Contacts of the strand formed by residues 159 - 169 (chain C) in PDB entry 2RFQ
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 ARG 159 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C ILE* 3.8 4.9 - - - +
156C LYS 2.9 32.6 + - - +
157C ASP 3.3 4.0 - - - +
158C GLY* 1.3 80.3 - - - +
160C PRO* 1.4 76.1 - - + +
161C VAL* 3.5 5.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C PRO* 4.1 15.5 - - + -
154C VAL 3.2 9.0 - - - +
155C ILE* 3.8 15.9 - - + -
158C GLY 4.6 2.2 - - - +
159C ARG* 1.4 89.3 - - + +
161C VAL* 1.3 61.3 + - - +
162C ASP 3.8 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C VAL* 2.9 34.9 + - + +
156C LYS* 3.9 35.9 - - + +
159C ARG* 3.7 12.8 - - + +
160C PRO* 1.3 78.8 - - - +
162C ASP* 1.3 65.9 + - + +
392C 1PS 3.7 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C PRO* 3.3 8.5 - - - +
154C VAL* 3.1 37.5 + - + +
160C PRO* 3.8 2.3 - - - +
161C VAL* 1.3 82.2 + - + +
163C PHE* 1.3 74.2 + - - +
164C VAL* 3.6 12.4 - - + +
206C SER* 2.7 29.3 + - - -
392C 1PS 3.3 43.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C TYR 4.0 17.5 - - - -
119C PRO* 3.7 28.7 - - + -
152C GLY* 3.7 35.4 - - - -
153C PRO* 3.8 9.9 - - + -
162C ASP* 1.3 85.3 + - - +
164C VAL* 1.3 60.9 + - - +
206C SER* 3.8 0.2 + - - -
207C PHE* 3.1 54.7 + + + +
208C LYS 4.6 0.3 + - - -
392C 1PS 3.2 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C GLY* 3.3 4.2 - - - -
152C GLY 3.0 35.6 + - - +
154C VAL* 3.7 15.0 - - + -
162C ASP* 3.6 23.8 - - - +
163C PHE* 1.3 79.2 - - - +
165C SER* 1.3 62.9 - - - +
166C PHE* 3.4 35.4 - - + -
204C VAL* 3.6 24.2 - - + -
205C LEU 3.2 10.3 - - - +
206C SER* 3.7 11.2 - - - +
207C PHE* 3.8 8.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C HIS* 3.2 23.5 - - - -
96C PHE* 3.8 14.1 - - - -
117C TYR* 3.7 7.4 - - - -
149C VAL* 4.3 10.1 - - - -
150C LEU 3.3 8.7 + - - -
151C GLY* 4.6 0.3 - - - -
164C VAL* 1.3 73.4 - - - +
166C PHE* 1.3 61.8 + - - +
204C VAL* 3.4 5.2 - - - +
205C LEU 2.9 32.1 + - - -
207C PHE* 3.1 27.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C ALA* 4.3 5.4 - - - -
123C GLY* 3.5 33.2 - - - -
130C TYR* 3.9 18.6 - + + -
132C VAL* 3.7 28.7 - - + -
136C TRP* 4.7 4.0 - + - -
148C ALA 3.2 5.9 - - - +
149C VAL* 3.4 1.7 - - - -
150C LEU* 2.9 43.7 + - + +
152C GLY* 4.0 16.6 - - - -
153C PRO 3.8 6.3 - - - -
154C VAL* 4.3 3.1 - - + -
164C VAL* 3.4 26.7 - - + -
165C SER* 1.3 72.7 - - - +
167C LEU* 1.3 59.2 + - - +
168C ILE* 3.7 21.1 + - + +
199C VAL* 4.3 6.3 - - + -
203C ARG 3.9 3.4 - - - -
204C VAL* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C LEU* 3.8 19.5 - - + -
96C PHE* 3.9 10.8 - - + -
100C ALA* 3.9 22.0 - - + +
104C VAL* 3.8 23.1 - - + -
113C ILE* 4.5 3.8 - - + -
147C TRP* 3.6 36.3 - - + -
148C ALA 3.4 7.9 - - - +
149C VAL* 3.8 19.7 - - + -
165C SER 4.0 0.8 + - - -
166C PHE* 1.3 70.3 - - - +
168C ILE* 1.3 60.9 + - - +
169C PRO* 4.5 0.5 - - - +
199C VAL* 3.7 14.1 - - - +
203C ARG* 2.9 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C VAL* 4.1 9.4 - - + -
147C TRP* 3.3 5.3 - - - -
148C ALA 2.8 37.2 + - - +
150C LEU* 3.9 23.1 - - + -
166C PHE* 3.9 12.8 - - + +
167C LEU* 1.3 80.5 - - - +
169C PRO* 1.4 82.0 - - + +
172C ASP* 3.7 17.9 - - + +
173C TYR* 3.3 16.1 - - + -
194C VAL* 3.9 20.9 - - + -
197C VAL* 4.2 7.2 - - + -
199C VAL* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C SER 3.7 4.3 - - - +
147C TRP* 3.4 40.5 - - + -
167C LEU 4.5 0.2 - - - +
168C ILE* 1.4 89.8 - - + +
170C ARG* 1.3 59.8 + - - +
171C GLU* 3.9 24.7 - - + +
172C ASP* 2.9 40.3 + - - +
173C TYR* 3.4 9.6 - - - -
199C VAL* 6.4 0.2 - - + -
203C ARG* 3.9 15.3 - - - +
----------------------------------------------------------
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