Contacts of the helix formed by residues 696 - 702 (chain B) in PDB entry 2O8C
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 696 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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515B ARG* 3.4 33.0 - - - +
521B THR* 3.5 32.3 - - - +
523B THR* 3.9 9.9 - - + +
563B THR* 4.5 1.3 - - - -
691B LEU* 3.0 34.2 + - + +
694B CYS* 4.4 6.7 - - + +
695B LEU* 1.3 83.0 - - - +
697B ASP* 1.3 65.0 + - - +
698B GLN 3.4 2.9 - - - +
699B GLU* 3.5 30.7 + - - +
700B LEU* 3.3 34.8 + - + +
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Residues in contact with ASP 697 (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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640B GLU* 5.3 1.0 - - - +
642B TYR* 2.8 27.1 + - - +
688B VAL 4.6 1.3 - - - +
691B LEU* 3.0 28.0 + - + +
692B LYS* 3.3 36.9 - - + +
695B LEU* 4.3 4.9 - - - +
696B ILE* 1.3 77.3 + - - +
698B GLN* 1.3 70.2 + - - +
700B LEU* 4.9 1.8 - - - -
701B LEU* 2.9 51.5 + - + +
837B HIS* 6.1 0.7 - - - -
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Residues in contact with GLN 698 (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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640B GLU* 4.9 11.4 + - - +
642B TYR* 4.2 7.2 - - + -
695B LEU 6.5 0.2 - - - -
696B ILE 3.4 0.4 - - - -
697B ASP* 1.3 92.0 + - - +
699B GLU* 1.3 52.7 + - + +
702B SER* 2.7 36.7 + - - -
830B SER* 4.2 3.5 + - - -
832B LEU* 3.7 41.3 + - + +
833B LYS* 3.4 27.9 - - + +
836B ASN* 3.9 21.3 + - - +
837B HIS* 3.8 20.4 - - + +
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Residues in contact with GLU 699 (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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515B ARG* 5.7 0.3 - - - -
523B THR* 4.3 9.5 + - - +
695B LEU 3.9 1.1 - - - +
696B ILE* 3.5 37.6 - - - +
697B ASP 3.2 0.2 - - - -
698B GLN* 1.3 76.4 - - + +
700B LEU* 1.3 62.2 + - + +
702B SER* 2.7 19.8 + - - -
703B MET* 3.4 1.2 - - - +
826B HIS* 2.9 16.5 + - - -
827B ASN* 3.1 46.4 + - + +
830B SER* 4.4 7.8 + - - -
833B LYS* 2.8 47.6 + - + -
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Residues in contact with LEU 700 (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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523B THR* 5.1 4.3 - - + -
563B THR* 3.3 51.4 - - + +
564B SER 5.6 0.4 - - - -
565B LEU 5.1 0.2 - - - -
566B GLY* 3.8 24.2 - - - +
568B PHE* 3.8 25.1 - - + -
691B LEU* 4.0 14.1 - - + -
696B ILE* 3.3 31.6 + - + +
697B ASP* 4.1 2.7 - - - +
699B GLU* 1.3 81.9 - - + +
701B LEU* 1.3 61.9 + - - +
703B MET* 3.4 27.8 - - - +
704B ALA 4.3 1.4 + - - -
705B ASN 5.1 0.3 + - - -
823B SER* 6.6 0.2 - - - -
827B ASN* 5.0 7.0 - - - +
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Residues in contact with LEU 701 (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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568B PHE* 3.7 28.0 - - + -
637B LEU* 4.6 4.3 - - + -
642B TYR* 3.6 50.7 - - + -
643B PHE* 3.5 19.2 - - + -
684B LEU* 5.3 0.2 - - + -
688B VAL* 4.0 32.3 - - + -
691B LEU* 5.5 2.2 - - + -
697B ASP* 2.9 26.5 + - + +
700B LEU* 1.3 68.7 - - - +
702B SER* 1.3 57.1 + - - +
703B MET 3.0 5.4 - - - -
704B ALA* 2.9 17.4 + - - +
705B ASN 6.0 0.2 - - - +
706B PHE* 3.7 26.2 - - + -
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Residues in contact with SER 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B TYR* 3.3 23.0 - - - +
645B GLU* 5.2 10.9 - - - +
646B LYS* 3.6 23.7 + - - +
698B GLN 2.7 17.8 + - - -
699B GLU* 2.7 22.9 + - - -
701B LEU* 1.3 77.6 - - - +
703B MET* 1.3 60.4 + - - +
704B ALA* 3.2 0.8 - - - +
826B HIS* 2.9 19.9 + - - -
830B SER* 3.9 7.1 + - - -
831B PRO* 6.5 0.2 - - - -
832B LEU* 4.3 11.9 - - - -
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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