Contacts of the strand formed by residues 192 - 199 (chain B) in PDB entry 1FTA
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 GLU 192 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B THR* 3.6 33.1 - - + -
13B LEU* 6.0 0.2 - - - +
14B THR* 4.0 15.6 + - - -
42B LYS* 5.0 2.6 + - - +
185B MET 3.4 1.2 - - - +
186B LEU* 3.4 5.7 - - - +
187B ASP 2.9 27.0 + - - -
190B ILE* 3.6 21.8 - - + +
191B GLY* 1.3 75.7 - - - +
193B PHE* 1.3 64.1 + - - +
194B ILE* 3.6 12.7 - - + +
39D THR* 3.1 32.4 + - + +
42D LYS* 2.8 29.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B THR* 3.2 7.1 - - - -
13B LEU* 2.9 50.7 + - + +
38B CYS* 4.0 30.3 - - - -
41B VAL* 3.8 24.7 - - + -
42B LYS* 3.8 24.5 - - + -
171B THR* 4.0 10.1 - - + -
173B LEU* 3.9 24.9 - - + -
184B PHE* 3.8 22.0 - - + -
185B MET 3.3 1.1 - - - -
186B LEU* 3.6 39.7 - - + -
192B GLU* 1.3 75.0 + - - +
194B ILE* 1.3 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 4.1 10.1 - - + -
54A ALA* 3.9 30.7 - - + -
57A TYR* 3.9 34.1 - - + -
59A ILE* 6.1 0.2 - - + -
10B VAL* 4.7 10.5 - - + -
11B VAL 3.6 10.1 - - - +
12B THR* 4.8 3.8 - - + -
184B PHE* 3.3 2.7 - - - -
185B MET 2.8 34.3 + - - +
187B ASP* 4.3 7.2 - - + -
190B ILE* 4.5 1.1 - - + -
192B GLU* 3.6 39.5 - - + +
193B PHE* 1.3 71.9 - - - +
195B LEU* 1.3 67.3 + - - +
196B VAL* 3.1 7.7 + - + +
39D THR* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 4.2 7.6 - - - -
11B VAL* 3.0 38.9 + - + +
16B PHE* 3.9 31.2 - - + -
182B ASN* 4.1 5.4 - - + +
183B CYS 3.2 20.2 - - - +
184B PHE* 3.7 29.8 - - + -
193B PHE 4.0 0.2 + - - -
194B ILE* 1.3 74.7 - - - +
196B VAL* 1.3 60.4 + - - +
197B ASP 3.3 20.2 - - - +
198B LYS* 3.7 29.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 5.2 0.7 - - + -
57A TYR* 3.8 42.8 + - + +
172B MET* 3.6 28.7 - - + -
183B CYS* 3.1 16.4 + - + +
185B MET* 3.5 29.6 - - + +
194B ILE* 3.1 8.9 + - + +
195B LEU* 1.3 79.0 - - - +
197B ASP* 1.3 65.3 + - + +
198B LYS* 5.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ASN* 3.4 3.5 - - - -
183B CYS* 3.0 39.4 + - + -
195B LEU* 3.3 7.1 - - - +
196B VAL* 1.3 81.5 - - + +
198B LYS* 1.3 71.1 + - - +
200B VAL* 3.8 25.4 - - + +
257B VAL* 6.1 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 5.1 9.7 - - - +
16B PHE* 6.1 1.6 - - + -
182B ASN* 3.1 10.3 - - - +
195B LEU* 3.7 31.6 - - + -
196B VAL 5.5 0.2 - - - -
197B ASP* 1.3 83.1 + - - +
199B ASP* 1.3 82.5 + - - +
200B VAL* 3.3 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B CYS* 4.2 21.1 - - - +
180B GLY* 5.1 2.1 - - - -
181B VAL 3.3 10.8 - - - +
182B ASN* 3.2 13.7 + - - +
198B LYS* 1.3 84.1 - - - +
200B VAL* 1.3 66.7 + - - +
201B LYS* 3.6 16.9 + - - +
----------------------------------------------------------
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