Contacts of the strand formed by residues 812 - 818 (chain B) in PDB entry 1QCO
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 ALA 812 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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802B SER* 3.1 4.0 - - - -
803B LEU 2.9 31.2 + - - -
808B MET* 4.4 0.9 - - + -
810B GLN 3.9 0.6 + - - -
811B ALA* 1.3 73.3 - - - +
813B THR* 1.3 64.6 + - - +
814B ILE* 3.3 7.6 + - + +
874B ASP 5.2 1.1 - - - +
875B VAL* 3.4 45.8 - - + +
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Residues in contact with THR 813 (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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800B SER* 4.8 6.3 - - - -
801B VAL 3.5 8.7 - - - +
802B SER* 4.1 7.2 - - - +
811B ALA 4.2 1.5 + - - -
812B ALA* 1.3 72.7 - - - +
814B ILE* 1.3 62.2 + - - +
815B CYS 3.8 19.5 - - - +
816B ARG* 3.6 44.7 + - + +
874B ASP 5.8 0.3 - - - +
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Residues in contact with ILE 814 (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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698B MET* 3.5 27.4 - - + -
801B VAL* 2.9 24.1 + - + +
803B LEU* 4.2 32.5 - - + -
812B ALA* 3.3 17.9 + - + +
813B THR* 1.3 75.4 - - - +
815B CYS* 1.3 62.1 + - - +
857B GLU* 4.3 3.7 - - - +
862B MET* 4.3 7.9 - - + -
865B LEU* 3.4 33.0 - - + +
873B ILE* 4.1 24.0 - - + +
874B ASP 5.0 3.6 - - - +
875B VAL* 4.7 8.1 - - + -
890B VAL* 6.1 0.7 - - + -
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Residues in contact with CYS 815 (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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698B MET* 5.4 1.8 - - + -
700B LEU* 4.1 24.7 - - - -
799B LEU 5.4 0.2 - - - -
800B SER* 3.4 3.5 - - - -
801B VAL* 2.9 43.1 + - + +
813B THR* 3.6 3.7 - - - +
814B ILE* 1.3 82.1 - - + +
816B ARG* 1.3 67.8 + - - +
817B SER* 4.1 4.0 - - - -
857B GLU 3.4 6.5 - - - +
858B SER 3.9 12.1 - - - -
859B PHE 3.2 32.8 - - - +
860B GLY* 4.3 1.6 - - - -
865B LEU* 4.4 4.9 - - + -
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Residues in contact with ARG 816 (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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799B LEU 3.4 7.4 - - - +
800B SER* 4.1 15.2 + - - +
813B THR* 3.6 34.7 + - + +
815B CYS* 1.3 78.1 - - - +
817B SER* 1.3 59.7 + - - +
857B GLU* 3.0 17.9 + - + +
858B SER* 3.1 20.8 + - - -
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Residues in contact with SER 817 (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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700B LEU* 4.0 23.6 - - - -
798B ASN* 3.7 5.0 - - - +
799B LEU* 2.9 30.9 + - - +
815B CYS* 4.1 2.4 - - - -
816B ARG* 1.3 75.3 - - - +
818B ASN* 1.3 69.2 + - - +
821B HIS* 4.0 3.4 + - - -
851B ILE* 3.6 16.7 + - - +
853B GLY 3.8 8.5 + - - -
858B SER* 3.2 27.6 + - - -
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Residues in contact with ASN 818 (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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796B ASP* 2.9 24.0 + - - -
797B ILE 3.1 23.7 + - - +
798B ASN* 3.3 21.4 + - - -
799B LEU* 4.3 1.8 - - - -
817B SER* 1.3 80.0 + - - +
819B PHE* 1.3 66.8 + - - +
820B LYS* 2.9 43.4 + - + +
821B HIS* 3.3 31.0 + - + -
851B ILE* 3.4 16.0 - - - +
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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