Contacts of the helix formed by residues 336 - 347 (chain A) in PDB entry 5CEO
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 PRO 336 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LEU* 4.7 2.0 - - + -
334A SER 3.8 2.9 - - - +
335A CYS* 1.4 89.4 - - - +
337A ASP* 1.4 66.2 - - - +
338A GLY 3.3 2.0 - - - +
339A PHE* 3.1 24.7 + - + +
340A LYS 3.1 17.8 + - - -
367A ALA 5.7 0.2 - - - +
370A ASP* 3.7 20.9 - - + +
371A VAL* 3.6 26.2 - - + -
379A TYR* 5.4 1.8 - - + -
386A TRP* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A CYS 3.4 2.0 + - - +
336A PRO* 1.4 69.8 - - - +
338A GLY* 1.3 56.0 + - - +
340A LYS* 3.4 28.9 + - - +
341A ILE* 2.9 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A PRO* 3.2 3.0 + - - +
337A ASP* 1.3 75.9 - - - +
339A PHE* 1.3 57.4 + - - +
341A ILE* 3.4 10.3 + - - +
342A LEU* 2.9 30.5 + - - +
363A HIS* 5.4 4.3 - - - +
367A ALA* 4.1 22.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LEU* 3.8 25.8 - - + -
214A VAL* 5.2 4.3 - - + -
217A SER* 5.0 0.4 - - - -
300A LEU* 3.9 26.6 - - + +
304A LEU* 3.8 24.7 - - + -
335A CYS* 3.9 6.5 - - - -
336A PRO* 3.1 26.1 + - + +
338A GLY* 1.3 72.6 - - - +
340A LYS* 1.4 58.4 + - - +
342A LEU* 3.3 5.2 + - + +
343A LEU* 2.9 37.4 + - - +
364A LEU* 3.8 24.7 - - + -
367A ALA* 3.7 24.0 - - + -
368A SER 4.9 1.1 - - - -
371A VAL* 3.6 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A VAL* 3.7 22.4 - - + +
332A PRO 3.4 19.7 - - - +
333A SER* 2.9 20.6 + - - +
335A CYS* 3.4 32.5 - - - +
336A PRO 3.1 7.5 + - - +
337A ASP* 3.4 30.6 + - - +
339A PHE* 1.4 75.2 - - - +
341A ILE* 1.4 62.8 + - + +
343A LEU* 3.5 1.7 + - - +
344A ARG* 3.1 55.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ASP* 2.9 37.0 + - + +
338A GLY* 3.5 9.2 - - - +
340A LYS* 1.4 77.6 - - + +
342A LEU* 1.4 56.1 + - - +
344A ARG* 3.4 8.5 + - - +
345A GLN* 3.0 56.0 + - - +
363A HIS* 6.5 1.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
296A PHE* 4.6 0.2 - - + -
300A LEU* 3.8 20.9 - - + -
338A GLY 2.9 17.3 + - - +
339A PHE* 3.3 7.2 + - + +
341A ILE* 1.4 73.6 - - - +
343A LEU* 1.4 58.2 + - - +
345A GLN* 3.3 16.0 + - - +
346A CYS* 2.9 42.3 + - - -
355A PRO* 4.6 5.4 - - + -
360A ILE* 4.0 38.8 - - + +
363A HIS* 4.3 16.2 - - + +
364A LEU* 3.8 37.5 - - + +
367A ALA* 6.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLY* 3.1 29.8 - - - +
300A LEU* 3.8 20.4 - - + -
301A TRP* 3.9 18.8 - - + +
304A LEU* 4.2 16.6 - - + -
331A VAL* 4.2 22.2 - - + -
332A PRO* 5.1 2.0 - - + -
335A CYS* 5.1 3.6 - - - -
339A PHE 2.9 25.5 + - - +
340A LYS 3.8 3.8 - - - +
342A LEU* 1.4 71.3 - - - +
344A ARG* 1.3 57.5 + - - +
346A CYS* 3.4 4.9 + - - +
347A TRP* 3.1 60.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A HIS* 5.1 12.9 + - + +
331A VAL* 3.6 43.9 + - + +
333A SER* 6.1 0.8 - - - +
340A LYS* 3.1 48.3 + - - +
341A ILE* 3.7 7.6 - - - +
343A LEU* 1.3 74.2 - - - +
345A GLN* 1.4 62.3 + - + +
347A TRP* 3.6 14.1 + - - +
348A ASN* 3.7 14.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ILE* 3.0 43.0 + - + +
342A LEU* 3.3 18.9 + - - +
344A ARG* 1.4 73.5 - - + +
346A CYS* 1.4 63.7 + - - +
347A TRP 3.2 0.6 + - - -
348A ASN* 3.4 25.5 + - - +
353A ASN 4.3 2.6 - - - +
354A ARG* 3.6 1.7 - - - -
355A PRO* 3.3 29.8 - - + +
363A HIS* 4.7 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ILE* 3.4 29.6 - - - +
294A TRP* 3.4 12.6 + - - -
296A PHE* 4.2 12.6 - - - -
297A GLY* 3.9 16.2 - - - -
300A LEU* 5.7 0.4 - - - -
342A LEU* 2.9 32.5 + - - +
343A LEU 3.4 4.7 + - - +
345A GLN* 1.4 71.7 - - - +
347A TRP* 1.3 58.9 + - + +
348A ASN 3.4 0.7 - - - -
354A ARG* 3.4 22.3 + - - -
355A PRO* 3.8 4.5 - - - +
360A ILE* 3.9 26.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A TRP* 3.2 61.0 + + + -
297A GLY* 3.4 24.0 - - - -
298A VAL* 3.4 19.8 - - + +
301A TRP* 3.8 17.5 - + + -
328A HIS* 3.5 43.3 + + + +
329A LEU* 3.4 42.0 - - + -
331A VAL* 3.7 18.2 - - + -
343A LEU* 3.1 32.4 + - + +
344A ARG 3.6 8.3 + - - +
345A GLN 3.2 0.8 - - - -
346A CYS* 1.3 79.7 - - + +
348A ASN* 1.3 61.8 + - - +
349A SER* 3.5 2.3 + - - -
----------------------------------------------------------
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