Contacts of the helix formed by residues 143 - 151 (chain A) in PDB entry 1VRR
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 143 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASN* 4.9 0.4 - - - +
139A TYR* 3.0 42.2 + - + +
141A LEU 3.4 0.2 - - - -
142A PHE* 1.3 84.1 - - - +
144A LYS* 1.3 65.0 + - + +
146A MET* 3.9 1.3 - - - +
147A ALA* 2.9 30.1 + - - +
138B ALA* 3.9 26.0 - - + -
142B PHE* 4.3 11.9 - - + -
183B ASN* 4.0 18.4 - - + +
186B ARG* 3.8 24.6 + - - +
187B GLN* 4.8 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASN* 4.4 12.3 - - + +
117A GLN 2.8 29.7 + - - +
118A THR* 3.6 6.4 - - - +
128A GLU* 3.0 31.4 + - - +
136A PHE* 6.2 0.4 - - - -
139A TYR* 3.2 33.0 + - + +
140A ASP* 3.3 27.1 + - - +
143A VAL* 1.3 77.0 - - + +
145A HIS* 1.3 70.2 + - + +
146A MET 3.0 0.9 - - - -
147A ALA* 2.8 16.4 + - - +
148A PHE* 3.0 20.0 + - + +
5D A 4.0 18.4 + - - -
6D G 4.9 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ALA* 3.3 34.8 + - + +
128A GLU* 3.5 17.4 - - + +
140A ASP* 2.9 31.1 + - + +
141A LEU* 3.9 16.4 - - + +
144A LYS* 1.3 73.0 - - + +
146A MET* 1.3 57.6 + - - +
148A PHE* 3.3 7.7 + - - +
149A TYR* 2.8 30.0 + - - +
154A ILE* 3.9 3.7 - - - +
157A GLY* 3.2 16.6 - - - -
158A VAL 3.4 17.8 + - - -
159A GLU* 2.9 27.4 + - - -
194A VAL* 4.3 4.9 - - + -
196A LEU* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU 3.8 9.2 + - - +
142A PHE* 3.5 20.2 - - - +
143A VAL 4.1 0.4 - - - +
144A LYS 3.0 0.2 - - - -
145A HIS* 1.3 80.6 - - - +
147A ALA* 1.3 63.1 + - - +
149A TYR* 3.2 5.3 + - - +
150A VAL* 2.9 48.3 + - + +
192A PRO* 3.6 15.7 - - + -
193A ALA* 3.4 50.3 - - + +
194A VAL* 3.7 9.1 - - + +
187B GLN* 3.5 25.6 - - + +
191B VAL* 5.8 5.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
116A ASN* 6.0 1.3 - - + -
143A VAL 2.9 22.5 + - - +
144A LYS* 2.8 9.9 + - - +
146A MET* 1.3 77.1 - - - +
148A PHE* 1.3 66.4 + - + +
150A VAL* 3.2 7.2 - - - +
151A SER* 2.9 31.1 + - - +
186B ARG* 3.7 35.2 - - - +
187B GLN* 6.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A SER* 4.0 26.7 - - - -
78A THR* 3.8 21.8 - - + -
116A ASN* 5.6 4.5 - - + -
117A GLN 5.6 0.4 - - - -
118A THR* 3.4 39.9 - - + -
121A VAL* 4.3 8.5 - - + -
126A ALA* 4.2 16.4 - - + -
144A LYS* 3.0 18.4 + - + -
145A HIS* 3.7 4.9 - - - +
147A ALA* 1.3 80.1 - - + +
149A TYR* 1.3 65.0 + - - +
151A SER* 3.1 5.0 + - - -
152A ASP 3.1 4.3 + - - -
153A LYS* 3.0 48.2 + - + -
154A ILE* 3.4 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A HIS 2.8 14.5 + - - +
146A MET* 3.2 8.3 + - - +
148A PHE* 1.3 73.5 - - - +
150A VAL* 1.3 67.1 + - + +
152A ASP* 3.0 14.7 + - - -
154A ILE* 3.1 23.9 - - + +
155A ASP* 4.2 12.3 - - - -
193A ALA 3.5 26.0 - - - -
194A VAL* 3.3 24.5 - - + -
195A PRO* 3.3 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A MET* 2.9 38.7 + - + +
147A ALA* 3.2 14.8 - - - +
149A TYR* 1.3 72.6 - - + +
151A SER* 1.3 67.6 + - - +
152A ASP* 3.0 12.7 + - - +
186B ARG* 5.2 13.7 - - + +
187B GLN* 5.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ALA* 2.9 23.4 + - - +
148A PHE* 3.1 6.5 + - - -
150A VAL* 1.3 80.2 - - - +
152A ASP* 1.3 70.0 + - - +
153A LYS* 3.5 29.0 + - - +
186B ARG* 6.0 2.1 - - - -
----------------------------------------------------------
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