Contacts of the strand formed by residues 167 - 173 (chain A) in PDB entry 2CX9
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 VAL 167 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA* 5.6 0.4 - - + -
100A ILE* 4.0 27.4 - - + -
112A PHE* 4.0 20.2 - - + +
115A LYS* 5.8 0.4 - - + -
116A LEU* 3.8 31.2 - - + -
121A ALA* 4.2 8.3 - - + -
122A LEU 3.2 3.2 + - - +
123A GLY* 3.4 3.6 - - - -
124A ALA 3.0 23.7 + - - -
165A ALA* 3.6 4.0 - - - +
166A GLY* 1.3 83.7 - - - +
168A TYR* 1.3 71.5 + - - +
169A VAL* 4.8 2.0 - - + -
192A PHE 3.6 7.9 - - - +
193A PHE* 4.1 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ALA* 3.5 21.8 - - + -
126A GLY 6.3 0.4 - - - -
162A GLY 2.7 30.3 + - - -
163A SER* 4.4 4.0 + - - -
165A ALA* 3.5 31.9 + - + +
167A VAL* 1.3 77.8 - - - +
169A VAL* 1.3 63.6 + - - +
170A VAL* 4.1 6.5 - - + -
190A PHE 3.4 1.7 - - - +
191A ALA* 3.2 5.0 - - - +
192A PHE* 2.9 55.3 + + + -
194A ARG* 4.1 26.4 - - + +
199A LEU* 3.5 33.9 - - + +
201A VAL* 4.5 4.0 - - - +
218A LEU* 3.8 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA* 3.8 30.3 - - + +
99A HIS* 3.7 24.0 - - + +
100A ILE* 4.0 22.7 - - + -
124A ALA 2.9 9.1 + - - +
125A TRP* 3.4 27.3 - - + +
126A GLY 2.7 32.1 + - - +
167A VAL* 4.8 1.1 - - + -
168A TYR* 1.3 77.7 - - - +
170A VAL* 1.3 57.1 + - - +
171A MET* 4.2 5.5 - - - +
189A ALA* 4.7 2.5 - - + -
190A PHE 3.2 6.1 - - - +
191A ALA* 4.2 3.6 - - + -
231A LEU* 4.2 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLY* 3.6 9.2 - - - +
141A THR* 4.7 3.1 - - + -
152A LEU* 5.1 5.2 - - + -
156A LYS* 3.5 28.7 - - + -
168A TYR* 4.5 9.0 - - + -
169A VAL* 1.3 81.5 - - - +
171A MET* 1.3 72.2 + - - +
172A ALA* 5.0 2.0 - - + -
189A ALA* 3.4 0.9 - - - -
190A PHE* 2.8 40.5 + - + -
192A PHE* 3.9 28.9 - - + -
218A LEU* 5.3 3.8 - - + -
220A LEU* 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A HIS* 3.7 12.6 - - - -
125A TRP* 3.4 44.6 - - + +
126A GLY 3.1 20.4 + - - +
127A LEU* 3.8 14.4 - - + -
139A LEU* 3.6 20.7 - - + +
141A THR* 4.0 0.5 - - - -
156A LYS* 2.8 29.3 + - - -
169A VAL* 4.2 5.2 - - - +
170A VAL* 1.3 76.9 - - - +
172A ALA* 1.3 63.3 + - - +
187A ILE* 4.2 7.6 - - + -
188A SER 3.3 8.3 - - - +
189A ALA* 3.6 21.3 - - + -
237A GLY 5.1 0.7 - - - +
241A VAL* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 4.6 2.9 - - - -
141A THR* 3.5 28.3 - - + +
142A LYS 3.9 12.6 - - - +
143A ALA* 4.0 12.6 - - + -
152A LEU* 4.7 6.5 - - + -
170A VAL* 3.9 2.6 + - + -
171A MET* 1.3 76.5 - - - +
173A ARG* 1.3 64.2 + - - +
174A THR* 3.5 2.8 + - - +
187A ILE* 3.6 5.9 - - - +
188A SER* 2.8 33.6 + - - +
190A PHE* 4.7 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ALA 3.8 7.3 + - - -
138A ALA* 5.6 0.2 - - - +
139A LEU* 4.9 17.1 + - + +
141A THR 2.9 19.5 + - - +
142A LYS* 3.5 16.7 - - + +
143A ALA 3.0 24.3 + - - +
172A ALA* 1.3 70.3 - - - +
174A THR* 1.3 60.6 + - - +
175A ASP 3.0 35.3 + - - +
176A PRO* 4.4 2.5 - - + -
177A PRO* 3.9 15.0 - - - +
183A LYS* 2.8 41.9 + - - +
185A GLN 3.0 22.8 + - - -
186A GLY* 3.3 12.2 - - - -
187A ILE* 4.1 11.9 - - + +
----------------------------------------------------------
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