Contacts of the helix formed by residues 301 - 307 (chain A) in PDB entry 4A14
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 SER 301 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLU* 3.0 22.8 + - - -
275A SER* 3.4 11.4 - - - -
278A ALA* 3.8 21.1 - - - -
299A ARG 3.3 1.2 - - - -
300A ASP* 1.3 79.1 - - - +
302A LYS* 1.3 62.5 + - - +
303A ILE* 3.0 22.5 + - - +
304A THR* 3.2 9.7 + - - -
305A ARG* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A VAL* 4.5 7.6 - - + -
148A GLU* 2.7 57.2 + - - +
149A GLU* 4.4 7.6 + - - +
150A PHE* 3.2 46.0 - - + +
163A ILE 5.5 3.4 - - - -
164A GLN* 6.4 0.4 - - - +
165A LEU* 3.7 4.8 - - + +
301A SER* 1.3 72.7 + - - +
303A ILE* 1.3 58.1 + - - +
305A ARG* 4.0 31.3 - - - +
306A ILE* 2.9 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A VAL* 4.8 9.0 - - + +
148A GLU* 4.6 0.8 + - - -
215A HIS* 4.2 30.5 - - + +
217A VAL* 3.8 28.9 - - + -
248A VAL* 4.2 10.3 - - + -
250A LEU* 4.2 15.7 - - + -
275A SER* 3.9 25.4 - - - +
276A LEU* 6.4 0.4 - - + -
279A LEU* 4.7 9.0 - - + -
301A SER* 3.0 17.7 + - - +
302A LYS* 1.3 79.5 - - - +
304A THR* 1.3 69.7 + - + +
306A ILE* 3.5 8.2 - - + +
307A LEU* 3.2 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ALA* 4.0 4.0 - - + +
279A LEU* 3.5 48.5 - - + +
282A VAL* 3.8 15.7 - - + -
297A PRO 4.5 1.0 + - - -
298A TYR* 2.6 40.4 + - - -
300A ASP 4.4 0.5 + - - -
301A SER* 3.2 14.4 + - - -
303A ILE* 1.3 80.5 - - + +
305A ARG* 1.3 63.9 + - - +
307A LEU* 3.5 4.5 + - - +
308A LYS* 3.1 23.2 + - - +
311A LEU* 4.7 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLU* 5.6 0.2 + - - -
165A LEU* 3.1 56.3 + - + +
166A ARG* 4.3 6.5 - - - +
173A VAL* 3.5 10.9 - - - +
298A TYR* 3.3 17.9 - - + +
299A ARG* 3.7 24.3 + - - +
301A SER 2.9 18.1 + - - +
302A LYS* 3.3 26.2 + - - +
304A THR* 1.3 74.4 - - - +
306A ILE* 1.3 65.0 + - - +
308A LYS* 3.2 22.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 3.7 30.1 - - + -
150A PHE* 4.1 15.3 - - + -
165A LEU* 3.5 21.0 - - + +
173A VAL* 3.7 15.4 - - + +
175A LEU* 3.9 20.0 - - + -
217A VAL* 4.7 18.8 - - + -
219A THR* 5.3 2.5 - - - +
244A LYS* 5.8 0.2 + - - -
246A HIS* 4.1 19.7 + - + -
302A LYS 2.9 20.9 + - - +
303A ILE* 3.5 19.5 - - + +
305A ARG* 1.3 78.2 - - - +
307A LEU* 1.3 71.1 + - + +
309A ASP* 4.3 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR* 3.9 21.3 - - + +
88A PHE* 5.6 3.6 - - + -
217A VAL* 4.8 1.3 - - + -
246A HIS* 3.5 42.6 - - + +
248A VAL* 4.3 15.9 - - + -
279A LEU* 5.3 7.2 - - + -
303A ILE* 3.2 31.9 - - + +
304A THR 3.5 2.4 + - - +
305A ARG 3.1 0.8 - - - -
306A ILE* 1.3 87.3 - - + +
308A LYS* 1.3 56.9 + - - +
309A ASP 3.2 2.9 - - - -
310A SER* 2.8 23.6 + - - -
311A LEU* 3.1 35.9 + - + +
----------------------------------------------------------
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