Contacts of the strand formed by residues 144 - 149 (chain A) in PDB entry 3CJR
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 LYS 144 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLY* 3.7 30.2 + - - +
122A ASP 2.7 12.9 + - - +
123A LYS* 3.4 17.4 - - + +
124A VAL* 2.9 23.0 + - - +
139A GLU* 3.5 4.3 - - - +
142A GLY 4.7 2.0 - - - +
143A GLY* 1.3 74.2 - - - +
145A ALA* 1.3 60.6 - - - +
146A LEU 4.0 0.2 + - - -
185A PHE* 5.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 3.3 9.4 - - + +
126A ASP* 5.9 0.4 - - + -
135A ALA* 3.5 35.7 - - + +
138A ALA* 4.0 13.0 - - + -
139A GLU* 2.7 17.5 + - + +
144A LYS* 1.3 73.1 - - - +
146A LEU* 1.3 60.5 + - - +
147A GLY 4.2 0.2 - - - -
169A PRO* 3.6 7.9 - - + +
170A ARG* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL 2.8 12.7 + - - +
125A LEU* 3.5 4.6 - - + +
126A ASP* 2.8 28.9 + - - +
144A LYS 4.0 0.4 + - - -
145A ALA* 1.3 75.0 - - - +
147A GLY* 1.3 58.5 + - - +
148A VAL* 3.8 9.6 - - + -
170A ARG* 3.3 40.8 - - + +
172A LEU* 3.9 22.7 - - + -
179A ALA* 3.8 27.4 - - + -
182A PHE* 3.9 15.9 - - + -
185A PHE* 3.7 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASP* 3.5 11.7 - - - -
129A THR* 3.7 22.2 - - - +
135A ALA* 4.4 3.7 - - - +
145A ALA 4.2 0.6 - - - -
146A LEU* 1.3 72.5 - - - +
148A VAL* 1.3 61.8 + - - +
170A ARG 2.7 12.1 + - - -
171A PHE* 3.2 15.0 - - - +
172A LEU 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 4.0 14.4 - - + -
126A ASP 3.1 5.4 + - - +
127A LEU* 3.7 28.0 - - + -
128A GLY 2.8 26.2 + - - -
129A THR* 2.9 7.5 + - - -
146A LEU* 3.8 26.8 - - + -
147A GLY* 1.3 78.6 - - - +
149A ASP* 1.3 61.7 + - - +
172A LEU* 3.1 26.5 - - + +
174A GLY 3.7 14.4 - - - +
175A SER 3.9 10.5 - - - +
178A ALA* 5.2 0.4 - - + -
179A ALA* 4.3 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A THR* 3.4 10.5 + - + +
130A GLY* 2.8 26.7 + - - -
148A VAL* 1.3 75.2 - - - +
150A ILE* 1.3 64.1 + - - +
151A ASP* 2.9 25.2 + - - +
154A VAL* 3.6 23.3 - - + -
155A LEU* 4.3 4.0 - - + +
172A LEU 3.1 6.9 + - - -
173A GLU* 3.3 10.0 - - - +
174A GLY 2.9 19.8 + - - -
255A SFG 2.7 43.6 + - - -
----------------------------------------------------------
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