Contacts of the strand formed by residues 664 - 669 (chain D) in PDB entry 2OX8
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 HIS 664 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621D PHE* 3.7 31.6 - + + -
622D SER 4.1 5.4 - - - -
658D MET* 5.0 6.4 - - + +
662D GLU* 2.4 39.6 + - - -
663D SER* 1.3 73.9 - - - +
665D TRP* 1.3 66.8 + - - +
666D ILE* 5.6 0.2 - - + -
710D GLY* 4.4 0.9 - - - -
711D LEU* 2.7 40.3 + - + +
727D ASN* 3.0 28.8 + - + +
728D PHE* 3.1 24.8 + - - -
729D ILE* 2.9 30.7 - - + +
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Residues in contact with TRP 665 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626D GLU 3.0 22.6 + - - -
627D ILE 4.3 0.7 - - - -
628D PHE* 3.7 37.0 - + + +
631D ALA* 4.3 2.0 - - + -
642D LEU* 4.7 7.6 - - + -
643D VAL* 4.3 2.8 - - - +
663D SER 4.1 0.2 + - - -
664D HIS* 1.3 83.4 - - - +
666D ILE* 1.3 68.5 + - - +
708D CYS* 3.0 33.0 - - + -
709D ALA 3.4 22.9 - - - +
710D GLY* 4.2 2.7 - - - -
720D PHE* 3.5 16.2 - + + -
721D GLN 3.6 22.0 - - - -
722D CYS* 4.1 3.8 - - - -
724D ASP* 3.4 22.7 - - + -
726D ASN* 3.4 28.7 + - + +
727D ASN 2.9 26.9 + - - -
728D PHE* 3.6 15.9 - - + +
729D ILE 4.0 9.9 + - - +
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Residues in contact with ILE 666 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628D PHE* 3.8 5.9 - - - -
642D LEU* 3.9 6.3 - - - -
643D VAL* 3.8 26.7 - - + +
645D ILE* 4.3 10.3 - - + -
664D HIS* 4.1 6.5 - - + +
665D TRP* 1.3 85.8 - - - +
667D GLY* 1.3 52.4 + - - +
668D LEU* 2.4 29.9 + - + +
679D TRP* 4.6 6.7 - - + -
709D ALA* 3.3 33.2 + - + +
710D GLY 4.0 6.1 - - - +
711D LEU* 4.1 14.4 - - + -
717D TRP* 3.7 46.9 - - + +
729D ILE* 5.8 0.4 - - + -
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Residues in contact with GLY 667 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642D LEU* 3.2 25.9 - - - +
643D VAL 3.3 7.5 + - - -
644D PHE* 3.7 9.7 - - - -
666D ILE* 1.3 67.4 - - - +
668D LEU* 1.3 57.0 + - - -
679D TRP* 2.9 16.3 - - - +
680D LEU* 2.8 43.5 + - - -
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Residues in contact with LEU 668 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666D ILE* 2.4 22.8 + - + +
667D GLY 1.3 70.5 - - - +
669D THR* 1.3 70.3 + - - +
677D TRP* 3.4 22.9 - - + +
678D LYS 3.3 39.0 - - - +
679D TRP* 3.7 19.5 - - + +
685D PRO* 4.4 12.6 - - + -
690D TRP* 3.9 14.6 - - + -
709D ALA* 2.9 38.3 + - + +
717D TRP* 3.7 36.3 - - + -
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Residues in contact with THR 669 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628D PHE* 3.2 37.5 - - + -
668D LEU* 1.3 82.6 - - - +
670D ASP* 1.3 58.9 + - - +
671D SER* 3.1 22.3 + - - +
676D GLU 3.2 0.9 - - - +
677D TRP* 3.3 8.5 - - - -
678D LYS* 2.9 35.9 + - - +
680D LEU* 4.5 10.4 - - + +
707D ASP 2.8 22.0 - - - +
708D CYS* 4.2 3.1 - - - -
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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