Contacts of the strand formed by residues 806 - 814 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B SER* 3.4 16.6 - - - +
288B TRP* 3.7 17.9 - - + -
780B ASN 3.8 0.2 - - - +
781B VAL* 3.4 3.5 - - - +
782B ASN* 2.7 68.3 + - - +
783B ASN* 5.1 0.8 - - - +
803B ASP* 4.0 17.7 + - - +
804B PRO 2.9 15.2 + - - -
805B ARG* 1.3 73.9 - - - +
807B LEU* 1.3 70.3 + - - +
808B MET* 5.9 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 807 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769A TYR* 3.7 39.0 - - + +
771A ILE* 5.4 1.1 - - + -
286B GLY* 3.1 22.1 - - - -
287B SER* 3.0 20.3 + - - +
779B VAL* 4.6 2.0 - - + -
780B ASN 3.0 5.6 - - - +
781B VAL* 4.0 31.2 - - + -
782B ASN* 5.9 0.2 - - - -
805B ARG* 5.1 9.4 - - + +
806B ASN* 1.3 87.1 - - - +
808B MET* 1.3 64.3 + - - +
809B PHE* 3.7 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 808 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLY* 5.9 7.0 - - - +
183B ASN* 5.2 12.3 - - - +
284B GLY* 4.2 7.0 - - - -
285B ALA 3.5 28.9 - - - +
286B GLY* 4.1 3.4 - - - +
290B ASN* 3.3 46.2 - - + +
292B ARG* 5.6 5.2 - - + -
316B GLN* 4.4 6.5 - - - +
778B SER 4.4 0.3 - - - -
779B VAL* 3.3 4.9 - - - -
780B ASN* 2.7 49.9 + - + +
782B ASN* 5.8 3.6 - - - +
806B ASN* 5.9 0.4 - - - +
807B LEU* 1.3 77.1 - - - +
809B PHE* 1.3 64.4 + - - +
810B SER* 3.9 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 809 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769A TYR* 3.8 32.1 - + + -
771A ILE* 3.4 29.4 - - + -
777A ALA* 3.9 18.8 - - + -
1817A N8E 3.7 39.1 - - - +
284B GLY* 3.1 4.5 - - - -
285B ALA 2.7 43.2 + - - +
778B SER 3.7 1.1 - - - -
779B VAL* 3.7 24.7 - - + -
807B LEU* 3.7 33.4 - - + -
808B MET* 1.3 73.7 - - - +
810B SER* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 810 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1817A N8E 3.7 6.0 - - - +
282B GLU* 2.9 31.3 + - - +
283B LEU 3.7 4.3 + - - -
284B GLY* 4.3 3.9 - - - -
777B ALA* 3.4 3.3 - - - -
778B SER* 2.8 53.3 + - - +
780B ASN* 5.7 1.6 - - - -
808B MET* 4.7 8.8 - - - +
809B PHE* 1.3 75.2 - - - +
811B THR* 1.3 62.3 + - - +
812B ARG 4.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 811 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811A THR* 5.1 2.8 + - - -
1817A N8E 3.0 28.1 + - - -
281B VAL 3.9 0.7 - - - +
282B GLU* 3.3 6.0 - - - +
283B LEU* 3.1 37.2 + - - +
775B LEU* 4.0 29.8 - - + -
776B SER 3.5 13.0 - - - +
777B ALA* 4.8 4.7 - - + -
810B SER* 1.3 71.7 + - - +
812B ARG* 1.3 62.2 + - - +
813B TRP* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 812 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASP* 5.9 0.4 + - - -
178B ASP* 3.6 20.4 + - - -
278B LYS* 5.6 2.6 - - - +
279B GLY 5.4 0.2 - - - -
280B HIS* 3.1 30.7 + - + +
281B VAL 3.6 9.0 - - - +
282B GLU* 3.8 28.1 + - - +
768B ARG* 6.4 1.1 - - - +
774B LYS 3.6 0.9 - - - +
775B LEU* 3.5 6.0 - - - +
776B SER* 3.0 46.7 + - - +
810B SER 4.2 0.6 - - - -
811B THR* 1.3 74.6 - - - +
813B TRP* 1.3 61.3 + - - +
814B ASP* 2.9 35.9 + - - +
1818B PO4 2.3 34.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 813 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B HIS* 3.2 3.5 - - - -
281B VAL* 2.9 55.7 + - + +
774B LYS* 3.2 25.5 - - + +
775B LEU* 3.7 20.6 - - + -
811B THR* 4.2 0.6 + - + -
812B ARG* 1.3 72.5 - - - +
814B ASP* 1.3 79.9 + - - +
815B PHE* 3.9 28.2 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 814 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B GLY 3.3 9.6 - - - +
280B HIS* 3.8 2.6 - - - +
770B GLN* 5.0 6.8 + - - +
773B ASP 5.3 1.5 - - - +
774B LYS* 2.9 41.6 + - - +
776B SER* 5.4 0.9 + - - -
812B ARG* 2.9 46.8 + - - +
813B TRP* 1.3 83.2 - - - +
815B PHE* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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