Contacts of the strand formed by residues 168 - 175 (chain A) in PDB entry 2CND
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 168 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ARG* 2.9 37.0 + - + +
138A ARG* 3.2 23.4 - - - +
139A LEU* 2.6 35.7 + - - +
166A HIS 3.7 2.1 + - - +
167A THR* 1.3 71.9 - - - +
169A MET* 1.3 55.0 + - - +
170A HIS* 2.8 34.1 + - - +
196A ASP 4.1 8.1 - - - +
197A ARG* 3.3 7.2 - - - +
199A LYS* 3.4 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 3.6 15.5 - - + -
141A MET* 4.1 19.1 - - - -
155A ILE* 3.8 49.1 - - + +
158A VAL* 4.0 26.2 - - + -
159A LEU* 4.1 15.0 - - + -
167A THR* 4.0 7.4 - - + +
168A GLU* 1.3 78.7 - - - +
170A HIS* 1.3 61.8 + - - +
171A LEU 4.0 0.4 - - - -
197A ARG 2.6 13.7 + - - +
198A LEU* 3.4 31.5 - - + -
199A LYS* 2.8 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ARG* 4.5 0.6 - - + +
139A LEU 2.8 14.7 + - - +
140A ALA* 3.5 1.4 - - - -
141A MET* 2.8 34.1 + - - +
168A GLU* 2.8 37.3 + - - -
169A MET* 1.3 76.4 - - - +
171A LEU* 1.3 56.5 + - - +
172A VAL* 4.1 0.6 + - - -
199A LYS* 3.1 35.8 - - + +
229A HIS 3.3 26.4 + - - +
230A VAL* 4.2 3.7 - - - +
231A PRO* 3.4 45.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A MET* 3.1 39.0 - - + +
143A CYS* 4.1 19.7 - - - -
148A ILE* 4.2 9.6 - - + -
151A MET* 4.5 3.4 - - + -
155A ILE* 4.5 4.0 - - + -
169A MET 4.0 0.4 - - - -
170A HIS* 1.3 73.6 - - - +
172A VAL* 1.3 61.6 + - - +
173A TYR* 4.2 16.8 - - + -
187A LEU* 4.1 36.3 - - + -
198A LEU* 4.5 10.5 - - + -
199A LYS 2.8 17.4 + - - +
200A VAL* 4.4 14.1 - - + -
201A TRP* 3.1 27.2 + - - +
229A HIS 5.0 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A MET 2.8 8.7 + - - +
142A ILE* 3.4 13.4 - - + +
143A CYS* 3.0 27.9 + - - +
171A LEU* 1.3 75.9 - - - +
173A TYR* 1.3 59.6 + - - +
201A TRP* 3.6 5.4 - - + +
203A VAL* 4.2 10.1 - - + -
221A VAL* 4.2 21.8 - - + -
225A VAL* 4.1 20.4 - - + -
226A LEU* 4.2 7.9 - - + -
229A HIS* 4.1 22.2 - - + -
230A VAL* 3.6 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A CYS* 3.6 18.4 - - - -
145A GLY 3.0 36.8 + - - -
148A ILE* 3.6 20.7 - - + +
171A LEU* 3.8 15.2 - - + -
172A VAL* 1.3 71.3 - - - +
174A ALA* 1.3 61.9 + - - +
175A ASN* 3.4 20.4 + - - -
181A ILE* 3.7 20.6 - - + -
182A LEU* 3.1 43.0 + - - +
183A LEU 4.4 0.7 - - - -
187A LEU* 4.1 20.6 - - + -
201A TRP 3.0 9.6 + - - +
202A TYR* 3.3 19.5 - + + +
203A VAL* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A CYS 2.9 17.5 + - - +
144A GLY* 3.3 17.4 - - - -
145A GLY 3.3 0.7 + - - -
172A VAL 3.8 1.2 + - - +
173A TYR* 1.3 71.4 - - - +
175A ASN* 1.3 76.8 + - - +
203A VAL* 3.5 13.2 - - + -
220A PHE* 6.1 1.1 - - - -
221A VAL* 3.7 30.3 - - + +
247A MET* 4.0 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLY* 3.0 25.3 + - - +
173A TYR* 3.4 28.1 - - - -
174A ALA* 1.3 86.7 + - - +
176A ARG* 1.3 62.3 + - - +
177A THR 4.1 13.9 - - - +
180A ASP* 3.8 15.5 - - + +
181A ILE* 3.3 31.4 - - + +
203A VAL 2.9 10.5 + - - +
204A ILE* 3.7 1.2 - - + -
205A ASP* 3.1 27.4 + - - +
219A GLY 4.6 1.7 - - - +
----------------------------------------------------------
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