Contacts of the strand formed by residues 806 - 814 (chain A) in PDB entry 2W77
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 ASN 806 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A SER* 3.3 13.7 - - - +
288A TRP* 3.6 20.4 - - + -
780A ASN 3.7 0.5 - - - +
781A VAL* 3.5 1.7 - - - +
782A ASN* 2.8 66.5 + - - +
783A ASN* 5.0 1.0 - - - +
803A ASP* 4.1 14.7 + - - +
804A PRO 3.0 14.8 + - - -
805A ARG* 1.3 77.1 - - - +
807A LEU* 1.3 69.1 + - - +
808A MET* 5.8 0.9 - - - +
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Residues in contact with LEU 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A ALA 4.9 0.2 - - - -
286A GLY* 3.1 22.7 - - - -
287A SER* 2.7 20.0 + - - +
779A VAL* 4.9 0.4 - - + -
780A ASN 3.1 5.2 - - - +
781A VAL* 4.0 22.7 - - + -
782A ASN* 5.6 0.2 - - - -
805A ARG* 4.8 1.1 - - - -
806A ASN* 1.3 86.9 - - - +
808A MET* 1.3 63.0 + - - +
809A PHE* 3.8 29.2 - - + -
1817A N8E 3.8 54.7 - - + +
769B TYR* 3.8 29.6 - - + +
771B ILE* 5.7 1.3 - - + -
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Residues in contact with MET 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A GLY* 6.3 2.9 - - - -
183A ASN* 5.1 7.0 - - - +
284A GLY* 3.5 15.3 - - - +
285A ALA* 3.4 24.5 - - - +
286A GLY* 3.6 20.9 - - - +
290A ASN* 4.5 17.7 - - - +
292A ARG* 4.3 22.4 - - + -
316A GLN* 5.2 1.8 - - - +
778A SER 4.1 0.5 - - - +
779A VAL* 3.3 5.2 - - - -
780A ASN* 2.8 51.6 + - + +
782A ASN* 5.5 4.0 - - - +
806A ASN* 5.8 0.9 - - - +
807A LEU* 1.3 74.3 - - - +
809A PHE* 1.3 65.9 + - - +
810A SER* 4.8 7.1 + - - +
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Residues in contact with PHE 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A GLY* 3.0 2.6 - - - -
285A ALA* 2.7 37.0 + - + +
778A SER 3.7 4.3 - - - +
779A VAL* 3.5 28.9 - - + -
807A LEU* 3.8 23.3 - - + -
808A MET* 1.3 76.8 - - - +
810A SER* 1.3 62.8 + - - +
1817A N8E 3.8 43.3 - - - -
769B TYR* 3.8 36.8 - + + -
771B ILE* 3.5 38.8 - - + -
777B ALA* 4.4 10.3 - - + -
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Residues in contact with SER 810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A GLU* 5.1 10.1 + - - -
283A LEU 3.1 15.0 - - - -
284A GLY* 3.8 4.9 - - - -
777A ALA* 3.5 4.7 - - - +
778A SER* 3.0 47.2 + - - +
780A ASN* 5.2 2.8 + - - -
808A MET* 4.8 8.5 + - - +
809A PHE* 1.3 78.6 - - - +
811A THR* 1.3 65.1 + - - +
1817A N8E 5.0 3.6 - - - +
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Residues in contact with THR 811 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A VAL 4.0 0.5 - - - +
282A GLU* 3.3 5.6 - - - +
283A LEU* 3.0 37.5 + - - +
775A LEU* 3.6 28.3 - - + -
776A SER 3.0 18.8 - - - +
777A ALA* 4.1 2.2 - - + -
810A SER* 1.3 76.5 - - - +
812A ARG* 1.3 60.9 + - - +
1817A N8E 3.7 30.6 + - - +
811B THR* 5.1 1.7 + - - -
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Residues in contact with ARG 812 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ASP* 3.7 9.9 + - - -
280A HIS* 3.1 21.5 + - + -
281A VAL 3.5 7.2 - - - +
282A GLU* 4.0 24.1 + - - +
768A ARG* 6.4 0.9 - - - +
774A LYS 3.7 0.9 - - - +
775A LEU* 3.5 6.0 - - - +
776A SER* 3.0 44.5 + - - +
811A THR* 1.3 75.3 - - - +
813A TRP* 1.3 60.5 + - - +
814A ASP* 2.7 37.5 + - - +
1820A PO4 2.9 42.2 + - - -
1822A PO4 3.1 14.5 + - - -
1823A PO4 3.7 12.7 + - - -
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Residues in contact with TRP 813 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A HIS* 3.0 6.4 - - - -
281A VAL* 2.7 52.1 + - + +
774A LYS* 3.2 34.9 - - + +
775A LEU* 4.5 17.5 - - + +
811A THR* 4.2 0.4 - - - -
812A ARG* 1.3 74.0 - - - +
814A ASP* 1.4 70.7 + - - +
815A PHE* 3.6 37.5 + + + -
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Residues in contact with ASP 814 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A GLY 3.4 7.0 - - - +
280A HIS* 3.8 2.0 - - - +
770A GLN* 5.2 6.1 + - - +
773A ASP 5.3 2.5 - - - +
774A LYS* 2.8 44.8 + - - +
776A SER* 5.5 0.9 + - - -
812A ARG* 2.7 50.2 + - - +
813A TRP* 1.4 73.5 - - - +
815A PHE* 1.3 65.1 + - - +
1822A PO4 3.5 11.0 + - - +
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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