Contacts of the helix formed by residues 140 - 149 (chain A) in PDB entry 2NPP
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 TRP 140 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A THR* 5.2 4.7 - - + -
100A GLU* 5.1 6.1 - - + -
138A GLY* 3.3 0.6 - - - -
139A ASP* 1.3 93.1 - - + +
141A PHE* 1.3 90.8 - + - +
142A THR* 3.0 19.7 - - + +
143A SER* 2.7 39.1 + - - +
144A ARG* 3.3 7.8 + - - -
199B TYR* 3.0 34.8 - + - -
235B ILE* 3.9 23.0 - - + +
239B LYS* 3.3 52.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 4.4 12.6 - - - -
140A TRP* 1.3 100.7 - + - +
142A THR* 1.3 74.3 + - + +
144A ARG* 3.2 24.0 - - - +
145A THR* 2.8 38.9 + - - -
178A THR* 4.2 6.5 - - + +
180A MET* 3.9 29.8 - - + -
181A VAL* 4.0 13.2 - - + +
199B TYR* 3.3 50.9 - + + -
203B TYR* 4.1 18.4 - + + -
204B GLU* 6.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ALA 4.5 1.3 - - - -
98A THR* 3.0 27.7 + - - +
99A VAL 4.1 1.1 - - - -
100A GLU* 4.2 17.4 - - + +
105A ARG* 2.8 34.6 - - - +
140A TRP* 2.9 14.7 + - + +
141A PHE* 1.3 99.6 - - + +
143A SER* 1.3 72.0 + - - +
145A THR* 3.2 6.9 - - - +
146A SER* 3.0 26.0 + - - -
203B TYR* 5.7 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ALA 4.4 9.0 - - - -
98A THR* 3.0 28.1 + - - +
135A LEU* 3.1 31.5 - - - +
138A GLY* 4.3 13.0 - - - -
140A TRP* 2.7 21.9 + - - +
142A THR* 1.3 76.2 + - - +
144A ARG* 1.3 63.9 + - - -
146A SER* 3.0 7.1 + - - -
147A ALA* 3.0 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU 3.1 7.4 + - - +
136A ALA 3.0 28.7 - - - +
137A GLY 4.9 0.2 - - - -
138A GLY 3.1 21.4 + - - +
139A ASP 3.2 17.2 + - - -
140A TRP 3.3 9.0 + - - -
141A PHE* 3.2 30.5 - - - +
143A SER* 1.3 77.8 - - - +
145A THR* 1.3 67.6 + - - +
147A ALA* 3.0 17.6 + - - +
148A CYS* 3.3 12.8 + - - -
173A LEU* 3.9 14.1 - - + +
176A ASP* 2.7 39.9 + - - +
177A ASP* 4.8 6.7 + - - +
178A THR* 3.0 14.8 + - - +
181A VAL* 3.6 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 4.5 19.4 + - - +
141A PHE* 2.8 33.5 + - - -
142A THR* 3.2 9.9 - - - +
144A ARG* 1.3 75.6 - - - +
146A SER* 1.3 70.4 + - - +
148A CYS* 3.2 23.2 + - - +
149A GLY 4.2 0.9 + - - -
180A MET* 4.1 16.5 + - - +
181A VAL* 4.2 6.6 - - - +
184A ALA* 4.3 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ALA* 2.8 33.7 + - - -
105A ARG* 3.9 13.7 - - - +
109A VAL* 3.6 28.1 - - - +
135A LEU* 4.9 2.9 - - - -
142A THR 3.0 6.3 + - - -
143A SER 3.0 7.6 + - - -
145A THR* 1.3 80.9 - - - +
147A ALA* 1.3 68.2 + - - +
148A CYS 2.9 1.4 + - - -
149A GLY* 2.9 13.9 + - - -
150A LEU* 3.7 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL* 4.1 4.8 - - + +
135A LEU* 3.6 9.8 - - + +
136A ALA* 3.5 41.1 - - + +
143A SER 3.0 4.9 + - - -
144A ARG 3.0 11.0 + - - +
146A SER* 1.3 76.8 - - - +
148A CYS* 1.3 65.0 + - - +
150A LEU* 2.9 28.5 + - - +
151A PHE* 3.3 14.9 - - + -
173A LEU* 4.4 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ARG 3.4 16.4 - - - -
145A THR* 3.3 11.4 - - - +
146A SER 2.9 1.0 + - - -
147A ALA* 1.3 76.9 - - - +
149A GLY* 1.3 57.9 + - - +
150A LEU 3.1 5.0 + - - -
151A PHE* 3.4 24.2 + - - +
170A PHE* 4.4 3.5 - - + -
173A LEU* 3.6 19.7 - - - +
181A VAL* 4.4 3.1 - - - -
184A ALA* 3.9 8.7 - - + -
185A ALA* 3.7 31.9 - - - +
188A LYS* 3.8 26.6 - - + +
191A GLU* 4.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A VAL* 4.6 6.5 - - - -
113A ARG* 3.2 34.4 + - - +
145A THR 4.2 1.0 + - - -
146A SER 2.9 9.8 + - - -
148A CYS* 1.3 76.9 - - - +
150A LEU* 1.3 62.1 + - - +
151A PHE 3.5 1.0 + - - -
153A VAL* 4.6 2.1 - - - +
188A LYS* 3.9 25.9 - - - +
191A GLU* 4.0 4.1 - - - +
----------------------------------------------------------
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