Contacts of the strand formed by residues 138 - 144 (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 ARG 138 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA* 3.9 3.5 - - - +
137A ARG* 1.3 114.7 - - + +
139A LEU* 1.3 62.0 + - - +
168A GLU* 3.2 22.7 - - + +
170A HIS* 4.5 1.3 - - - +
231A PRO* 3.9 15.9 - - + +
232A GLU* 2.6 60.1 + - - +
233A GLY 3.4 3.0 + - - -
236A ASP 3.5 3.1 + - - +
237A THR* 2.9 31.8 + - + +
238A LEU 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TYR* 5.7 0.2 - - + -
127A PHE* 3.9 29.2 - - + -
136A ALA* 4.2 4.0 - - + -
138A ARG* 1.3 75.8 - - - +
140A ALA* 1.3 60.3 + - - +
141A MET* 3.9 25.8 - - + -
154A ILE* 4.3 8.1 - - + -
158A VAL* 5.1 1.3 - - + -
167A THR* 3.8 25.6 - - + -
168A GLU 2.6 13.7 + - - +
169A MET* 4.2 14.1 - - + -
170A HIS* 2.8 34.3 + - - -
231A PRO* 4.7 0.9 - - - -
238A LEU* 3.4 20.4 - - + -
240A LEU* 3.5 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 1.3 72.8 - - - +
141A MET* 1.3 58.1 + - - +
142A ILE* 3.8 9.4 - - + +
170A HIS 3.5 4.9 - - - -
230A VAL* 3.7 17.7 - - + -
231A PRO* 4.0 3.4 - - + -
238A LEU 2.9 13.8 + - - +
239A ALA* 3.3 11.3 - - + -
240A LEU 2.7 34.0 + - - +
261A TYR* 3.5 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 3.9 26.0 - - + -
140A ALA* 1.3 73.5 - - - +
142A ILE* 1.3 62.2 + - - +
151A MET* 3.9 25.6 - - - +
154A ILE* 3.9 29.6 - - + -
155A ILE* 3.7 37.0 - - + -
169A MET* 4.1 16.8 - - - -
170A HIS 2.8 11.8 + - - +
171A LEU* 3.1 21.1 - - + +
172A VAL 2.8 25.1 + - - -
240A LEU* 3.4 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ALA* 3.8 22.9 - - + +
141A MET* 1.3 73.6 - - - +
143A CYS* 1.3 64.1 + - - +
151A MET* 4.0 0.8 - - - +
172A VAL* 3.4 22.4 - - + +
221A VAL* 4.8 7.0 - - + -
226A LEU* 4.6 4.5 - - + -
230A VAL* 3.9 26.7 - - + -
239A ALA* 4.9 1.1 - - + -
240A LEU 3.1 9.8 + - - +
241A ALA* 3.1 31.9 - - + +
242A CYS 3.3 2.3 + - - -
247A MET* 4.3 7.9 - - + -
252A ILE* 3.8 32.4 - - + +
256A LEU* 3.8 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ILE* 1.3 74.7 - - - +
144A GLY* 1.3 60.1 + - - +
147A GLY 3.5 12.3 - - - +
148A ILE* 3.6 30.3 - - - -
151A MET* 4.1 8.3 - - + -
171A LEU* 4.1 13.2 - - - -
172A VAL 3.0 9.4 + - - +
173A TYR* 3.6 24.7 - - - -
174A ALA 2.9 23.9 + - - -
242A CYS 3.1 17.7 - - - +
247A MET* 3.6 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A CYS* 1.3 77.1 - - - +
145A GLY* 1.3 61.3 + - - -
146A SER 3.6 0.2 + - - -
147A GLY* 2.9 20.8 + - - -
173A TYR* 4.3 0.9 - - - -
174A ALA* 3.3 12.6 - - - -
242A CYS 3.3 6.5 + - - +
243A GLY* 4.2 6.7 - - - -
244A PRO* 4.3 10.5 - - - +
247A MET* 4.2 13.9 - - - -
----------------------------------------------------------
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