Contacts of the strand formed by residues 642 - 646 (chain E) in PDB entry 3E20
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 ARG 642 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583E ILE* 2.9 26.3 - - - +
634E PHE* 3.2 30.2 - - + -
638E GLN* 2.9 37.0 + - - +
639E TYR* 4.0 16.3 + - - +
640E MET 3.6 0.4 - - - -
641E GLY* 1.3 78.8 - - - +
643E PHE* 1.3 65.5 + - - +
644E THR* 6.3 0.7 - - + -
655E GLY 3.7 5.8 - - - +
656E LYS* 4.4 5.3 - - + +
488J ILE 4.8 0.2 + - - -
489J GLU* 2.6 43.0 + - - +
490J ALA* 4.4 1.4 - - - +
526J CYS* 3.4 25.1 - - - -
527J GLY* 5.7 3.0 - - - +
637J TYR* 5.8 5.4 - - - -
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Residues in contact with PHE 643 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560E PHE* 3.8 11.4 - + - -
562E ALA* 3.7 32.1 - - + -
564E ILE* 4.3 4.5 - - + -
581E MET* 3.5 18.2 - - + -
582E HIS 3.2 17.3 - - - +
583E ILE* 3.6 21.8 - - + -
623E LEU* 4.1 8.5 - - + -
641E GLY 4.0 5.4 - - - -
642E ARG* 1.3 78.3 - - - +
644E THR* 1.3 68.3 + - - +
645E LEU* 3.5 38.8 - - + -
654E VAL* 3.7 2.8 - - - +
655E GLY* 3.0 55.4 + - - +
657E VAL* 4.0 6.1 - - + -
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Residues in contact with THR 644 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580E VAL 3.8 0.5 - - - +
581E MET* 3.6 1.6 - - - -
582E HIS* 3.0 43.7 + - + +
642E ARG* 6.3 0.9 - - + -
643E PHE* 1.3 82.1 - - - +
645E LEU* 1.3 68.2 + - - +
646E ARG* 5.4 4.0 + - - +
651E THR* 4.7 5.3 + - - -
653E ALA 3.4 10.5 - - - -
654E VAL* 4.4 4.0 - - + -
525J ILE* 3.7 30.0 - - + +
526J CYS 4.3 9.6 - - - +
527J GLY* 5.5 4.5 - - - -
528J ASP* 5.4 3.2 + - - +
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Residues in contact with LEU 645 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564E ILE* 4.0 13.5 - - + -
577E TYR* 6.0 0.2 - - + -
579E CYS* 3.6 15.9 - - - -
580E VAL 3.5 1.3 - - - -
581E MET* 4.0 18.4 - - + -
590E VAL* 4.5 6.3 - - + -
592E PHE* 3.6 33.0 - - + -
623E LEU* 5.0 2.5 - - + -
643E PHE* 3.5 28.0 - - + -
644E THR* 1.3 75.7 + - - +
646E ARG* 1.3 62.9 + - - +
651E THR* 3.7 6.1 - - - +
652E VAL* 3.1 36.1 + - + -
653E ALA* 2.6 33.3 + - + +
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Residues in contact with ARG 646 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579E CYS* 3.4 4.9 - - - +
580E VAL* 2.6 46.7 + - - +
582E HIS* 3.5 28.3 + - + +
644E THR* 5.4 4.1 + - - +
645E LEU* 1.3 77.7 - - - +
647E ASP* 1.3 58.0 + - - +
648E GLN* 2.7 65.7 + - + +
650E THR* 3.1 19.7 + - - +
651E THR* 4.5 10.4 + - - +
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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