Contacts of the helix formed by residues 244 - 258 (chain A) in PDB entry 4UC5
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 ASP 244 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A PRO 5.9 0.2 - - - -
242A ASN 3.5 0.4 - - - -
243A TYR* 1.3 89.7 - - + +
245A ALA* 1.3 65.6 + - - +
246A GLU* 3.3 10.4 + - - +
247A HIS* 2.8 39.5 + - - -
248A VAL* 2.9 19.1 + - - +
286A ASP* 3.8 16.2 - - - +
290A GLN* 3.7 5.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
244A ASP* 1.3 74.5 - - - +
246A GLU* 1.3 56.2 + - - +
248A VAL* 3.4 3.4 + - - +
249A SER* 2.9 31.5 + - - -
286A ASP* 4.4 1.0 + - - -
290A GLN* 3.5 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ASP* 3.1 10.3 + - - +
245A ALA* 1.3 76.7 - - - +
247A HIS* 1.3 61.7 + - + +
249A SER* 3.4 5.1 + - - -
250A GLU* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LEU* 4.8 2.5 - - + +
240A GLU* 5.6 6.6 + - - +
241A PRO 3.8 15.8 + - - -
242A ASN* 3.1 44.4 - - + +
244A ASP* 2.8 37.2 + - - +
246A GLU* 1.3 78.4 - - + +
248A VAL* 1.3 64.0 + - - +
250A GLU* 3.6 5.6 + - + +
251A ALA* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LEU* 4.3 12.8 - - + -
243A TYR 3.6 23.6 - - - +
244A ASP 2.9 8.2 + - - +
245A ALA* 3.7 7.0 - - - +
247A HIS* 1.3 76.4 - - - +
249A SER* 1.3 58.3 + - - +
251A ALA* 3.3 6.5 + - - +
252A ALA* 2.9 26.9 + - - +
264A LEU* 4.2 8.7 - - + +
266A ILE* 4.0 16.2 - - + -
290A GLN* 3.6 15.5 - - - +
295A GLY* 6.3 1.3 - - - -
297A ASN* 4.0 25.6 - - + +
298A ILE* 4.3 12.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
245A ALA 2.9 18.5 + - - -
246A GLU* 3.9 5.8 - - - -
247A HIS 3.3 0.2 - - - -
248A VAL* 1.3 74.7 - - - +
250A GLU* 1.3 67.6 + - - +
252A ALA* 3.8 5.6 - - - +
253A GLU* 3.0 25.7 + - - +
256A ARG* 5.0 1.6 + - - -
297A ASN* 5.5 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 6.0 0.4 - - + -
246A GLU 3.0 18.0 + - - +
247A HIS* 3.9 6.5 - - + +
249A SER* 1.3 74.7 + - - +
251A ALA* 1.3 58.8 + - - +
253A GLU* 3.3 18.3 + - - +
254A GLN* 3.0 52.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 3.6 31.5 - - + +
235A LEU* 4.4 8.3 - - + -
247A HIS 3.0 19.5 + - - +
248A VAL* 3.4 5.2 - - - +
250A GLU* 1.3 76.7 - - - +
252A ALA* 1.3 57.4 + - - +
254A GLN* 3.3 2.8 + - - +
255A LEU* 2.9 35.3 + - + +
264A LEU* 3.6 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A VAL 2.9 16.0 + - - +
249A SER* 3.3 5.8 + - - +
251A ALA* 1.3 72.3 - - - +
253A GLU* 1.3 66.2 + - - +
255A LEU* 3.3 11.2 + - - +
256A ARG* 2.9 40.1 + - - +
262A ASP* 3.8 4.2 - - - +
264A LEU* 4.6 1.1 - - + +
297A ASN* 3.4 40.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A SER* 3.0 15.0 + - - +
250A GLU* 3.6 20.8 - - - +
252A ALA* 1.3 78.3 - - - +
254A GLN* 1.3 62.9 - - + +
256A ARG* 3.3 21.8 + - - +
257A ALA* 3.0 25.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 3.7 25.4 - - - +
196A LYS* 4.8 4.9 + - - +
199A ILE* 3.5 21.6 - - + +
250A GLU* 3.0 51.0 + - - +
251A ALA 3.7 2.9 - - - +
253A GLU* 1.3 75.8 - - + +
255A LEU* 1.3 63.0 + - - +
257A ALA* 3.3 8.6 + - - +
258A ALA* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 5.9 0.7 - - + -
199A ILE* 3.8 22.9 - - + +
202A ILE* 4.2 2.5 - - + -
233A VAL* 3.8 35.4 - - + -
251A ALA* 2.9 30.4 + - + +
252A ALA* 3.6 4.9 - - - +
254A GLN* 1.3 76.1 - - - +
256A ARG* 1.3 61.5 + - - +
258A ALA* 3.1 11.0 + - - -
260A VAL* 3.2 40.0 + - + +
261A THR 3.4 27.4 - - - +
262A ASP* 3.7 14.6 - - - -
263A LYS 4.8 0.7 - - - +
264A LEU* 4.1 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A SER 5.0 1.6 + - - -
252A ALA* 2.9 32.6 + - - +
253A GLU* 3.6 30.2 - - + +
255A LEU* 1.3 75.9 - - - +
257A ALA* 1.3 57.1 + - - +
259A GLY* 3.0 18.2 + - - -
260A VAL 4.3 6.7 - - - +
262A ASP* 2.9 36.5 + - + +
297A ASN* 3.9 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A GLU* 3.0 16.1 + - + +
254A GLN* 3.5 11.9 - - - +
255A LEU 3.2 0.4 - - - -
256A ARG* 1.3 75.2 - - - +
258A ALA* 1.3 57.6 + - - +
259A GLY 3.3 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ILE* 3.4 33.9 - - + +
254A GLN 3.1 7.6 + - - +
255A LEU 3.1 6.4 + - - +
257A ALA* 1.3 75.3 - - - +
259A GLY* 1.3 61.9 + - - +
260A VAL* 3.2 14.2 + - + +
----------------------------------------------------------
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