Contacts of the helix formed by residues 141 - 153 (chain A) in PDB entry 2V3V
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 MET 141 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PRO* 2.7 13.8 + - + +
140A CYS* 1.3 86.6 - - + +
142A ALA* 1.3 61.5 + - - -
143A SER 3.2 3.4 - - - -
144A ALA* 3.1 9.0 + - + +
145A VAL* 3.1 19.1 + - - +
308A MET* 3.5 26.9 - - - -
311A ASN* 4.0 6.1 - - - +
342A SER* 3.5 17.0 - - - +
343A LEU 3.3 17.9 - - - +
344A THR* 3.5 31.2 - - + +
349A ALA* 4.2 7.2 - - + -
354A ARG* 3.3 32.3 - - - +
813A UNX 4.1 2.5 - - - -
814A LCP 2.9 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ARG* 3.6 22.9 - - - +
141A MET* 1.3 76.5 - - - +
143A SER* 1.3 56.5 + - - +
145A VAL* 3.5 2.5 + - - +
146A GLY 3.1 21.5 + - - -
708A SER* 3.4 27.6 - - - +
710A GLU* 3.3 3.5 + - + +
814A LCP 3.2 28.4 + - - +
815A LCP 3.1 17.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
142A ALA* 1.3 75.1 - - - +
144A ALA* 1.3 52.2 + - - +
146A GLY* 3.4 1.2 + - - -
147A GLY* 2.8 30.8 + - - -
311A ASN* 2.9 31.0 + - - -
313A ARG 4.3 1.0 + - - -
316A GLY* 3.7 26.1 - - - -
317A VAL* 3.8 6.1 - - - -
320A ASN* 3.7 6.9 + - - -
705A ASP* 4.2 0.9 + - - -
708A SER* 3.0 22.0 + - - -
710A GLU* 2.9 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A MET* 3.1 15.4 + - + +
143A SER* 1.3 77.4 - - - +
145A VAL* 1.3 59.7 + - - +
147A GLY 3.8 0.4 - - - -
148A TYR* 2.9 39.5 + - + -
311A ASN* 3.7 13.9 - - - +
320A ASN* 3.3 20.8 - - - +
342A SER* 3.4 28.7 - - - +
354A ARG* 4.6 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A MET 3.1 3.4 + - - +
142A ALA 3.6 5.8 - - - +
143A SER 3.3 0.2 - - - -
144A ALA* 1.3 74.0 - - - +
146A GLY* 1.3 58.9 + - - +
148A TYR* 3.2 1.7 + - - +
149A VAL* 2.9 34.7 + - + +
155A ASP* 3.4 10.8 - - - +
354A ARG* 3.3 24.0 - - + +
814A LCP 3.1 37.7 - - - +
815A LCP 3.7 19.5 - - - +
816A LCP 3.3 38.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA 3.1 11.5 + - - -
143A SER 3.8 2.9 - - - -
145A VAL* 1.3 76.5 - - - +
147A GLY* 1.3 53.2 + - - +
149A VAL* 4.7 2.7 - - - -
150A THR* 2.6 40.3 + - - +
317A VAL* 3.9 12.8 - - - -
707A VAL* 5.1 3.1 - - - -
815A LCP 3.3 24.1 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
143A SER 2.8 20.1 + - - -
144A ALA 4.0 0.7 - - - -
145A VAL 3.3 0.2 - - - -
146A GLY* 1.3 73.9 - - - +
148A TYR* 1.3 60.0 + - - +
150A THR* 3.9 3.4 - - - -
151A SER* 3.1 30.7 + - - -
317A VAL* 4.0 5.2 - - - +
320A ASN* 3.6 21.1 - - - -
321A ASN* 3.4 6.8 + - - -
324A HIS* 3.6 6.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ALA 2.9 27.6 + - - +
145A VAL 3.2 3.1 + - - +
147A GLY* 1.3 77.1 - - - +
149A VAL* 1.3 53.9 + - - +
152A PHE* 2.7 45.0 + + - +
154A LYS 3.2 20.5 - - - +
155A ASP* 3.7 17.3 - - - +
156A GLU* 3.8 17.9 - - - -
157A PRO* 3.4 25.5 - - + +
158A MET* 4.0 11.7 - - + -
306A TRP* 4.7 2.2 - + - -
324A HIS* 3.5 27.1 - + - -
340A SER 2.8 25.3 + - - -
342A SER* 3.0 37.3 + - - -
354A ARG* 4.2 4.3 - - - -
565A TYR* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A VAL* 2.9 21.7 + - + +
146A GLY* 4.2 4.3 - - - +
148A TYR* 1.3 75.2 - - - +
150A THR* 1.3 65.6 + - + +
153A GLY* 2.7 39.5 + - - +
154A LYS* 4.0 4.0 - - - +
155A ASP 3.9 12.8 - - - +
586A LYS* 3.7 3.6 + - - -
815A LCP 5.2 6.1 - - - +
816A LCP 3.0 31.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLY* 2.6 27.2 + - - +
149A VAL* 1.3 81.0 - - + +
151A SER* 1.3 53.5 + - - +
317A VAL* 4.3 5.7 - - + +
321A ASN* 3.0 23.8 + - - -
586A LYS* 2.7 26.9 + - - +
592A VAL* 4.0 0.7 - - - +
594A TRP* 2.9 33.1 + - + -
596A ARG* 4.1 10.8 + - - +
707A VAL* 5.7 5.8 - - + -
----------------------------------------------------------
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 GLY 3.1 14.1 + - - -
150A THR* 1.3 76.9 - - - +
152A PHE* 1.3 78.0 + - - +
321A ASN* 2.9 26.7 + - - -
324A HIS* 3.4 21.3 - - - +
328A LEU* 5.0 0.4 - - - -
586A LYS* 3.9 2.8 - - - -
591A ALA* 3.4 8.8 - - - +
592A VAL 2.9 41.3 + - - -
594A TRP* 4.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TYR* 2.7 29.7 + + + +
151A SER* 1.3 81.5 - - - +
153A GLY* 1.3 55.5 + - - +
154A LYS* 3.2 6.8 + - - +
158A MET* 3.4 29.6 - - + -
324A HIS* 3.7 34.5 - + + -
327A HIS* 6.1 0.2 - - + -
328A LEU* 4.0 14.6 - - + -
333A ILE* 3.6 25.8 - - + -
340A SER* 5.4 0.4 - - - -
565A TYR* 4.0 19.7 + + + +
583A PHE* 3.6 31.3 - + - +
585A GLY* 3.4 20.3 + - - -
586A LYS* 3.9 9.7 + - - +
591A ALA* 3.7 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TYR 3.4 0.2 + - - -
149A VAL* 2.7 37.6 + - - +
152A PHE* 1.3 70.9 - - - +
154A LYS* 1.3 70.2 + - - +
585A GLY* 3.3 22.4 - - - +
586A LYS* 3.7 6.8 - - - +
----------------------------------------------------------
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