Contacts of the strand formed by residues 672 - 676 (chain A) in PDB entry 3OJW
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 TYR 672 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLU* 5.4 1.6 - - - +
627A ILE* 3.4 31.6 - - + -
629A VAL* 4.0 8.0 - - + +
637A ALA 4.9 0.7 + - - -
640A VAL* 3.7 8.5 - - - +
641A GLN* 3.5 23.3 + - + +
644A PHE* 3.4 33.2 - + - -
663A VAL* 3.8 28.9 - - + -
666A LEU* 3.5 8.4 + - + -
667A MET* 3.6 54.7 - - + +
670A GLY 3.5 2.1 - - - -
671A ARG* 1.3 80.5 - - - +
673A SER* 1.3 62.3 + - - +
674A LEU* 3.6 26.7 + - + +
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Residues in contact with SER 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A GLN 4.5 12.1 + - - -
518A PHE* 3.9 12.1 - - - -
519A ARG 5.3 0.5 + - - -
627A ILE 2.8 7.2 + - - +
628A TYR* 3.4 31.8 - - - -
629A VAL* 3.0 23.4 + - - +
670A GLY* 4.3 13.0 + - - -
672A TYR* 1.3 76.0 + - - +
674A LEU* 1.3 67.1 + - - +
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Residues in contact with LEU 674 (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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141A GLY* 6.0 1.6 - - - -
142A GLU* 3.1 47.8 - - + +
518A PHE* 3.5 9.1 - - - -
629A VAL* 3.3 34.3 - - + -
637A ALA* 4.7 12.8 - - + +
641A GLN* 6.0 3.6 - - - +
667A MET* 4.1 14.1 - - + -
672A TYR* 3.6 21.5 - - + +
673A SER* 1.3 75.9 - - - +
675A ASP* 1.3 64.5 + - - +
676A VAL* 4.0 15.3 - - + +
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Residues in contact with ASP 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A GLY 5.5 0.8 - - - +
319A HIS* 2.9 29.4 + - - -
457A SER* 2.9 27.0 + - - -
518A PHE* 3.5 29.3 - - + +
539A PRO* 4.9 1.9 - - - +
629A VAL 2.8 9.3 + - - +
630A CYS* 3.2 27.2 - - + -
631A GLY 3.3 4.0 + - - -
674A LEU* 1.3 76.4 - - - +
676A VAL* 1.3 62.3 + - - +
677A TRP* 3.0 16.1 + - - -
752A FAD 4.3 5.4 - - - +
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Residues in contact with VAL 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLY* 5.6 3.5 - - - -
629A VAL* 5.0 4.3 - - + +
631A GLY 3.2 16.4 - - - +
632A ASP 4.4 1.1 - - - -
633A ALA 3.7 27.1 - - - +
634A ARG* 3.9 19.3 - - + +
636A MET* 5.4 1.1 - - + -
637A ALA* 3.9 23.8 - - + -
674A LEU* 4.0 16.7 - - + +
675A ASP* 1.3 82.1 - - - +
677A TRP* 1.3 63.4 + - - +
678A SER 3.4 7.4 + - - +
751A FMN 3.6 15.1 - - - +
752A FAD 5.5 2.1 - - - +
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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