Contacts of the strand formed by residues 597 - 601 (chain B) in PDB entry 1OFD
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 597 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522B LEU* 3.8 26.2 - - + -
523B GLY 4.5 0.2 - - - +
539B ILE* 3.9 16.2 - - + -
554B ILE* 3.8 23.3 - - + -
559B LEU* 3.9 15.3 - - + -
560B GLN 3.2 2.7 + - - +
561B VAL* 4.0 25.8 - - + -
562B ALA* 2.8 31.9 + - - +
595B ALA* 3.6 0.4 - - - +
596B GLU* 1.3 84.8 - - - +
598B LEU* 1.3 67.0 + - - +
599B VAL* 4.4 1.3 - - + -
639B SER* 3.5 7.6 - - - +
641B ILE* 3.7 30.1 - - + -
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Residues in contact with LEU 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B ALA* 3.5 3.6 - - + -
564B VAL* 4.0 13.5 - - + -
587B ALA* 3.7 31.2 - - + +
590B THR* 3.8 14.6 - - + -
591B VAL* 4.0 22.9 - - + -
595B ALA* 3.8 27.4 - - + -
597B ILE* 1.3 73.2 - - - +
599B VAL* 1.3 56.7 + - - +
600B LEU* 3.7 11.0 + - + +
625B VAL* 4.7 0.2 - - + -
629B LEU* 4.6 2.0 - - + -
638B ALA* 4.8 3.6 - - + -
639B SER 2.9 12.6 + - - +
640B LEU* 3.5 24.4 - - + +
641B ILE* 2.8 33.3 + - - +
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Residues in contact with VAL 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B LEU* 4.5 13.9 - - + -
554B ILE* 6.1 1.1 - - + -
555B LYS* 4.7 20.0 - - + -
561B VAL* 3.9 21.5 - - + -
562B ALA 2.8 19.5 + - - +
563B GLU* 3.7 7.3 - - + -
564B VAL 2.9 28.6 + - - +
597B ILE* 4.4 7.4 - - + -
598B LEU* 1.3 73.4 - - - +
600B LEU* 1.3 58.5 + - - +
601B THR* 3.2 22.0 + - - +
641B ILE* 3.5 16.4 - - + +
643B ASP* 3.7 19.3 - - + +
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Residues in contact with LEU 600 (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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564B VAL* 3.4 29.2 - - + -
566B THR* 4.0 16.3 - - + +
583B LEU* 4.4 11.0 - - + -
587B ALA* 5.3 0.2 - - + -
598B LEU* 4.4 19.5 - - + +
599B VAL* 1.3 69.6 - - - +
601B THR* 1.3 56.0 + - - +
621B ALA* 4.1 7.6 - - + +
622B VAL* 3.9 37.7 - - + +
625B VAL* 4.0 22.7 - - + -
640B LEU* 4.6 6.3 - - + -
641B ILE 2.8 17.2 + - - +
642B VAL* 3.6 7.9 - - + +
643B ASP 2.8 30.5 + - - +
644B THR* 5.3 0.3 - - - -
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Residues in contact with THR 601 (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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555B LYS* 5.9 0.2 + - - -
563B GLU* 4.3 13.9 - - + +
564B VAL 3.0 9.2 + - - -
565B SER* 3.5 5.9 - - - -
566B THR* 3.0 26.5 + - - +
599B VAL* 3.2 30.8 + - - +
600B LEU* 1.3 71.0 - - - +
602B ASP* 1.3 57.8 + - - +
603B ARG* 3.1 37.0 - - + +
604B PRO* 3.5 7.3 - - + +
643B ASP* 2.9 29.4 + - - +
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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