Contacts of the helix formed by residues 354 - 359 (chain A) in PDB entry 3QEV
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 354 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 4.9 4.3 - - - -
6A LEU 6.2 0.2 - - - -
7A THR* 6.3 1.8 - - - +
8A VAL* 2.8 42.8 - - + +
9A GLU* 3.3 18.2 - - - +
89A LYS* 3.6 26.6 - - + +
90A LEU* 4.8 4.0 - - + +
93A LEU* 4.6 2.0 - - + +
269A SER* 5.0 1.1 - - - +
353A ILE* 1.3 77.0 - - - +
355A ILE* 1.3 69.0 + - - +
356A GLN* 3.5 30.3 + - - +
357A SER* 2.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 4.5 1.5 - - + +
6A LEU 4.5 14.8 + - - +
211A VAL* 6.2 0.2 - - + -
212A ILE* 3.9 24.2 - - + -
269A SER* 4.1 5.6 + - - +
271A LEU* 3.8 26.4 - - + +
344A SER* 3.9 17.7 - - - +
345A LEU* 4.2 11.7 - - + +
348A GLY* 3.8 28.3 - - - -
349A TYR* 4.1 29.8 - - + +
353A ILE 3.4 4.9 + - - +
354A GLN* 1.3 71.0 - - - +
356A GLN* 1.3 64.9 + - - +
357A SER 3.0 1.4 + - - -
358A VAL* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLU* 4.6 4.9 + - - -
268A ILE 4.0 13.7 + - - -
269A SER* 2.6 31.5 + - - -
270A VAL 3.8 25.1 - - - +
271A LEU* 3.6 13.1 - - + +
354A GLN* 3.5 40.9 + - + +
355A ILE* 1.3 71.2 - - - +
357A SER* 1.3 60.8 + - - +
358A VAL 3.2 1.6 - - - -
359A PHE* 3.3 26.0 + - + +
3T G 4.5 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ILE* 3.7 17.7 - - - +
354A GLN* 2.8 33.9 + - - +
356A GLN* 1.3 77.5 - - - +
358A VAL* 1.3 54.7 + - - +
359A PHE 3.0 5.6 - - - -
360A SER* 2.9 33.0 + - - +
363A LYS* 3.7 26.6 - - - +
364A THR* 3.4 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 4.6 9.4 - - + -
276A LEU* 5.0 1.1 - - + -
279A LYS* 3.3 17.8 - - - -
280A PHE* 4.2 12.1 - - + -
344A SER* 3.4 47.1 - - - +
347A MET* 4.0 21.8 - - + +
348A GLY* 3.6 20.4 - - - +
353A ILE* 4.3 4.0 - - + -
355A ILE 3.0 18.4 + - - +
356A GLN 4.7 0.2 - - - +
357A SER* 1.3 76.7 - - - +
359A PHE* 1.3 64.6 + - + +
360A SER* 3.1 3.9 + - - -
361A PRO* 4.7 0.3 - - - +
364A THR* 4.0 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A VAL 4.4 5.2 - - - -
271A LEU* 3.8 28.0 - - + -
272A ASP 4.3 4.0 - - - -
275A ASP* 3.5 44.9 - - + -
276A LEU* 3.7 27.8 - - + -
279A LYS* 3.9 28.0 + - + +
280A PHE* 5.4 0.2 - + - -
356A GLN* 3.3 22.2 + - + +
357A SER 3.0 0.8 - - - -
358A VAL* 1.3 78.7 - - + +
360A SER* 1.3 58.1 + - - +
361A PRO* 3.5 9.0 - - - +
3T G 3.3 67.6 + + + +
----------------------------------------------------------
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