Contacts of the helix formed by residues 240 - 255 (chain A) in PDB entry 3VVK
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 PRO 240 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A VAL* 5.1 1.8 - - + -
237A ALA* 5.2 4.0 - - + +
238A VAL 3.3 10.3 - - - +
239A LEU* 1.3 86.1 - - + +
241A VAL* 1.3 64.7 + - - +
242A GLY 3.4 1.1 - - - +
243A TYR* 3.1 35.6 + - + -
244A THR* 2.8 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 5.6 4.0 - - + -
34A LEU* 4.6 19.3 - - + -
107A VAL* 5.8 4.7 - - + -
117A VAL* 4.9 3.6 - - + -
118A VAL* 3.8 43.5 - - + +
120A MET* 5.3 5.8 - - + -
233A VAL* 4.2 24.2 - - + +
240A PRO* 1.3 73.0 - - - +
242A GLY* 1.3 66.1 + - - +
244A THR* 2.9 22.4 - - + +
245A SER* 3.1 11.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 5.3 2.7 - - - -
33A LEU* 3.7 29.3 - - - +
34A LEU* 4.5 12.3 - - - -
240A PRO* 3.4 1.2 - - - +
241A VAL* 1.3 80.6 - - - +
243A TYR* 1.3 59.9 + - - +
245A SER* 3.4 7.8 - - - -
246A TRP* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.7 26.0 - - + +
239A LEU* 4.2 15.6 - - + +
240A PRO* 3.1 44.1 + - + +
242A GLY* 1.3 76.1 - - - +
244A THR* 1.3 66.4 + - - +
245A SER 3.0 1.6 - - - -
246A TRP* 3.2 6.4 + - - +
247A ALA* 2.9 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A VAL* 3.9 4.0 - - - +
232A GLY* 3.9 23.3 - - - -
233A VAL* 3.7 21.0 + - + +
234A GLU* 4.7 2.8 + - - -
239A LEU* 3.7 9.5 - - - +
240A PRO 2.8 22.5 + - - +
241A VAL* 2.9 22.7 - - - +
243A TYR* 1.3 71.3 - - - +
245A SER* 1.3 61.3 + - - +
247A ALA* 3.2 9.4 + - - +
248A TYR* 3.0 43.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 3.6 21.5 - - - +
37A SER* 3.1 13.9 + - - -
38A LEU* 4.1 2.9 - - - +
120A MET* 4.4 7.7 - - - +
123A ARG* 2.9 38.6 + - - +
241A VAL 3.1 13.3 + - - -
242A GLY 3.4 10.5 - - - -
243A TYR 3.0 0.2 - - - -
244A THR* 1.3 78.6 - - - +
246A TRP* 1.3 58.3 + - - +
248A TYR* 3.1 2.6 + - - -
249A SER* 2.8 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.1 42.5 + - + +
36A SER* 3.0 31.1 + - - -
37A SER* 3.4 28.2 - - - -
40A ILE* 4.6 18.4 - - + -
242A GLY 3.1 11.4 + - - +
243A TYR* 3.2 9.1 + - - +
245A SER* 1.3 75.3 - - - +
247A ALA* 1.3 57.4 + - - +
249A SER* 3.9 13.5 - - - -
250A ALA* 2.8 41.2 + - + +
253A ILE* 4.6 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A VAL* 3.6 26.9 - - + +
239A LEU* 5.6 5.4 - - + -
243A TYR 2.9 13.6 + - - +
244A THR* 3.3 11.7 - - - +
245A SER 3.1 0.2 - - - -
246A TRP* 1.3 78.5 - - - +
248A TYR* 1.3 60.6 + - - +
250A ALA* 3.4 5.6 + - - +
251A LEU* 3.2 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ARG* 3.5 36.1 - - - +
124A TYR* 6.3 0.2 - + - -
127A TRP* 3.5 32.5 - + + -
225A TYR* 3.9 26.0 - + + -
228A VAL* 3.6 20.6 - - + -
229A TRP* 3.2 25.8 - - - +
234A GLU* 2.9 32.1 + - - -
244A THR* 3.0 36.5 + - - -
245A SER* 3.5 5.8 - - - +
247A ALA* 1.3 76.8 - - - +
249A SER* 1.3 56.6 + - - +
251A LEU* 3.3 6.2 + - + +
252A ASP* 2.9 33.8 + - - +
301A RET 4.2 0.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 2.7 40.3 + - - -
41A ASN* 3.8 4.7 - - - +
82A TYR* 3.7 13.6 + - - -
123A ARG* 3.0 20.3 + - - +
245A SER 2.8 14.7 + - - -
246A TRP* 3.3 13.7 + - - -
248A TYR* 1.3 73.3 - - - +
250A ALA* 1.3 61.0 + - - +
252A ASP* 3.5 2.3 + - - +
253A ILE* 3.1 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TRP* 2.8 27.5 + - + +
247A ALA* 3.7 6.7 - - - +
249A SER* 1.3 75.6 - - - +
251A LEU* 1.3 65.9 + - + +
253A ILE* 3.5 17.0 + - - +
254A VAL* 3.5 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A MET* 3.9 27.6 - - - +
224A GLY* 3.6 34.1 - - - -
225A TYR* 3.4 33.7 - - + +
228A VAL* 3.7 18.8 - - + -
247A ALA 3.2 11.6 + - - +
248A TYR* 3.6 7.6 - - + +
250A ALA* 1.3 75.0 - - + +
252A ASP* 1.3 62.5 + - - +
254A VAL* 3.1 6.8 + - - +
255A ALA* 2.8 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASN* 3.8 5.8 - - - +
82A TYR* 2.7 38.2 + - + +
123A ARG* 4.1 3.2 + - - -
126A THR* 4.7 2.3 - - - +
127A TRP* 3.6 13.8 + - - -
225A TYR* 2.6 38.2 + - - -
248A TYR 2.9 15.5 + - - +
249A SER 3.6 3.6 - - - +
250A ALA 3.3 0.2 - - - -
251A LEU* 1.3 77.9 - - - +
253A ILE* 1.3 55.7 + - - +
255A ALA 4.5 0.2 - - - +
256A LYS* 2.7 59.7 + - + +
257A TYR* 5.0 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 4.8 3.6 - - + -
41A ASN* 3.2 27.4 - - - +
44A LEU* 3.9 19.1 - - + -
246A TRP* 4.6 16.6 - - + -
249A SER 3.1 17.6 + - - +
250A ALA* 3.7 10.8 - - - +
251A LEU 3.2 0.2 - - - -
252A ASP* 1.3 76.1 - - - +
254A VAL* 1.3 61.5 - - + +
257A TYR* 3.4 22.7 + - + +
258A ILE* 3.0 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 4.0 7.2 - - + +
221A MET* 3.5 34.3 - - + -
250A ALA 3.5 14.6 + - - +
251A LEU* 3.1 6.3 + - - +
253A ILE* 1.3 80.0 - - + +
255A ALA* 1.3 60.8 + - - +
258A ILE* 2.9 52.2 - - + +
259A PHE* 3.0 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ILE* 3.7 14.4 - - - +
217A LEU* 6.0 0.4 - - - -
218A THR* 6.4 0.7 - - - +
221A MET* 4.0 23.3 - - + +
222A TRP* 4.5 6.7 + - - +
225A TYR* 3.7 16.4 - - + +
251A LEU 2.8 20.4 + - - +
252A ASP* 4.4 0.4 - - - +
254A VAL* 1.3 74.3 - - - +
256A LYS* 1.3 57.5 + - - +
259A PHE* 3.1 22.6 - - - +
301A RET 3.8 18.6 - - + -
----------------------------------------------------------
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