Contacts of the strand formed by residues 695 - 699 (chain D) in PDB entry 1O23
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 VAL 695 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651D VAL* 4.0 4.7 - - + -
652D PHE 3.2 8.5 - - - +
653D SER* 3.4 24.9 - - - +
657D LEU* 3.9 22.2 - - + -
666D TYR* 3.9 26.0 - - + +
674D HIS* 3.6 5.6 - - - -
675D ILE* 2.8 49.1 + - + -
676D SER* 2.7 26.2 + - - +
693D GLY 3.6 1.0 + - - -
694D GLY* 1.3 79.0 - - - +
696D SER* 1.3 63.1 + - - +
744D CYS* 5.8 0.9 - - - -
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Residues in contact with SER 696 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630D ARG* 5.4 4.2 + - - -
650D PHE 3.6 0.3 - - - +
651D VAL* 3.3 4.0 - - - +
652D PHE* 2.8 49.4 + - - +
673D ARG 3.2 10.3 - - - -
674D HIS* 4.6 1.1 - - - -
675D ILE* 4.2 5.4 - - - +
692D PHE* 3.4 41.4 + - - -
694D GLY 5.6 0.2 - - - -
695D VAL* 1.3 75.6 - - - +
697D ALA* 1.3 61.3 + - - +
698D LEU* 4.3 1.8 - - - +
709D PHE* 5.0 2.6 - - - -
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Residues in contact with ALA 697 (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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650D PHE 3.2 8.3 - - - +
651D VAL* 4.0 6.5 - - + -
667D ARG 3.3 31.9 - - - +
668D CYS* 4.2 5.5 - - - -
671D GLN 4.6 0.3 - - - +
672D PRO* 3.8 0.7 - - - +
673D ARG* 2.7 45.3 + - + +
675D ILE* 4.0 14.6 - - + +
696D SER* 1.3 77.1 - - - +
698D LEU* 1.3 63.7 + - - +
702D GLN* 4.0 0.9 - - - +
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Residues in contact with LEU 698 (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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650D PHE* 2.9 32.7 + - - +
652D PHE* 4.4 7.6 - - + -
668D CYS* 3.4 4.5 - - - -
672D PRO* 4.3 7.2 - - + -
692D PHE* 3.9 30.7 - - + -
696D SER* 4.5 2.9 - - - +
697D ALA* 1.3 82.4 - - - +
699D SER* 1.3 69.5 + - - +
702D GLN* 3.3 13.7 - - + +
703D PHE* 3.8 29.8 - - + +
706D ILE* 3.9 21.8 - - + -
709D PHE* 4.3 19.5 - - + -
727D LEU* 4.1 10.1 - - + -
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Residues in contact with SER 699 (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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648D ASN 3.8 7.6 - - - -
668D CYS* 3.5 21.1 - - - -
669D PHE 4.9 1.3 - - - -
698D LEU* 1.3 75.6 - - - +
700D LYS* 1.3 65.4 + - - +
701D GLN* 3.5 21.1 + - - +
702D GLN* 2.8 42.9 + - - +
703D PHE* 2.9 20.1 + - - +
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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