Contacts of the helix formed by residues 240 - 252 (chain A) in PDB entry 1V2E
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 PHE 240 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A PHE* 4.0 20.4 - + - -
212A GLU 4.4 6.3 - - - -
215A PHE* 3.8 23.8 - + + -
237A PRO* 3.3 32.4 + - + +
239A GLU* 1.3 98.8 - - + +
241A MET* 1.3 66.3 + - - +
242A PRO* 3.1 3.8 - - - -
243A ARG* 2.9 24.5 + - - +
244A LEU* 3.5 6.6 + - + +
1B MET* 4.2 25.1 - - + -
2B ARG* 5.0 1.1 - - - -
3B LEU* 3.6 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU 3.6 15.3 - - - +
80A SER* 3.8 11.4 - - - +
82A VAL* 3.5 37.2 - - + +
215A PHE* 3.9 14.4 - - - -
234A ILE* 3.8 21.8 - - + +
236A GLY 3.4 28.5 - - - +
237A PRO 3.2 15.0 - - - +
238A LYS* 3.6 9.6 - - - +
240A PHE* 1.3 77.0 - - - +
242A PRO* 1.3 68.4 - - + +
243A ARG 3.1 0.3 + - - -
244A LEU* 3.1 20.7 + - + +
245A ALA* 3.0 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU 5.7 1.1 - - - +
238A LYS 3.1 14.8 - - - +
239A GLU* 3.0 21.3 - - - +
240A PHE 3.1 1.6 - - - +
241A MET* 1.3 91.3 - - + +
243A ARG* 1.3 60.8 + - + +
245A ALA* 3.6 9.1 + - + +
246A GLY* 3.3 14.7 + - - -
10B ALA 4.4 2.1 - - - +
12B GLU* 5.4 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLU 5.4 2.2 - - - +
240A PHE* 2.9 11.8 + - - +
242A PRO* 1.3 75.6 - - + +
244A LEU* 1.3 56.8 + - + +
246A GLY* 2.6 22.5 + - - -
247A MET* 2.8 16.8 + - - +
3B LEU* 3.6 27.3 - - + +
7B THR* 3.2 39.3 + - + -
8B GLU* 4.0 5.6 + - - +
10B ALA* 3.4 20.8 + - + +
11B LYS* 3.9 27.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL* 4.7 2.7 - - + -
93A VAL* 4.2 13.3 - - + +
94A LEU* 3.8 23.1 - - + -
97A SER* 3.5 32.3 - - - +
98A LEU* 5.8 1.3 - - + -
215A PHE* 3.6 32.3 - - + -
234A ILE* 3.9 13.2 - - + -
240A PHE* 4.0 10.3 - - + +
241A MET* 3.1 26.2 + - + +
243A ARG* 1.3 81.6 - - + +
245A ALA* 1.3 62.1 + - - +
246A GLY 3.0 0.7 + - - -
247A MET* 3.1 4.4 + - - +
248A ARG* 3.1 27.2 + - - +
3B LEU* 5.5 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PRO* 4.1 5.5 - - + +
61A ALA* 4.3 22.0 - - + +
82A VAL* 4.1 17.6 - - + +
241A MET 3.0 13.1 + - - +
242A PRO* 3.7 11.9 - - + +
244A LEU* 1.3 75.2 - - - +
246A GLY* 1.3 60.7 + - - +
248A ARG* 3.8 11.8 - - - +
249A GLN* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PRO 3.3 4.4 + - - -
243A ARG 2.6 19.0 + - - -
245A ALA* 1.3 73.5 - - - +
247A MET* 1.3 63.7 + - - +
249A GLN* 2.6 31.7 + - - +
250A TRP* 3.4 9.2 - - - -
10B ALA* 3.8 21.1 - - - -
11B LYS 4.8 2.5 - - - -
12B GLU* 4.9 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A VAL* 3.3 22.7 - - + -
96A GLN* 3.2 40.6 - - + +
97A SER* 3.1 26.7 - - - +
243A ARG 2.8 14.0 + - - +
244A LEU* 3.1 3.8 + - - +
246A GLY* 1.3 68.2 - - - +
248A ARG* 1.3 53.8 + - - +
249A GLN 2.8 4.2 + - - -
250A TRP* 2.8 36.2 + - - +
251A THR* 3.5 6.3 + - - +
6B ARG* 4.6 4.3 - - + -
7B THR* 4.4 11.4 - - + -
10B ALA* 3.6 25.4 - - + -
121B LEU* 4.2 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PRO 3.2 15.5 + - - -
82A VAL* 4.3 11.2 - - + -
83A VAL 3.1 17.1 + - - -
84A THR* 3.1 15.0 - - + +
85A SER* 3.0 31.3 + - - +
89A GLU* 2.6 45.8 + - - +
93A VAL* 3.8 14.5 - - + +
244A LEU 3.1 16.2 + - - +
245A ALA* 3.8 12.1 - - - +
247A MET* 1.3 78.0 - - - +
249A GLN* 1.3 59.1 + - - +
251A THR* 2.5 23.9 + - - +
252A SER* 3.1 17.2 + - - -
253A PHE 3.2 20.4 + - - -
254A SER* 3.7 0.7 - - - -
255A ALA 3.4 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PRO* 4.0 19.0 - - + +
245A ALA 3.2 13.0 + - - +
246A GLY* 2.6 33.1 + - - +
247A MET 2.8 1.0 + - - -
248A ARG* 1.3 82.3 - - - +
250A TRP* 1.3 77.4 + - + +
253A PHE* 3.3 38.3 + - + +
11B LYS 3.5 9.9 - - - +
12B GLU* 3.7 2.6 - - - +
13B SER* 2.5 53.0 + - - +
16B PRO* 4.6 0.4 - - - +
88B THR* 4.0 3.8 - - - +
114B VAL* 5.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLY 3.4 17.3 + - - -
247A MET* 2.8 11.7 + - - +
249A GLN* 1.3 97.1 + - + +
251A THR* 1.3 65.3 + - - +
253A PHE* 6.1 1.6 - + - -
9B ALA 3.3 25.2 + - - -
10B ALA* 4.0 3.3 - - - +
11B LYS 3.8 17.7 - - - -
13B SER* 4.1 16.2 - - - -
88B THR* 3.3 14.2 - - - +
92B TYR* 3.5 17.8 - - + +
113B ASP* 3.0 43.5 - - + -
114B VAL* 4.0 21.9 - - + +
117B PRO* 3.8 21.3 - - + +
118B ASP* 3.8 14.9 - - - +
121B LEU* 3.9 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU* 3.0 16.3 + - + -
92A TYR* 3.9 28.9 - - + -
93A VAL* 4.0 12.3 - - + -
247A MET 3.5 4.9 + - - +
248A ARG* 2.5 32.1 + - - -
250A TRP* 1.3 80.2 - - - +
252A SER* 1.3 58.4 + - - -
89B GLU* 3.0 35.3 - - - +
92B TYR* 4.0 26.0 - - + +
251B THR* 5.1 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A SER* 2.9 20.6 + - - -
89A GLU* 2.4 26.3 + - - -
248A ARG* 3.1 2.4 + - - -
251A THR* 1.3 80.8 + - - +
253A PHE* 1.3 59.8 + - - +
254A SER 3.3 5.0 + - - -
85B SER* 3.6 28.5 - - - -
88B THR* 3.8 8.5 - - - -
89B GLU* 4.3 4.7 - - - -
230B ARG* 2.5 34.0 + - - -
252B SER* 5.4 0.4 - - - -
----------------------------------------------------------
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