Contacts of the helix formed by residues 254 - 265 (chain A) in PDB entry 3V3Q
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 254 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLN* 5.5 3.1 - - - +
76A TYR* 3.6 34.8 - - + +
77A ASP* 5.8 0.4 - - - +
80A SER* 3.1 29.2 - - - +
252A PRO 4.4 0.4 - - - +
253A PRO* 1.4 89.2 - - + +
255A PRO* 1.3 69.6 - - + +
256A ILE* 3.4 2.0 - - + +
257A ILE* 3.2 17.1 + - + +
258A ASP* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A PRO 3.4 4.9 - - - +
254A PRO* 1.3 86.7 - - + +
256A ILE* 1.3 58.9 + - + +
258A ASP* 3.2 7.6 + - + +
259A LYS* 2.7 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.7 24.7 - - + -
84A GLU* 4.9 12.1 - - - +
87A ARG* 4.0 20.2 - - - +
109A GLU* 4.3 17.3 - - + +
254A PRO* 3.4 2.2 - - + +
255A PRO* 1.3 81.2 - - + +
257A ILE* 1.3 63.6 + - + +
259A LYS* 3.3 11.6 + - + +
260A ILE* 3.0 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TYR* 4.9 6.3 - - + -
79A LEU* 4.1 38.4 - - + +
80A SER* 3.9 19.7 - - - +
83A LEU* 4.0 20.6 - - + -
112A PHE* 3.8 29.8 - - + -
242A ILE* 4.2 17.2 - - + +
253A PRO* 5.4 1.3 - - + -
254A PRO* 3.2 23.3 + - + +
256A ILE* 1.3 74.4 - - - +
258A ASP* 1.3 61.8 + - - +
260A ILE* 3.3 8.3 + - + +
261A PHE* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 6.1 0.9 - - - -
246A LYS* 2.4 44.3 + - - +
253A PRO* 4.0 18.8 - - + +
254A PRO 2.9 17.5 + - - +
255A PRO* 3.5 8.7 - - + +
257A ILE* 1.3 76.8 - - - +
259A LYS* 1.3 57.5 + - - +
261A PHE* 3.5 4.1 + - - +
262A MET* 3.0 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLU* 2.9 33.0 + - - +
255A PRO 2.7 17.9 + - - +
256A ILE* 3.8 12.6 - - + +
257A ILE 3.2 0.2 - - - -
258A ASP* 1.3 74.2 - - - +
260A ILE* 1.3 55.0 + - - +
262A MET* 3.2 5.5 + - - +
263A ASP* 2.6 72.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.9 25.1 - - + -
109A GLU* 3.6 45.3 - - + +
112A PHE* 4.1 19.3 - - + -
113A LEU* 5.3 1.3 - - + -
256A ILE* 3.0 22.1 + - + +
257A ILE* 3.3 8.5 + - + +
259A LYS* 1.3 72.4 - - - +
261A PHE* 1.3 59.9 + - - +
263A ASP* 4.0 4.8 - - - +
264A THR* 2.3 36.0 + - - -
301A TMY 3.0 42.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 3.3 38.8 - - + -
242A ILE* 3.6 25.8 - - + +
243A PHE* 3.7 28.5 - + + -
246A LYS* 3.7 24.9 - - - -
257A ILE 2.9 16.1 + - - +
258A ASP* 3.6 5.6 - - - +
260A ILE* 1.3 80.2 - - - +
262A MET* 1.3 79.0 + - + +
264A THR* 3.4 4.7 + - - -
265A LEU* 3.2 39.2 - - + +
301A TMY 4.0 7.6 - - - -
243B PHE* 3.7 23.6 - + - -
267B PHE* 4.4 6.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LYS* 3.3 33.0 - - - +
258A ASP* 3.0 32.2 + - - +
259A LYS* 3.7 5.6 - - - +
261A PHE* 1.3 93.1 - - + +
263A ASP* 1.3 64.3 + - - +
264A THR 3.2 0.9 + - - -
265A LEU* 3.3 27.9 + - - +
268A LEU* 3.7 27.1 - - + +
267B PHE* 3.4 28.5 - - + -
269B GLU 6.1 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 6.1 0.7 - - - +
109A GLU* 3.9 7.2 - - + +
259A LYS* 2.6 58.3 + - - +
260A ILE* 4.0 5.8 - - - +
262A MET* 1.3 75.1 - - - +
264A THR* 1.3 60.7 + - - +
265A LEU 3.5 5.0 + - - +
301A TMY 4.8 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 4.1 6.1 - - + -
260A ILE* 2.3 14.6 + - - +
261A PHE 3.8 3.1 - - - -
262A MET 3.2 0.4 - - - -
263A ASP* 1.3 75.7 - - - +
265A LEU* 1.3 65.8 + - - +
266A PRO* 3.2 5.2 - - - +
301A TMY 2.2 116.6 + - + +
247B LEU* 4.8 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 4.9 4.0 - - + -
261A PHE* 3.2 48.0 - - + +
262A MET* 3.3 19.4 + - - +
263A ASP 4.1 4.3 - - - +
264A THR* 1.3 81.3 - - - +
266A PRO* 1.4 66.0 - - + +
267A PHE* 3.2 24.9 + - + -
268A LEU* 3.5 44.7 + - + +
243B PHE* 4.0 21.1 - - + -
247B LEU* 4.7 8.1 - - + -
267B PHE* 6.1 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