Contacts of the helix formed by residues 302 - 314 (chain A) in PDB entry 3SMZ
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 302 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A CYS* 3.9 0.9 - - - -
268A GLU* 3.5 20.6 - - - +
300A GLY 3.6 5.1 - - - +
301A PRO* 1.4 84.7 - - + +
303A GLY* 1.3 66.5 + - - +
304A ARG* 3.2 7.0 - - + +
305A SER* 3.0 30.5 + - - +
306A MET* 3.0 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A CYS* 3.4 15.3 - - - -
250A PHE* 3.5 25.2 - - - -
266A VAL* 3.4 14.0 - - - +
268A GLU* 2.7 23.0 + - - -
302A PRO* 1.3 68.6 - - - +
304A ARG* 1.3 56.2 + - - +
307A LEU* 3.1 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A PHE* 3.6 23.0 - - + -
252A GLN* 5.6 2.9 - - - +
302A PRO* 3.0 6.6 + - + +
303A GLY* 1.3 72.9 - - - +
305A SER* 1.3 72.0 + - - +
307A LEU* 3.4 7.0 + - + +
308A ALA* 3.3 46.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PRO* 3.5 14.1 - - - +
302A PRO* 3.0 29.0 + - - +
304A ARG* 1.3 88.5 - - - +
306A MET* 1.4 63.0 + - - +
308A ALA* 3.7 2.8 + - - +
309A ALA* 3.3 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A TYR* 4.2 16.4 - - - +
206A HIS* 3.9 15.0 - - + -
222A CYS* 4.7 2.5 - - - -
266A VAL* 4.0 11.2 - - + -
297A CYS* 3.7 32.3 - - + -
298A ALA* 3.4 28.7 - - + +
301A PRO* 3.7 31.5 - - + +
302A PRO 3.0 14.1 + - - +
303A GLY 4.6 0.2 - - - -
305A SER* 1.4 72.8 - - - +
307A LEU* 1.4 65.9 + - - +
309A ALA* 3.4 3.5 + - + -
310A LEU* 3.1 44.3 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
250A PHE* 4.6 3.4 - - + -
252A GLN* 3.5 42.0 - - + +
253A LEU 4.5 3.4 - - - +
254A ALA* 3.9 33.4 - - + +
264A PHE* 4.5 0.4 - - + -
266A VAL* 3.8 33.3 - - + +
303A GLY 3.1 19.0 + - - +
304A ARG* 3.6 8.1 - - + +
305A SER 3.4 0.2 - - - -
306A MET* 1.4 76.4 - - - +
308A ALA* 1.3 62.9 + - - +
310A LEU* 3.4 1.9 + - - +
311A ILE* 3.1 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ARG* 3.3 39.1 + - - +
305A SER 4.1 3.4 - - - +
307A LEU* 1.3 78.8 - - - +
309A ALA* 1.4 56.0 + - - +
311A ILE* 3.5 9.5 + - - +
312A ALA* 2.9 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A TYR* 3.3 27.6 - - + +
206A HIS* 6.2 0.2 - - + -
305A SER 3.3 17.1 + - - +
306A MET* 3.8 10.1 - - + +
307A LEU 3.3 0.2 - - - -
308A ALA* 1.4 77.4 - - - +
310A LEU* 1.3 52.3 + - - +
312A ALA* 3.3 7.4 + - - +
313A ALA* 2.8 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A TYR* 3.7 38.8 - - + -
224A CYS* 4.4 11.7 - - + -
264A PHE* 3.7 24.2 - - + -
266A VAL* 3.8 25.8 - - + -
297A CYS* 4.3 9.9 - - - -
306A MET* 3.1 32.9 + - + +
307A LEU 3.9 0.7 - - - +
309A ALA* 1.3 73.0 - - - +
311A ILE* 1.4 62.4 + - - +
313A ALA* 3.4 16.5 + - + +
314A GLN* 3.5 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ALA* 3.8 14.6 - - + -
255A CYS 3.8 18.6 - - - +
256A GLY* 4.2 22.7 - - - -
257A GLN 5.5 0.2 - - - +
262A LYS* 4.3 16.0 + - + +
264A PHE* 3.7 18.2 - - + -
307A LEU* 3.1 41.4 + - + +
308A ALA* 3.8 7.4 - - - +
310A LEU* 1.4 74.2 - - - +
312A ALA* 1.4 62.9 + - - +
314A GLN* 3.1 17.3 + - - +
315A ALA* 3.3 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ALA 2.9 18.5 + - - +
309A ALA* 3.5 8.7 - - - +
311A ILE* 1.4 78.3 - - - +
313A ALA* 1.4 59.6 + - - +
315A ALA* 3.3 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 4.6 16.5 - - + +
195A GLY* 6.0 2.1 - - - -
204A TYR* 4.0 25.8 - - + -
309A ALA 2.8 13.7 + - - +
310A LEU* 3.4 15.7 - - + +
311A ILE 3.2 0.4 - - - -
312A ALA* 1.4 78.1 - - - +
314A GLN* 1.3 59.3 + - + +
315A ALA 3.4 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A THR* 6.5 0.7 - - + -
262A LYS* 4.0 37.5 + - + +
264A PHE* 3.4 32.1 - - - -
310A LEU 3.5 7.8 + - - +
311A ILE* 3.1 11.2 + - - +
313A ALA* 1.3 77.5 - - + +
315A ALA* 1.4 61.1 + - - +
316A THR* 3.7 10.7 + - - +
----------------------------------------------------------
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