Contacts of the strand formed by residues 783 - 789 (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 MET 783 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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781D THR* 6.4 1.1 - - - -
782D TYR* 1.3 86.5 - - - +
784D VAL* 1.3 64.3 + - - +
785D LEU* 3.5 10.7 + - + +
798D VAL* 3.3 4.9 - - - -
799D ASP* 2.9 59.5 + - + +
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Residues in contact with VAL 784 (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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167B LEU* 4.8 16.4 - - + +
389B PRO* 5.3 4.7 - - - +
640D GLU* 3.6 29.4 - - - +
643D LYS* 5.1 4.9 - - - +
782D TYR* 3.6 15.7 - - + -
783D MET* 1.3 72.3 - - - +
785D LEU* 1.3 62.5 + - - +
786D GLU* 3.8 7.9 - - - +
787D VAL* 3.7 30.5 - - + -
796D ILE* 4.0 8.5 - - + -
797D THR 3.9 3.1 - - - -
798D VAL* 4.0 6.5 - - + -
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Residues in contact with LEU 785 (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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156B LYS* 5.8 10.8 - - - +
167B LEU* 5.5 0.9 - - - -
388B TYR* 4.0 6.6 - - - -
389B PRO* 3.6 24.8 - - - +
811B UDP 5.9 0.9 - - - -
623D ALA* 3.5 30.7 - - + -
783D MET* 3.9 17.7 - - + +
784D VAL* 1.3 79.5 - - - +
786D GLU* 1.3 63.9 + - + +
797D THR* 2.9 21.2 + - + +
799D ASP* 4.2 18.2 - - + +
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Residues in contact with GLU 786 (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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167B LEU* 5.3 0.4 - - - -
386B GLN* 2.7 29.6 - - - +
387B ARG 3.5 11.7 - - - +
388B TYR* 3.1 29.6 + - + -
811B UDP 4.9 3.5 + - - -
784D VAL* 3.5 3.4 - - - +
785D LEU* 1.3 84.8 - - + +
787D VAL* 1.3 69.9 + - - +
788D GLN* 3.3 34.8 + - + +
795D LYS 3.9 0.3 - - - +
796D ILE* 3.6 5.7 - - - +
797D THR* 3.0 39.1 + - + +
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Residues in contact with VAL 787 (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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167B LEU* 4.5 13.5 - - + -
385B VAL 3.7 1.4 - - - +
386B GLN* 3.5 1.7 - - - -
387B ARG* 2.7 52.7 + - + +
640D GLU* 4.8 6.1 - - - +
784D VAL* 3.7 20.4 - - + -
786D GLU* 1.3 79.6 - - - +
788D GLN* 1.3 63.1 + - - +
789D ARG* 3.9 33.8 - - + +
794D THR* 4.4 9.2 - - + -
795D LYS 4.0 1.6 - - - -
796D ILE* 4.3 13.0 - - + +
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Residues in contact with GLN 788 (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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384B GLU* 2.9 24.0 - - - +
385B VAL 3.5 4.7 - - - +
386B GLN* 4.2 5.6 - - + +
786D GLU* 3.3 41.0 + - + +
787D VAL* 1.3 73.6 - - - +
789D ARG* 1.3 62.3 + - - +
790D TYR* 3.0 30.6 + - + -
794D THR* 3.4 6.9 - - - +
795D LYS* 2.9 65.4 + - + +
797D THR* 4.4 5.7 + - - -
812D UDP 3.8 15.0 + - - -
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Residues in contact with ARG 789 (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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384B GLU* 3.6 8.1 - - - +
385B VAL* 2.7 46.9 + - + +
387B ARG* 5.7 4.0 - - - +
569D LEU* 3.6 30.2 - - + +
570D GLY* 4.2 8.9 - - - -
572D ARG* 6.2 1.8 - - - +
618D TYR* 5.1 0.2 - - - -
644D ASP* 2.5 44.8 + - - -
787D VAL* 3.9 21.2 - - + +
788D GLN* 1.3 73.5 - - - +
790D TYR* 1.3 60.7 + - - +
793D TYR 4.1 2.7 - - - -
794D THR* 3.1 34.8 + - - +
796D ILE* 6.3 0.8 - - - +
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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