Contacts of the strand formed by residues 805 - 813 (chain B) in PDB entry 1GYW
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 SER 805 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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801B ASN* 3.4 4.6 - - - -
802B HIS* 2.9 35.9 + - - +
803B LYS* 3.0 5.7 + - - -
804B GLY* 1.3 79.0 - - - +
806B ALA* 1.4 62.9 + - - +
807B MET* 3.6 13.5 + - - +
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Residues in contact with ALA 806 (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 TYR 3.7 0.4 - - - +
801B ASN* 3.2 20.3 - - - +
804B GLY 4.4 0.6 + - - -
805B SER* 1.4 70.8 - - - +
807B MET* 1.3 64.9 + - - +
808B GLN 4.2 0.2 + - - -
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Residues in contact with MET 807 (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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713B ASN* 4.6 21.5 - - + +
798B LEU 4.4 0.2 - - - -
799B THR* 3.3 8.5 - - - -
800B TYR* 2.6 78.7 + - + +
802B HIS* 4.2 13.0 - - + +
805B SER* 4.1 19.1 - - - +
806B ALA* 1.3 80.4 - - - +
808B GLN* 1.3 66.1 + - - +
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Residues in contact with GLN 808 (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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797B LYS* 3.5 30.2 + - - +
798B LEU 3.3 8.7 - - - +
799B THR* 3.8 13.1 - - + +
800B TYR* 6.0 1.1 - - - -
806B ALA 5.5 0.2 - - - +
807B MET* 1.3 82.1 - - - +
809B ASP* 1.3 74.4 + - - +
810B LEU* 5.2 7.4 - - + +
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Residues in contact with ASP 809 (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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710B TYR* 2.4 43.8 + - + +
712B LYS* 3.3 24.6 + - - +
713B ASN* 4.5 6.5 + - - +
796B ILE 4.0 0.4 - - - +
797B LYS* 3.4 5.0 - - - +
798B LEU* 2.9 40.1 + - + +
800B TYR* 6.2 2.0 - - + -
808B GLN* 1.3 78.2 - - - +
810B LEU* 1.3 77.2 + - - +
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Residues in contact with LEU 810 (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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710B TYR* 5.6 0.2 - - - -
712B LYS* 4.6 4.2 + - - -
796B ILE 3.3 5.4 - - - +
797B LYS* 3.1 47.3 - - + -
808B GLN* 5.2 8.7 - - + +
809B ASP* 1.3 88.6 + - - +
811B ALA* 1.3 62.7 + - - +
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Residues in contact with ALA 811 (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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709B ALA 5.7 2.9 - - - +
710B TYR* 4.2 22.2 - - + -
712B LYS* 5.0 6.7 - - - +
795B ARG* 3.3 7.5 - - - +
796B ILE* 2.8 49.5 + - + +
810B LEU* 1.3 75.1 - - - +
812B GLU* 1.3 64.6 + - - +
813B VAL* 4.2 1.3 + - + -
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Residues in contact with GLU 812 (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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797A LYS* 4.9 5.4 + - - -
793B ARG* 3.2 31.3 + - - +
794B MET 3.6 13.7 - - - +
795B ARG* 3.6 36.1 + - + +
811B ALA* 1.3 78.3 - - - +
813B VAL* 1.3 67.9 + - - +
814B ASN* 3.4 32.4 + - - +
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Residues in contact with VAL 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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707B ILE* 4.5 2.7 - - + -
709B ALA* 4.5 23.8 - - + +
719B PHE* 4.5 13.9 - - + -
792B LEU 5.0 0.5 - - - +
793B ARG* 4.8 2.3 - - - -
794B MET* 2.9 19.8 + - + +
796B ILE* 4.5 24.7 - - + -
811B ALA* 5.3 1.1 - - + -
812B GLU* 1.3 72.6 - - - +
814B ASN* 1.4 65.1 + - - +
815B ASN* 3.4 22.7 - - - +
816B PHE* 3.6 49.3 - - + +
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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