Contacts of the strand formed by residues 89 - 94 (chain B) in PDB entry 4A8W
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 HIS 89 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B SER 4.9 1.6 - - - +
51B LEU* 4.5 4.7 - - - +
54B LYS* 3.8 15.6 + - - -
86B GLY 2.9 25.1 + - - -
87B MET 2.8 7.7 + - - -
88B ARG* 1.3 75.3 - - - +
90B MET* 1.3 64.3 + - - +
91B ASN* 3.3 20.4 + - - +
207B SER 3.5 15.5 - - - +
208B THR* 4.1 0.4 - - - -
209B ASP* 3.4 39.7 + - + -
211B ILE* 3.7 16.6 - - + +
247B LYS* 4.8 8.3 - - + -
264B PHE* 3.9 7.8 - - - -
265B PHE* 3.1 18.1 + - + +
266B CYS 3.3 24.0 + - - -
267B GLU* 4.1 12.9 - - + -
268B ARG 5.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B SER* 4.5 2.0 - - - -
46B VAL* 3.8 22.7 - - + -
51B LEU* 3.8 34.5 - - + -
89B HIS* 1.3 67.7 - - - +
91B ASN* 1.4 66.4 + - - +
93B PHE* 3.1 31.6 + - + +
249B ALA* 4.0 12.6 - - + -
252B LEU* 3.8 28.9 - - + -
258B ILE* 3.9 18.4 - - + -
259B ASP 3.9 7.0 - - - +
260B VAL* 4.1 10.1 - - + -
261B PRO* 4.6 0.2 - - - -
264B PHE* 3.9 21.5 - - + -
265B PHE 2.8 18.2 + - - +
266B CYS* 5.1 0.2 - - - -
267B GLU* 4.5 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ALA* 3.6 3.8 - - - -
37B ILE* 3.2 29.5 + - + +
39B THR* 4.9 0.8 + - - -
45B SER* 2.6 42.9 + - - -
50B PHE* 5.1 0.2 - - - -
54B LYS* 3.3 24.9 - - - +
89B HIS* 3.3 11.0 + - - +
90B MET* 1.4 68.4 - - - +
92B GLY* 1.3 57.4 + - - +
93B PHE* 4.4 0.7 - - - -
207B SER* 3.4 17.8 - - - +
267B GLU* 3.1 22.2 - - - +
526B PHE 3.7 2.8 + - - -
527B SER* 3.7 21.6 + - - +
528B PRO* 4.7 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLU* 3.7 8.0 - - - +
35B GLY 3.1 36.5 + - - +
37B ILE* 3.8 14.6 - - - +
91B ASN* 1.3 71.6 - - - +
93B PHE* 1.4 58.8 + - - +
94B PRO* 3.7 3.8 - - - +
267B GLU* 2.8 14.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLU* 3.7 19.5 - - + +
35B GLY* 3.6 14.4 - - - -
36B ALA* 3.4 32.1 - - + -
46B VAL* 3.9 16.2 - - + -
90B MET* 3.1 22.4 + - + +
91B ASN 4.4 0.7 - - - -
92B GLY* 1.4 77.2 - - - +
94B PRO* 1.4 65.3 - - - +
252B LEU* 3.5 37.7 - - + -
256B TYR* 3.8 25.8 - + - -
258B ILE* 3.5 24.9 - - + -
266B CYS* 3.4 9.0 - - - -
267B GLU* 2.8 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE* 3.5 24.2 - - + -
33B LYS 4.8 0.4 - - - +
34B GLU* 3.3 27.4 - - + +
92B GLY 3.7 4.5 - - - +
93B PHE* 1.4 84.6 - - - +
95B MET* 1.3 68.7 + - - +
96B ILE* 3.7 0.9 + - - +
251B ARG* 3.0 23.0 + - - -
266B CYS* 3.5 5.1 - - - +
267B GLU* 3.5 9.4 - - + +
269B ARG* 3.4 47.1 - - + +
----------------------------------------------------------
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