Contacts of the helix formed by residues 348 - 360 (chain B) in PDB entry 6EZG
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 348 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LYS 3.8 3.4 + - - -
347B ILE* 1.3 79.9 - - - +
349B ARG* 1.3 58.8 + - - +
350B GLU* 3.4 9.1 + - - +
351B ASP* 3.1 32.3 + - - +
352B PHE* 2.9 25.3 + - - +
382B ASN 6.0 0.9 - - - -
387B ASN* 4.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B SER* 1.3 71.3 - - - +
350B GLU* 1.3 65.1 + - - +
352B PHE* 3.3 26.2 + - - +
353B MET* 3.0 42.4 + - + +
372B THR* 3.4 21.6 - - - +
376B THR* 3.2 43.1 + - - +
378B TRP* 3.7 20.5 - - + -
381B ASP* 3.4 24.0 + - - +
382B ASN* 3.7 22.1 + - - +
387B ASN* 3.6 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B SER* 3.3 7.9 + - - +
349B ARG* 1.3 78.6 - - - +
351B ASP* 1.3 67.7 + - - +
353B MET* 3.4 10.4 + - - +
354B SER* 3.1 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B PRO* 3.6 37.5 - - - +
338B GLY* 3.8 17.9 + - - -
347B ILE* 3.7 14.1 - - + -
348B SER* 3.1 23.3 + - - +
350B GLU* 1.3 85.2 - - - +
352B PHE* 1.3 56.2 + - - +
354B SER* 3.5 7.3 + - - -
355B GLY* 2.7 32.7 + - - -
391B LEU* 4.1 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B ILE* 3.5 8.4 - - + +
348B SER 2.9 16.8 + - - +
349B ARG* 3.5 31.4 - - - +
351B ASP* 1.3 78.0 - - - +
353B MET* 1.3 66.0 + - - +
355B GLY* 3.2 2.3 + - - -
356B VAL* 3.0 40.3 + - + +
372B THR* 4.2 8.1 - - + -
375B TYR* 4.0 13.5 - - + -
376B THR* 3.7 23.3 - - - -
387B ASN* 3.2 41.7 - - + -
390B GLY* 4.2 5.2 - - - -
391B LEU* 3.9 27.3 - - + +
394B ILE* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B ARG* 3.0 51.0 + - + +
350B GLU* 3.5 10.1 - - - +
352B PHE* 1.3 79.2 - - - +
354B SER* 1.3 62.5 + - - +
356B VAL* 3.2 17.8 + - + +
357B LYS* 3.3 13.0 + - - +
368B LEU* 6.4 0.9 - - + -
369B ASP* 6.0 1.6 - - - +
372B THR* 3.4 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B PRO* 3.7 21.0 - - - +
350B GLU* 3.1 16.3 + - - +
351B ASP* 3.5 10.5 + - - -
353B MET* 1.3 77.1 - - - +
355B GLY* 1.3 62.7 + - - +
357B LYS* 3.4 8.0 + - - +
358B LEU* 3.1 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ILE* 5.2 0.3 - - - +
336B ALA* 4.7 13.5 - - - -
337B PRO* 4.8 0.6 - - - +
351B ASP 2.7 18.2 + - - -
352B PHE 3.5 4.0 - - - -
354B SER* 1.3 71.1 - - - +
356B VAL* 1.3 59.4 + - - +
358B LEU* 3.3 6.7 + - - +
359B SER* 2.8 32.6 + - - -
391B LEU* 3.6 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B PHE* 3.0 43.7 + - + +
353B MET* 3.2 12.1 + - + +
355B GLY* 1.3 75.6 - - - +
357B LYS* 1.3 62.6 + - + +
359B SER* 3.0 5.5 + - - -
360B VAL* 2.9 34.4 + - - +
368B LEU* 3.9 22.4 - - + +
371B VAL* 4.4 15.5 - - + -
372B THR* 3.7 21.1 - - - +
391B LEU* 3.9 12.3 - - + -
394B ILE* 4.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ASP 4.6 1.7 - - - +
353B MET 3.3 7.7 + - - +
354B SER* 3.6 11.2 - - - +
356B VAL* 1.3 83.9 - - + +
358B LEU* 1.3 65.6 + - + +
359B SER 3.4 0.2 + - - -
360B VAL 3.6 1.6 - - - +
361B PRO* 3.5 31.0 + - + +
363B ALA 4.9 7.2 + - - +
368B LEU* 3.7 36.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ASP* 3.8 37.9 - - + +
286B SER* 3.5 8.9 - - - +
287B ILE* 3.3 33.6 + - + +
335B GLY 3.6 26.2 - - - +
336B ALA* 4.0 6.3 - - + -
337B PRO* 3.8 21.3 - - + -
354B SER* 3.1 18.3 + - - +
355B GLY* 3.3 7.4 + - - +
357B LYS* 1.3 82.2 - - + +
359B SER* 1.3 60.7 + - - +
361B PRO* 3.6 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ILE* 3.6 18.9 - - - +
289B ARG* 4.5 1.2 + - - -
332B LEU* 4.3 2.4 - - - +
355B GLY 2.8 23.1 + - - -
356B VAL* 3.5 4.9 - - - -
358B LEU* 1.3 79.2 - - - +
360B VAL* 1.3 58.9 + - - +
361B PRO* 3.3 8.2 - - - +
391B LEU* 4.4 2.1 - - - +
394B ILE* 4.0 23.3 - - - -
395B VAL* 3.3 28.4 - - - +
398B HIS* 3.7 16.3 - - - -
399B ASN* 4.6 5.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B VAL* 2.9 13.5 + - + +
357B LYS* 3.6 5.6 - - - +
359B SER* 1.3 86.9 - - - +
361B PRO* 1.3 65.6 - - - +
362B HIS* 3.2 23.5 + - + +
363B ALA* 3.2 30.5 + - + +
368B LEU* 3.9 11.0 - - + +
371B VAL* 4.3 14.8 - - + -
394B ILE* 4.3 6.3 - - + -
398B HIS* 4.7 3.6 - - + +
524B TRP* 3.8 36.3 - - + -
528B LEU* 4.7 4.0 - - + -
----------------------------------------------------------
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