Contacts of the helix formed by residues 337 - 347 (chain A) in PDB entry 1Z6T
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 ARG 337 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LEU* 4.4 1.1 - - - +
334A PHE* 3.5 34.9 + - - +
335A PRO 3.5 3.2 - - - -
336A ASN* 1.3 82.2 - - - +
338A TRP* 1.3 59.7 + - - +
339A GLU 3.3 2.7 - - - -
340A TYR* 3.2 43.5 + - + -
341A TYR* 3.0 65.8 + - + -
374A MET* 3.7 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU* 4.2 8.7 - - + -
299A VAL* 3.9 30.2 - - + +
301A MET* 4.4 8.6 - - + +
306A LEU* 3.9 18.8 - - + -
307A PRO* 3.5 30.4 - - + +
309A GLN* 3.5 22.4 - - + +
310A ALA* 3.6 32.5 - - + -
313A ILE* 3.7 21.9 - - + +
331A LEU* 3.5 36.5 + - + +
335A PRO 3.3 27.3 + - - -
336A ASN* 3.7 5.4 + - - -
337A ARG* 1.3 78.5 - - - +
339A GLU* 1.3 59.3 + - - +
341A TYR 4.1 0.2 - - - -
342A LEU* 3.1 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A GLN* 3.7 26.5 + - + +
337A ARG 3.3 0.2 - - - -
338A TRP* 1.3 76.9 - - - +
340A TYR* 1.3 65.0 + - - +
342A LEU* 3.4 4.9 + - + +
343A LYS* 2.9 60.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ARG* 3.2 49.0 + - + +
339A GLU* 1.3 80.9 - - - +
341A TYR* 1.3 91.7 + + - +
343A LYS* 3.4 8.1 + - + +
344A GLN* 2.7 61.1 + - + +
374A MET* 4.0 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ILE* 5.2 3.4 - - + -
327A ILE* 5.6 7.9 - - + -
330A LEU* 4.3 22.9 - - + -
331A LEU* 3.9 23.1 - - + -
334A PHE* 3.4 30.6 - - + -
337A ARG* 3.0 61.7 + - + +
338A TRP 4.5 1.8 - - - +
340A TYR* 1.3 99.8 - + - +
342A LEU* 1.3 66.3 + - - +
344A GLN* 3.8 5.6 - - + +
345A LEU* 3.1 30.0 + - + +
370A ILE* 3.8 32.0 - - + +
374A MET* 3.6 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A GLN* 3.6 26.0 - - + -
312A SER* 3.5 49.6 - - - +
313A ILE* 3.9 16.6 - - + +
316A GLU* 4.2 4.0 - - + -
338A TRP 3.1 20.1 + - - +
339A GLU* 3.4 6.5 + - + +
341A TYR* 1.3 76.4 - - - +
343A LYS* 1.3 58.1 + - + +
345A LEU* 3.3 4.0 + - - +
346A GLN* 2.9 59.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLU* 2.9 52.1 + - + +
340A TYR* 3.6 7.2 - - + +
342A LEU* 1.3 75.6 - - + +
344A GLN* 1.3 56.6 + - + +
346A GLN* 3.2 13.8 + - - +
347A ASN* 2.8 51.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A TYR* 2.7 57.6 + - + +
341A TYR* 3.8 5.2 - - - +
342A LEU 3.4 0.2 - - - -
343A LYS* 1.3 77.3 - - + +
345A LEU* 1.3 59.9 + - - +
347A ASN* 3.1 24.1 - - - +
349A GLN* 5.6 3.8 + - - -
366A GLU* 3.7 13.7 - - - +
370A ILE* 3.5 41.9 - - + +
374A MET* 4.6 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ILE* 4.0 33.7 - - + +
316A GLU* 4.0 30.2 - - + +
317A CYS* 4.7 2.2 - - - -
323A VAL* 5.3 3.1 - - + -
327A ILE* 4.0 33.7 - - + -
341A TYR 3.1 16.4 + - - +
342A LEU* 3.5 8.7 - - - +
343A LYS 3.3 0.2 - - - -
344A GLN* 1.3 76.9 - - - +
346A GLN* 1.3 59.9 + - - +
348A LYS* 3.0 35.3 - - - +
363A ALA* 4.7 6.1 - - - +
366A GLU* 4.5 8.7 - - + -
367A ALA* 4.5 11.0 - - + +
370A ILE* 4.4 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A SER* 4.9 4.9 + - - -
315A LYS* 5.6 3.2 - - - +
316A GLU* 3.4 31.5 + - + +
342A LEU* 2.9 45.6 + - - +
343A LYS* 3.8 17.6 - - - +
345A LEU* 1.3 76.8 - - - +
347A ASN* 1.3 66.5 + - - +
348A LYS* 3.5 6.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LYS* 2.8 44.2 + - - +
344A GLN* 3.1 14.3 - - - +
346A GLN* 1.3 77.6 + - - +
348A LYS* 1.3 60.7 + - - +
349A GLN* 3.4 18.9 + - + +
366A GLU* 4.2 1.2 - - - +
----------------------------------------------------------
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