Contacts of the strand formed by residues 191 - 200 (chain C) in PDB entry 3OF6
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 TYR 191 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C GLY 3.1 23.9 + - - -
153C PHE* 2.9 49.9 + - + +
154C TYR* 3.3 30.7 - + - -
155C PRO* 4.1 0.9 - - + -
156C ASP* 3.5 48.2 + - + -
179C PRO* 3.9 11.2 - - + -
180C LEU 3.3 7.2 - - - -
181C LYS* 3.5 52.0 - - + -
182C GLU* 3.7 3.2 - - - +
189C SER 4.0 0.9 - - - -
190C ARG* 1.3 75.6 - - - +
192C CYS* 1.3 61.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 192 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C ALA 3.1 10.1 - - - +
151C THR* 4.2 12.3 - - + -
153C PHE* 3.6 1.6 - - - -
179C PRO* 3.2 6.6 - - - +
180C LEU* 2.7 37.7 + - - +
182C GLU* 4.3 9.2 - - + -
191C TYR* 1.3 75.8 - - - +
193C LEU* 1.3 61.6 + - - +
58F PHE* 4.0 15.3 - - + -
60F TYR* 4.0 19.4 - - + +
75F HIS* 5.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C CYS 4.4 0.2 - - - -
149C LEU* 3.4 3.8 - - - -
150C ALA* 2.8 40.2 + - + +
153C PHE* 4.1 9.2 - - + -
158C VAL* 3.8 26.0 - - + +
160C LEU* 4.3 28.5 - - + +
175C THR* 4.6 4.0 - - + -
176C ASP* 3.6 35.7 - - + +
177C PRO 5.4 0.2 - - - +
179C PRO* 4.2 22.7 - - + -
192C CYS* 1.3 76.5 - - - +
194C SER* 1.3 72.8 + - - +
215C VAL* 6.0 0.7 - - + -
60F TYR* 3.7 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 194 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C CYS 3.1 6.5 - - - -
149C LEU* 3.5 20.9 - - - -
160C LEU* 4.5 3.4 - - - -
175C THR* 3.6 3.3 - - - +
176C ASP* 2.7 56.9 + - - +
193C LEU* 1.3 80.5 - - - +
195C SER* 1.3 62.8 + - - +
196C ARG* 3.4 7.8 + - - -
60F TYR* 3.6 13.9 - - - +
73F LEU* 3.5 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 195 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C LEU 3.5 0.7 - - - +
147C VAL* 3.4 7.3 - - - +
148C CYS* 3.1 27.6 + - - -
160C LEU* 3.6 21.3 - - - -
162C TRP* 2.9 26.4 + - - -
173C VAL* 3.9 2.1 - - - +
174C SER 3.7 6.3 - - - -
175C THR* 2.8 28.6 + - - -
194C SER* 1.3 77.6 - - - +
196C ARG* 1.3 69.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 196 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C THR* 3.8 18.2 - - + -
146C LEU 3.4 3.8 - - - -
147C VAL* 4.2 12.3 - - + -
162C TRP* 4.6 0.7 - - - -
172C GLY 3.4 2.4 - - - +
173C VAL* 3.5 1.9 - - - -
174C SER* 2.8 70.7 + - - +
175C THR 4.5 0.4 - - - -
176C ASP* 2.9 26.5 + - - +
194C SER* 3.4 17.0 + - - -
195C SER* 1.3 83.6 + - - +
197C LEU* 1.3 60.9 + - - +
198C ARG* 4.2 0.7 - - + -
32F LEU* 3.9 21.5 - - - -
60F TYR* 5.8 0.4 - - - +
61F GLY 5.8 1.6 + - - -
63F SER* 3.4 22.5 + - - -
64F PRO 5.0 0.6 + - - -
71F THR* 3.2 29.2 + - - -
73F LEU* 4.1 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C ALA 3.2 5.5 - - - +
145C THR* 3.3 2.6 - - - +
146C LEU* 3.1 35.7 + - + +
162C TRP* 3.9 48.7 - - + +
164C VAL* 4.4 13.2 - - + -
169C VAL* 4.4 10.3 - - + -
171C SER 3.8 9.4 - - - +
172C GLY* 3.3 26.0 - - - +
173C VAL* 3.7 13.9 - - + -
196C ARG* 1.3 74.9 - - - +
198C ARG* 1.3 65.3 + - - +
199C VAL* 3.9 16.5 + - + +
211C PHE* 5.2 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 198 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C GLU* 3.8 2.4 + - - -
141C THR* 3.4 28.5 + - - +
143C LYS* 3.3 38.9 - - + +
144C ALA 3.3 3.8 - - - +
145C THR* 3.0 26.3 + - + +
171C SER 5.1 0.3 - - - +
172C GLY* 3.3 19.6 + - - +
196C ARG 4.2 0.6 - - - -
197C LEU* 1.3 77.8 - - - +
199C VAL* 1.3 65.8 + - - +
34F LEU* 3.3 38.6 - - - +
67F ASP* 3.6 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 199 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C LYS* 3.5 11.4 - - - +
144C ALA* 2.9 50.2 + - + +
146C LEU* 4.6 9.9 - - + -
164C VAL* 6.2 1.1 - - + -
197C LEU* 4.3 21.5 - - + +
198C ARG* 1.3 81.2 - - - +
200C SER* 1.3 68.9 - - - +
203C PHE* 4.3 22.7 - - + -
204C TRP* 4.2 13.5 - - + +
211C PHE* 4.9 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 200 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C GLN 4.5 3.4 - - - -
143C LYS* 4.9 8.6 - - - +
199C VAL* 1.3 78.0 - - - +
201C ALA* 1.3 66.5 + - - +
202C THR* 3.3 12.3 + - - -
203C PHE* 2.9 34.2 + - - +
204C TRP* 3.2 9.5 + - - +
----------------------------------------------------------
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