Contacts of the helix formed by residues 302 - 312 (chain A) in PDB entry 6T2C
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 ILE 302 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A GLY* 4.2 17.6 + - - +
300A GLU 3.6 0.6 + - - -
301A GLY* 1.3 75.0 - - - +
303A PRO* 1.3 75.0 - - + +
304A MET 4.2 4.3 - - - +
305A LYS* 3.2 20.8 + - + +
306A ASP* 3.0 22.7 + - - +
351A LYS* 3.8 61.0 - - + +
352A PHE* 6.0 1.3 - - + -
32V G 4.2 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A GLY 3.6 7.6 - - - +
302A ILE* 1.3 90.9 - - + +
304A MET* 1.3 57.5 + - + +
306A ASP* 3.4 6.9 + - + +
307A ALA* 2.9 28.1 + - - +
351A LYS 5.6 1.1 - - - +
352A PHE* 5.9 3.6 - - + -
479A PRO* 3.7 26.2 - - + +
481A ILE* 4.6 11.5 - - + +
31V U 4.8 13.9 - - - +
32V G 4.5 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ILE* 3.4 2.0 - - + +
303A PRO* 1.3 77.6 - - + +
305A LYS* 1.3 61.4 + - - +
307A ALA* 3.7 9.8 - - + +
308A LYS* 2.9 29.4 + - + +
345A ILE* 4.5 20.4 - - + -
348A MET* 3.7 42.7 - - + +
350A GLY 5.4 0.9 - - - +
351A LYS* 4.0 20.2 + - - +
352A PHE* 4.7 2.0 - - + -
353A LEU* 4.4 18.2 - - + +
477A VAL* 4.4 24.2 - - + +
479A PRO* 4.0 28.5 - - + -
498A PHE* 4.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A HIS* 4.2 9.8 + - + +
299A GLY* 4.0 31.0 - - - +
302A ILE* 3.2 23.3 + - + +
304A MET* 1.3 78.9 - - + +
306A ASP* 1.3 58.7 + - - +
308A LYS* 3.4 20.9 + - + +
309A ALA* 2.9 27.7 + - - +
348A MET* 5.6 9.6 + - - +
350A GLY 4.1 24.1 + - - +
351A LYS* 5.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A PRO* 6.1 1.3 - - - -
297A HIS* 2.6 40.9 + - + -
300A GLU 4.2 0.5 + - - -
301A GLY* 3.4 30.6 + - - +
302A ILE 3.0 14.5 + - - +
303A PRO* 3.8 7.0 - - + +
304A MET 3.3 0.2 - - - -
305A LYS* 1.3 73.0 - - - +
307A ALA* 1.3 60.4 + - - +
309A ALA* 3.3 1.4 + - - +
310A CYS* 2.9 34.9 + - - -
481A ILE* 4.9 8.5 - - + +
483A LYS* 4.6 10.4 - - - -
493A THR* 4.4 22.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A PRO 2.9 17.6 + - - +
304A MET* 3.7 11.9 - - + +
305A LYS 3.3 0.2 - - - -
306A ASP* 1.3 77.1 - - - +
308A LYS* 1.3 56.3 + - - +
310A CYS 3.4 0.3 + - - -
311A LEU* 2.9 35.1 + - + +
479A PRO* 4.0 13.0 - - + -
481A ILE* 4.7 3.1 - - + +
495A LEU* 3.8 15.1 - - + +
498A PHE* 4.0 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A MET* 2.9 18.5 + - + +
305A LYS* 3.7 22.0 - - + +
307A ALA* 1.3 76.2 - - - +
309A ALA* 1.3 57.6 + - - +
311A LEU* 3.3 7.5 + - + +
312A ASP* 3.0 53.1 + - - +
345A ILE* 4.7 24.2 + - + +
346A LYS* 4.3 27.6 + - - +
348A MET* 4.7 22.0 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
292A VAL* 3.7 12.5 - - + +
297A HIS* 3.7 33.4 - - + +
305A LYS 2.9 17.8 + - - +
306A ASP 3.7 4.5 - - - +
308A LYS* 1.3 77.2 - - - +
310A CYS* 1.3 61.5 + - - +
312A ASP* 3.9 8.0 + - - +
313A THR* 3.3 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LEU* 3.7 35.6 - - + +
292A VAL* 3.7 22.9 - - - -
306A ASP* 2.9 22.0 + - - +
309A ALA* 1.3 76.2 - - - +
311A LEU* 1.3 61.5 + - - +
312A ASP 3.3 0.2 - - - -
313A THR* 2.8 21.4 + - - -
493A THR* 3.8 23.1 - - - -
495A LEU* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LEU* 4.6 7.4 - - + -
307A ALA 2.9 20.8 + - - +
308A LYS* 3.8 5.4 - - + +
310A CYS* 1.3 78.8 - - - +
312A ASP* 1.3 64.3 + - - +
313A THR 3.3 0.7 + - - -
314A PHE* 3.4 20.3 + - - +
317A TRP* 3.6 38.7 + - + -
338A TRP* 5.8 1.8 - - + -
342A LEU* 5.7 7.0 - - + -
345A ILE* 3.9 27.8 - - + -
346A LYS* 4.8 11.3 + - - +
495A LEU* 4.5 2.7 - - + -
498A PHE* 3.6 27.8 - - + -
520A PHE* 4.3 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LYS* 3.0 38.0 + - - +
309A ALA* 4.3 7.3 - - - +
310A CYS 3.3 0.4 - - - -
311A LEU* 1.3 76.3 - - - +
313A THR* 1.3 58.7 + - + +
314A PHE 3.2 1.9 + - - -
315A TRP* 3.4 22.5 + - - -
346A LYS* 3.2 24.7 + - - +
----------------------------------------------------------
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