Contacts of the strand formed by residues 192 - 200 (chain Z) in PDB entry 6F0X
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 LYS 192 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103Z ASP 4.4 0.2 - - - -
104Z ILE* 3.5 0.9 - - - +
105Z GLU* 2.8 63.8 + - + +
185Z SER* 3.0 29.1 - - - -
186Z PHE* 3.3 13.0 - - - +
187Z THR* 3.3 19.1 - - + +
190Z ILE 4.1 0.4 + - - -
191Z HIS* 1.3 72.7 - - - +
193Z VAL* 1.3 71.1 + - - +
194Z ASN* 2.0 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Z VAL* 4.5 6.7 - - + -
24Z PHE* 3.7 25.4 - - + -
102Z PHE* 3.7 23.6 - - + -
103Z ASP 3.3 7.0 - - - +
104Z ILE* 4.2 16.8 - - + -
185Z SER* 4.1 1.4 - - - -
186Z PHE* 2.9 63.3 + - + +
191Z HIS* 5.4 2.9 - - + -
192Z LYS* 1.3 81.6 - - - +
194Z ASN* 1.3 75.3 + - - +
195Z SER* 3.8 3.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 194 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102Z PHE* 3.2 3.1 - - - -
103Z ASP* 2.9 49.7 + - + +
105Z GLU* 4.5 14.6 + - - +
182Z ARG* 5.8 12.8 - - - +
185Z SER* 3.6 8.6 - - - -
192Z LYS* 2.0 37.8 + - - +
193Z VAL* 1.3 73.7 - - - +
195Z SER* 1.3 66.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 195 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Z PHE* 5.6 1.0 - - - -
101Z GLN 3.3 5.4 - - - -
102Z PHE* 3.1 27.5 - - - -
131Z VAL* 5.6 3.5 - - - +
135Z ILE* 6.3 0.7 - - - -
182Z ARG* 3.3 7.7 - - - +
183Z LEU* 2.9 46.6 + - - +
184Z ARG 4.7 6.6 + - - -
186Z PHE* 3.9 10.8 - - - -
193Z VAL* 3.8 8.5 + - - +
194Z ASN* 1.3 82.4 + - - +
196Z MET* 1.3 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 196 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99Z ARG 3.8 0.3 - - - +
100Z TRP* 4.8 2.7 - - - -
101Z GLN* 2.9 53.4 + - + +
102Z PHE* 4.8 0.8 - - - -
103Z ASP* 5.7 3.1 - - - +
180Z GLU* 3.2 45.1 - - + +
181Z VAL 3.1 28.9 - - - +
182Z ARG* 3.7 29.2 - - + +
183Z LEU* 4.0 3.0 - - - +
195Z SER* 1.3 77.3 - - - +
197Z VAL* 1.3 60.4 + - - +
198Z ALA 4.0 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98Z GLU* 4.2 6.7 - - + -
99Z ARG 3.5 7.9 - - - +
100Z TRP* 3.4 56.1 - - + +
138Z THR* 5.9 0.7 - - - -
141Z PHE* 5.3 2.0 - - + -
142Z LEU* 4.4 16.4 - - + -
179Z GLU 3.6 1.4 - - - +
180Z GLU* 3.1 3.3 - - - -
181Z VAL* 2.9 56.2 + - + +
183Z LEU* 4.1 4.4 - - + +
196Z MET* 1.3 72.0 - - - +
198Z ALA* 1.3 73.1 + - - +
199Z TYR* 4.1 3.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 198 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98Z GLU* 3.5 0.9 - - - -
99Z ARG* 2.9 57.2 + - + +
175Z ILE* 4.2 6.7 - - + +
178Z SER* 4.1 14.1 - - - +
179Z GLU 3.1 7.9 - - - +
180Z GLU* 4.1 12.8 - - + +
196Z MET 4.0 0.6 + - - -
197Z VAL* 1.3 74.0 - - - +
199Z TYR* 1.3 64.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 199 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192P ARG* 4.0 18.0 + - - -
97Z LEU 3.1 11.9 - - - +
98Z GLU* 4.8 4.9 - - + -
141Z PHE* 5.0 6.1 - + - -
142Z LEU* 4.6 11.2 - - + -
143Z PRO* 3.8 33.9 - - + -
175Z ILE* 4.5 0.4 - - - -
178Z SER* 2.9 6.9 - - - -
179Z GLU* 2.2 95.0 + - + -
181Z VAL* 4.2 15.3 - - + -
197Z VAL* 4.1 15.0 - - + -
198Z ALA* 1.3 78.4 - - - +
200Z LYS* 1.3 77.2 + - - +
201Z ILE* 5.0 0.2 - - - -
202Z PRO* 4.8 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95Z GLU* 2.8 38.7 + - - +
96Z VAL 4.2 11.9 - - - +
97Z LEU* 2.9 33.3 + - + +
143Z PRO* 5.0 3.3 - - - +
175Z ILE* 4.4 6.7 - - + +
177Z ASN* 3.0 26.9 - - - +
178Z SER* 3.8 4.4 - - - +
199Z TYR* 1.3 79.2 - - - +
201Z ILE* 1.3 76.1 + - - +
202Z PRO* 3.4 4.7 - - - +
203Z VAL* 5.0 15.9 - - - +
----------------------------------------------------------
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