Contacts of the helix formed by residues 236 - 244 (chain A) in PDB entry 4YCV
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 GLN 236 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ILE* 2.3 49.4 + - + +
233A ARG* 3.2 15.1 - - - +
235A ARG* 1.3 74.1 - - + +
237A ARG* 1.3 62.1 + - - +
238A TYR* 3.5 32.7 + - + +
239A LEU* 3.2 35.1 + - + +
240A ASP 4.1 3.1 + - - -
313B MET* 5.0 0.2 - - - -
538B ALA* 6.6 0.4 - - + -
541B THR* 5.4 7.0 - - - +
545B TYR* 3.8 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ARG* 3.4 18.4 + - - +
234A TYR* 3.5 20.2 - - - +
235A ARG 3.7 3.4 + - - -
236A GLN* 1.3 70.7 - - - +
238A TYR* 1.3 68.9 + - - +
239A LEU 3.2 2.5 - - - -
240A ASP* 2.9 40.1 + - - +
241A LEU* 2.9 30.4 + - + +
247A SER* 4.0 3.4 + - - -
251A PHE* 3.6 21.8 - - - -
571A LYS 3.2 14.5 + - - -
572A ASP* 4.6 3.8 + - - +
574A ILE 2.4 30.5 + - - -
575A LEU* 2.4 32.5 + - + +
576A PHE* 3.6 31.4 - - + -
577A PRO* 3.6 3.6 - - - +
314B LEU* 4.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A GLN* 3.5 26.4 + - + +
237A ARG* 1.3 79.5 - - - +
239A LEU* 1.3 87.3 + - + +
241A LEU* 3.3 3.7 + - - +
242A LEU* 2.9 35.2 + - + +
576A PHE* 5.8 0.2 - - - -
313B MET* 3.5 46.8 + - + +
314B LEU* 6.1 0.6 - - - +
316B VAL* 3.9 15.9 - - + -
317B GLY* 3.5 21.5 - - - +
538B ALA* 4.6 1.6 + - + -
541B THR* 4.0 6.9 + - - +
542B SER* 3.4 33.2 + - - -
545B TYR* 3.3 42.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU* 4.8 4.3 - - + -
222A PRO* 4.3 25.4 - - + -
227A LEU* 4.2 13.9 - - + -
232A ILE* 4.7 11.0 - - + -
236A GLN* 3.2 34.8 - - + +
237A ARG 3.2 0.2 - - - -
238A TYR* 1.3 97.9 - - + +
240A ASP* 1.3 56.1 + - - +
242A LEU* 3.3 13.3 + - + +
243A ILE* 2.9 37.2 + - + +
545B TYR* 3.5 42.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 4.4 9.1 - - - +
233A ARG* 3.3 34.1 - - + +
236A GLN 4.1 1.2 + - - +
237A ARG* 2.9 35.6 + - - +
239A LEU* 1.3 79.3 - - - +
241A LEU* 1.3 58.5 + - - +
244A ASN* 2.8 53.0 + - - +
247A SER* 2.5 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ARG* 2.9 36.1 + - + +
238A TYR 3.8 2.2 - - - +
240A ASP* 1.3 75.8 - - - +
242A LEU* 1.3 61.4 + - - +
244A ASN 3.8 9.7 - - - +
245A GLU* 5.3 0.5 - - - -
247A SER* 4.1 2.9 - - - -
248A ARG* 3.7 38.2 - - + +
251A PHE* 3.7 30.3 - - + -
575A LEU* 4.7 3.6 - - + -
314B LEU* 4.0 22.2 - - + -
317B GLY* 3.3 27.2 - - - +
319B ILE* 4.2 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ARG* 3.4 46.9 - - + +
140A MET* 4.8 15.1 - - + +
155A VAL* 5.4 7.8 - - + +
221A LEU* 4.0 22.9 - - + -
238A TYR* 2.9 24.9 + - + +
239A LEU* 3.5 14.1 - - + +
241A LEU* 1.3 80.3 - - - +
243A ILE* 1.3 67.7 + - + +
244A ASN 4.9 0.7 - - - +
245A GLU* 5.9 0.2 - - - -
316B VAL* 4.2 7.0 - - + +
317B GLY 4.1 12.6 - - - +
318B GLY* 4.9 4.3 - - - +
545B TYR* 5.8 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A MET* 5.0 7.6 - - + -
186A ARG* 5.5 1.6 - - - +
221A LEU* 4.7 9.9 - - + -
222A PRO* 3.1 42.8 - - + +
223A MET 3.4 11.4 - - - +
224A LYS* 3.3 31.7 - - - +
226A GLY 5.4 0.2 - - - +
227A LEU* 3.5 26.5 - - + +
239A LEU* 2.9 16.6 + - + +
242A LEU* 1.3 83.6 - - + +
244A ASN* 1.3 69.8 + - - +
245A GLU 3.7 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LYS 4.3 5.3 - - - +
227A LEU* 4.4 24.3 + - - +
228A LYS* 4.5 8.7 - - - +
233A ARG* 4.2 12.3 - - - +
240A ASP* 2.8 40.9 + - - +
241A LEU 3.8 9.1 - - - +
242A LEU 4.9 0.7 - - - -
243A ILE* 1.3 88.9 - - - +
245A GLU* 1.3 64.1 + - - +
246A SER* 4.2 15.8 + - - +
247A SER* 3.8 5.8 + - - +
248A ARG 3.9 4.3 + - - -
----------------------------------------------------------
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