.6 - - - +
643A SER* 5.2 7.5 - - - +
681A PRO* 4.1 5.6 + - - +
682A LEU* 1.3 73.6 + - - +
684A SER* 1.3 54.7 + - - +
689A ASP* 2.4 44.0 + - - +
690A SER 3.1 23.6 + - - +
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Residues in contact with SER 684 (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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414A ARG* 2.9 26.0 + - - -
421A THR* 3.2 6.1 - - - -
422A ASP 3.4 5.0 + - - -
438A LEU* 3.4 20.3 - - - +
682A LEU* 3.6 7.0 + - - +
683A ASN* 1.3 74.6 + - - +
685A ASP* 1.3 59.4 + - - +
686A GLY* 3.1 5.4 - - - -
687A TYR* 2.9 48.5 + - - -
688A PRO* 3.0 8.3 - - - +
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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