Contacts of the helix formed by residues 235 - 249 (chain A) in PDB entry 3C5H
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 ASN 235 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A VAL* 3.7 7.3 - - + +
227A GLU* 2.8 34.3 + - - +
228A THR* 3.5 10.4 - - - +
233A ASN 4.3 0.8 + - - -
234A VAL* 1.3 83.3 - - - +
236A VAL* 1.3 62.6 + - - +
237A ASP 3.6 1.1 - - - -
238A LEU* 3.7 24.4 - - + +
239A ALA 3.1 17.5 + - - -
307A UNX 3.6 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.8 26.9 - - + +
41A ARG* 4.0 11.9 - - + +
42A PHE* 3.6 40.8 - - + +
228A THR* 4.7 0.7 - - - -
229A SER 3.7 24.7 - - - +
230A ALA* 4.1 7.9 - - - -
233A ASN* 4.0 19.9 + - - +
234A VAL 3.2 4.0 - - - +
235A ASN* 1.3 74.1 - - - +
237A ASP* 1.3 69.2 + - - +
239A ALA* 3.2 11.3 + - - +
240A PHE* 3.2 19.6 - - + -
307A UNX 3.9 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ARG 5.2 1.2 - - - +
42A PHE* 3.4 32.0 - - + +
45A PRO* 5.9 1.9 - - - +
235A ASN 3.6 0.2 - - - -
236A VAL* 1.3 78.6 - - - +
238A LEU* 1.3 52.1 + - - +
240A PHE* 3.2 3.6 + - - +
241A SER* 2.8 38.2 + - - -
307A UNX 3.5 11.1 - - - -
308A UNX 3.7 13.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A VAL* 4.1 13.9 - - + -
235A ASN* 3.7 31.4 - - - +
236A VAL 3.2 0.6 - - - -
237A ASP* 1.3 75.6 - - - +
239A ALA* 1.3 55.4 + - - +
241A SER* 3.0 10.7 + - - +
242A THR* 2.6 52.5 + - - +
307A UNX 3.1 16.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 5.2 1.6 - - + -
161A LEU* 3.7 19.4 - - + +
196A VAL* 4.5 2.1 - - - +
198A VAL* 3.9 26.5 - - + -
226A VAL* 3.8 18.8 - - + +
228A THR* 4.0 8.3 - - + -
235A ASN 3.1 13.8 + - - +
236A VAL* 3.2 10.5 + - - +
238A LEU* 1.3 77.0 - - - +
240A PHE* 1.3 64.5 + - + +
242A THR* 3.6 3.3 - - - -
243A LEU 3.4 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 4.0 20.3 - - + +
18A VAL* 4.1 13.7 - - + -
38A LEU* 4.1 22.9 - - + -
39A CYS* 4.7 2.7 - - - -
42A PHE* 3.5 58.8 - + + -
91A MET* 4.8 2.0 - - - -
93A ILE* 3.6 30.3 - - + -
161A LEU* 3.6 29.8 - - + -
236A VAL* 3.2 23.1 - - + -
237A ASP 3.2 4.6 + - - +
239A ALA* 1.3 77.6 - - + +
241A SER* 1.3 67.0 + - - +
243A LEU* 3.2 7.5 + - - +
244A VAL* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A MET* 5.7 1.3 - - - -
237A ASP* 2.8 24.6 + - - -
238A LEU* 3.0 22.9 + - - +
240A PHE* 1.3 72.5 - - - +
242A THR* 1.3 56.4 + - - +
244A VAL* 3.2 10.0 + - - +
245A GLN* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A VAL* 3.9 13.9 - - + -
224A GLN* 3.5 37.5 + - - +
226A VAL* 3.8 18.8 - - + +
238A LEU* 2.6 39.3 + - - +
239A ALA 3.6 5.4 - - - -
241A SER* 1.3 78.2 + - - +
243A LEU* 1.3 61.2 + - - +
245A GLN* 3.5 9.5 + - - +
246A LEU* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 3.5 40.6 - - + -
159A GLY* 3.8 4.9 - - - -
160A PHE 3.8 22.7 - - - +
161A LEU* 3.7 23.8 - - + -
194A PRO* 3.6 39.0 - - + +
196A VAL* 3.8 14.8 - - + +
239A ALA 3.4 1.8 + - - -
240A PHE* 3.2 9.0 + - - +
242A THR* 1.3 77.3 - - - +
244A VAL* 1.3 60.2 + - - +
246A LEU* 3.1 4.4 + - + +
247A ILE* 2.8 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 6.3 1.3 - - + -
14A TYR* 3.8 33.4 - - + -
16A ILE* 4.0 13.7 - - + -
91A MET* 3.7 32.3 - - + -
240A PHE 3.0 17.2 + - - +
241A SER* 3.6 10.8 - - - +
243A LEU* 1.3 73.4 - - - +
245A GLN* 1.3 63.4 + - - +
247A ILE* 3.2 19.9 + - + +
248A ASP* 3.2 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A SER 2.9 16.5 + - - +
242A THR* 3.6 9.1 - - - +
244A VAL* 1.3 77.5 - - - +
246A LEU* 1.3 63.4 + - + +
248A ASP* 3.3 15.3 + - - +
249A LYS* 3.3 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A PRO* 4.1 20.5 - - + +
195A ILE 4.1 11.7 - - - +
196A VAL* 3.5 30.7 - - + -
222A ASN 5.4 8.1 - - - +
224A GLN* 3.5 26.2 - - + +
242A THR 3.1 11.2 + - - +
243A LEU* 3.1 9.2 + - - +
245A GLN* 1.3 73.8 - - + +
247A ILE* 1.3 65.4 + - - +
248A ASP 3.3 0.5 + - - -
249A LYS* 3.3 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLN* 3.5 33.8 - - - +
14A TYR* 3.8 25.1 - - + -
16A ILE* 4.5 4.0 - - + -
158A ASP* 3.6 41.1 - - + +
159A GLY 4.1 1.8 - - - +
194A PRO* 3.9 16.3 - - + +
243A LEU* 2.8 35.3 + - + +
244A VAL* 3.2 11.4 + - - +
246A LEU* 1.3 76.7 - - - +
248A ASP* 1.3 60.8 + - - +
249A LYS 3.6 3.8 + - - +
303A MG 4.2 6.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR 3.8 23.0 - - - +
10A PHE* 3.3 17.3 - - + -
11A GLN* 3.2 26.2 + - - +
14A TYR* 2.6 38.4 + - - -
244A VAL* 3.2 9.3 + - - +
245A GLN* 3.3 8.3 + - - +
246A LEU 3.2 0.8 - - - -
247A ILE* 1.3 73.7 - - - +
249A LYS* 1.3 70.5 + - - +
303A MG 3.9 12.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLN* 3.3 46.4 + - - +
246A LEU* 3.3 29.8 + - + +
247A ILE 4.2 4.5 - - - +
248A ASP* 1.3 82.8 - - - +
----------------------------------------------------------
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