Contacts of the strand formed by residues 642 - 647 (chain B) in PDB entry 1D5J
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 ILE 642 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592B TRP* 5.1 1.6 - - + -
597B LEU* 4.4 13.0 - - + -
598B THR 2.8 16.6 + - - +
599B TYR* 3.1 6.0 - - + +
600B ARG 3.1 24.3 + - - -
621B LEU* 4.5 10.3 - - + -
632B PHE* 3.9 31.4 - - + -
640B ALA 3.9 2.7 - - - -
641B ASP* 1.3 79.6 - - + +
643B MET* 1.3 61.7 + - - +
644B ILE* 3.6 23.4 + - + -
676B GLY* 3.1 26.0 - - - +
677B ASP* 4.6 0.9 - - - -
678B ALA* 4.9 2.2 - - + +
703B ILE* 4.6 15.3 - - + -
706B SER* 4.5 13.9 - - - +
707B LEU* 5.1 1.6 - - + -
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Residues in contact with MET 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B ARG* 3.6 42.8 - - - +
602B VAL* 3.5 30.1 - - + -
638B GLY 3.9 3.1 - - - +
639B GLU* 3.7 25.8 - - - +
640B ALA* 3.4 33.2 - - - +
642B ILE* 1.3 70.7 - - - +
644B ILE* 1.3 60.4 + - - +
645B SER* 4.1 0.6 + - - -
673B GLY 5.6 0.2 - - - +
677B ASP* 3.2 30.2 + - - +
678B ALA 3.0 25.3 + - - +
679B HIS* 4.9 2.2 - - - +
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Residues in contact with ILE 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B TYR* 3.9 18.6 - - + -
600B ARG 2.8 13.6 + - - +
601B ILE* 3.3 15.8 - - + +
602B VAL* 2.7 32.2 + - - +
617B VAL* 3.5 40.4 - - + -
642B ILE* 3.8 24.2 - - + +
643B MET* 1.3 74.6 - - - +
645B SER* 1.3 62.5 + - - +
646B PHE* 5.4 4.7 - - + -
678B ALA* 3.7 8.3 - - + -
680B PHE* 3.7 27.8 - - + -
703B ILE* 4.4 12.1 - - + -
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Residues in contact with SER 645 (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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602B VAL* 4.0 17.3 - - - -
603B ASN* 3.7 17.3 - - - +
643B MET 4.1 0.6 + - - -
644B ILE* 1.3 77.3 - - - +
646B PHE* 1.3 71.5 + - - +
647B ALA* 5.4 1.4 - - - +
678B ALA 3.2 5.5 + - - -
679B HIS* 3.2 27.5 + - - -
680B PHE* 3.2 24.9 + - - -
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Residues in contact with PHE 646 (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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103A ASN* 4.6 6.6 + - + +
601B ILE* 5.0 3.8 - - + -
603B ASN* 3.0 46.8 + - - +
604B TYR 5.0 0.4 - - - -
605B THR* 3.6 45.3 - - + +
613B VAL* 4.1 16.2 - - + -
644B ILE* 5.4 4.9 - - + -
645B SER* 1.3 78.1 + - - +
647B ALA* 1.3 61.8 + - - +
680B PHE* 3.4 27.8 - + + +
682B ASP* 3.5 22.0 - - - +
686B TRP* 4.2 12.1 - + - -
695B LEU* 4.0 36.8 - - + -
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Residues in contact with ALA 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B SER* 4.1 2.8 + - - +
646B PHE* 1.3 75.5 - - - +
648B VAL* 1.3 63.0 + - - +
651B HIS* 3.3 44.4 - - + +
657B PHE* 3.4 12.7 - - + -
679B HIS* 4.9 4.9 - - + -
680B PHE 2.7 10.5 + - - -
681B ASP* 3.1 10.0 - - - -
682B ASP* 2.7 27.4 + - - -
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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