Contacts of the strand formed by residues 639 - 644 (chain B) in PDB entry 1XYZ
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 GLU 639 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555B MET* 4.5 5.3 - - - +
593B MET 4.0 0.4 + - - -
594B ARG* 2.8 49.5 + - + +
595B GLY 2.8 24.3 + - - -
637B ILE* 3.4 2.4 - - - +
638B VAL* 1.3 93.8 - - + +
640B TRP* 1.3 61.9 + - - +
683B LEU* 3.5 15.5 - - + +
685B PHE* 3.5 22.1 - - + -
749B ILE* 5.6 1.7 - - - +
751B SER* 2.9 21.0 + - - -
791B THR* 2.8 27.2 + - - +
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Residues in contact with TRP 640 (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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562B MET* 3.9 20.0 - - + -
595B GLY* 3.6 26.9 - - - -
596B HIS 4.3 0.7 - - - -
597B THR* 5.1 2.7 - - - -
598B LEU* 3.8 33.7 - - + -
629B VAL* 3.6 25.1 - - + -
630B MET* 3.7 41.9 + - + +
633B TYR* 4.4 10.9 + + + +
637B ILE* 3.5 42.1 + - + +
639B GLU* 1.3 73.5 - - - +
641B ASP* 1.3 65.5 + - - +
642B VAL* 3.1 15.7 + - + -
679B ASP* 5.1 3.8 + - - -
682B ALA* 3.8 17.0 - - + +
683B LEU 2.9 10.6 + - - +
684B LEU* 3.9 4.0 - - + -
685B PHE* 2.8 30.2 + - - +
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Residues in contact with ASP 641 (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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594B ARG* 2.8 42.0 + - - -
595B GLY 2.9 15.3 + - - +
596B HIS* 2.8 25.6 + - + +
597B THR* 2.9 30.9 + - - +
598B LEU* 3.2 12.0 + - - +
639B GLU 4.3 0.2 - - - -
640B TRP* 1.3 71.7 - - - +
642B VAL* 1.3 60.0 + - - +
643B ALA 3.4 2.7 - - - +
685B PHE* 3.7 10.7 - - - +
687B ASN* 3.7 31.2 + - + +
753B THR* 5.0 0.5 - - - -
754B GLU* 5.0 0.3 - - - +
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Residues in contact with VAL 642 (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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598B LEU* 3.4 18.9 - - + +
599B ILE* 2.9 27.6 + - - +
626B ILE* 4.9 2.2 - - + -
640B TRP* 3.1 11.6 + - + +
641B ASP* 1.3 72.8 - - - +
643B ALA* 1.3 57.1 + - - +
671B ALA* 3.9 39.3 - - + +
672B PHE* 3.8 20.9 - - + +
675B ALA* 4.0 11.7 - - + -
684B LEU* 3.9 36.8 - - + -
685B PHE 3.0 4.9 + - - -
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Residues in contact with ALA 643 (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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597B THR* 4.1 2.2 - - - -
599B ILE* 3.4 8.7 - - + +
641B ASP 4.4 1.6 - - - -
642B VAL* 1.3 79.9 - - + +
644B ASN* 1.3 61.7 + - - +
646B CYS* 3.9 8.5 - - - -
668B LEU* 3.5 32.5 - - + -
672B PHE* 4.1 8.7 - - + -
685B PHE 3.6 2.8 + - - +
686B TYR* 3.7 15.3 - - + -
687B ASN* 3.0 27.4 + - - +
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Residues in contact with ASN 644 (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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596B HIS* 3.9 22.4 + - - -
597B THR* 3.4 15.1 + - - +
599B ILE 3.0 9.2 + - - +
600B TRP* 3.1 49.6 + - + -
601B HIS* 4.3 0.7 - - - -
643B ALA* 1.3 75.4 - - - +
645B GLU* 1.3 76.1 + - - +
646B CYS* 3.3 8.6 + - - -
687B ASN* 2.8 41.7 + - - +
721B GLN* 3.8 6.5 + - - +
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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