Contacts of the helix formed by residues 246 - 258 (chain A) in PDB entry 3H60
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 246 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A THR* 3.1 15.0 + - - +
244A HIS 3.0 8.8 + - - +
245A GLY* 1.4 73.0 - - - +
247A PHE* 1.3 65.3 + - - +
248A TYR 3.2 2.9 - - - -
249A ASP* 2.7 38.0 + - + +
250A LEU* 2.9 19.2 + - - +
276A GLY* 4.8 6.0 - - - -
278A PHE* 5.0 3.4 - - - -
282A VAL* 3.8 3.5 - - - +
448A ALA* 3.5 19.6 - - + +
449A PRO* 2.9 16.8 - - - +
450A ASN 4.8 1.3 - - - -
451A TYR* 3.5 33.7 - - - +
452A CYS* 3.5 15.5 - - - +
453A ASP* 5.9 1.1 - - - -
481A HIS* 6.4 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A MET* 3.9 7.0 - - - -
198A TYR* 3.4 30.7 - + + -
199A LYS* 3.6 9.4 - - - -
245A GLY 3.1 5.7 + - - -
246A GLN* 1.3 75.4 - - - +
248A TYR* 1.3 78.0 + + + +
250A LEU* 3.2 7.6 + - + +
251A LEU* 3.0 65.9 + - + +
278A PHE* 3.5 25.7 - - + +
281A GLU* 3.6 25.8 - - + -
282A VAL* 3.5 15.5 - - + -
285A THR* 3.5 24.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TYR 3.2 9.4 + - - -
199A LYS* 2.6 55.2 + - + -
201A GLN* 3.6 6.1 - - - +
246A GLN 3.2 1.0 - - - -
247A PHE* 1.3 92.0 - + - +
249A ASP* 1.3 59.3 + - - +
251A LEU* 3.5 10.6 + - + +
252A ASN 3.1 19.9 + - - -
278A PHE* 3.8 29.2 - + - -
479A VAL* 3.3 18.5 - - + +
480A PRO 3.6 21.5 - - - +
481A HIS* 3.5 22.9 - - + -
482A PRO* 3.2 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLN* 2.7 38.8 + - + +
248A TYR* 1.3 77.8 - - - +
250A LEU* 1.4 59.3 + - - +
252A ASN* 3.1 8.3 + - - +
253A ILE* 2.9 32.5 + - - +
447A SER 5.0 2.7 - - - +
449A PRO* 3.4 33.0 - - + +
476A PHE* 4.4 3.5 - - + -
477A THR 4.5 0.9 - - - +
478A ALA* 3.5 7.8 - - - +
479A VAL* 3.0 34.1 + - - +
481A HIS* 5.4 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A THR* 4.8 10.5 - - + +
246A GLN 2.9 11.8 + - - +
247A PHE* 3.2 17.2 + - + +
249A ASP* 1.4 75.8 - - - +
251A LEU* 1.3 64.2 + - + +
253A ILE* 3.2 16.6 + - + +
254A PHE* 3.2 33.7 + - + -
268A PHE* 3.7 36.1 - - + -
282A VAL* 4.1 35.0 - - + +
285A THR* 4.1 26.0 - - + -
286A LEU* 4.3 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A MET* 3.9 33.7 - - + +
199A LYS* 4.0 32.8 - - + -
247A PHE* 3.0 58.6 + - + +
248A TYR* 3.7 12.8 - - + +
250A LEU* 1.3 78.4 - - + +
252A ASN* 1.3 58.7 + - - +
254A PHE* 3.2 11.3 + - + +
255A GLU* 3.0 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A TYR 3.1 15.1 + - - +
249A ASP* 3.1 11.6 + - - +
251A LEU* 1.3 76.1 - - - +
253A ILE* 1.3 56.0 + - - +
255A GLU* 3.1 21.8 + - - +
256A LEU* 2.8 59.7 + - - +
476A PHE* 3.9 9.3 - - - +
477A THR 3.7 15.0 + - - -
479A VAL* 3.5 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A CYS* 4.2 18.4 - - - -
243A THR* 4.6 4.0 - - + -
249A ASP 2.9 19.9 + - - +
250A LEU* 3.2 14.6 + - + +
252A ASN* 1.3 75.4 - - - +
254A PHE* 1.4 61.1 + - + +
256A LEU* 3.2 8.2 + - - +
257A ASN* 2.8 32.3 + - + +
266A TYR* 3.9 26.7 - - + +
268A PHE* 4.5 10.1 - - + -
447A SER* 4.1 21.5 - - - +
461A TYR* 4.4 11.9 - - + -
476A PHE* 3.6 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A MET* 4.0 17.9 - - - -
250A LEU* 3.2 37.9 + - + -
251A LEU* 3.2 11.6 + - + +
253A ILE* 1.4 78.8 - - + +
255A GLU* 1.3 59.6 + - + +
258A GLY* 2.9 30.6 + - - +
259A LEU* 3.7 19.4 + - + +
260A PRO* 3.8 25.1 - - + -
266A TYR* 3.5 28.5 - + - -
268A PHE* 3.9 21.3 - + - -
285A THR* 4.2 8.1 - - + -
286A LEU* 4.7 1.8 - - + -
289A PHE* 3.7 22.9 - + - -
297A PHE* 4.6 2.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LYS* 4.7 12.6 + - - -
251A LEU* 3.0 33.3 + - - +
252A ASN* 3.1 22.8 + - - +
254A PHE* 1.3 80.9 - - + +
256A LEU* 1.3 63.1 + - + +
257A ASN 3.6 0.2 + - - -
258A GLY* 4.1 2.3 + - - -
479A VAL* 5.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ASN* 2.8 39.7 + - - +
253A ILE* 3.7 2.9 - - - +
255A GLU* 1.3 78.6 - - + +
257A ASN* 1.3 60.4 + - - +
461A TYR* 3.5 24.7 + - + +
475A GLN 5.2 1.3 - - - +
476A PHE* 3.4 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LYS* 4.8 1.0 + - - -
238A THR* 2.9 27.3 + - - +
253A ILE* 2.8 15.6 + - + +
256A LEU* 1.3 78.4 - - - +
258A GLY* 1.3 58.9 + - - +
264A ASN* 3.2 18.9 + - - +
266A TYR* 3.0 26.7 + - + +
461A TYR* 3.5 22.4 + - + +
463A HIS* 2.7 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A PHE* 2.9 20.3 + - - +
255A GLU 4.1 2.3 + - - -
256A LEU 3.6 1.6 - - - -
257A ASN* 1.3 76.5 - - - +
259A LEU* 1.3 66.9 + - - +
264A ASN* 3.4 4.3 - - - +
266A TYR* 2.6 27.2 + - - -
----------------------------------------------------------
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