Contacts of the helix formed by residues 333 - 341 (chain A) in PDB entry 5M5R
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 ASN 333 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 3.6 35.5 - - + +
5A LEU 3.3 30.2 + - - +
330A GLU* 3.1 23.5 + - + +
332A GLU* 1.3 89.1 - - - +
334A ILE* 1.3 65.1 + - - +
335A ILE 3.3 2.9 + - - -
336A PRO* 3.4 8.3 - - - +
337A TYR* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PRO* 4.1 25.1 - - + +
272A VAL* 5.1 0.9 - - + -
284A LEU* 4.2 23.8 - - + -
293A ILE* 4.5 3.6 - - + -
329A VAL* 3.8 28.0 - - + -
330A GLU 3.1 16.4 + - - +
331A GLU* 4.4 6.0 + - - +
333A ASN* 1.3 77.0 - - - +
335A ILE* 1.3 62.4 + - + +
337A TYR* 3.4 1.2 + - - +
338A ILE* 3.0 44.9 + - + +
351A MET* 4.2 21.1 - - + -
357A LEU* 3.9 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A GLU 5.4 0.6 + - - +
334A ILE* 1.3 80.2 - - + +
336A PRO* 1.3 72.8 - - + +
337A TYR 3.3 0.2 + - - -
338A ILE* 3.3 8.8 + - + +
339A THR* 3.1 26.2 + - - +
348A ALA* 3.8 17.0 - - + +
351A MET* 3.9 15.3 - - + -
352A ALA* 3.7 27.6 - - + +
357A LEU* 3.8 25.4 - - + -
358A ALA 3.6 14.8 + - - +
359A GLY 3.5 26.7 - - - +
360A ALA* 3.6 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 4.6 7.6 - - + -
332A GLU 3.9 16.6 - - - +
333A ASN* 3.4 14.4 - - - +
335A ILE* 1.3 96.4 - - + +
337A TYR* 1.3 56.3 + - - +
339A THR* 4.4 3.6 - - - -
340A ASN* 2.9 49.0 + - - +
358A ALA 4.3 6.7 - - - +
359A GLY* 4.4 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 3.5 33.1 - - + +
5A LEU* 4.7 3.1 - - + -
6A PRO* 3.7 37.9 - - + -
293A ILE* 3.6 22.8 + - + -
294A TYR* 3.5 19.6 - + - -
333A ASN 3.0 20.0 + - - +
334A ILE 3.5 4.3 - - - +
336A PRO* 1.3 75.1 - - - +
338A ILE* 1.3 67.2 + - + +
341A VAL* 2.8 67.6 + - + +
342A LEU* 3.2 16.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ILE* 4.1 22.0 - - + -
334A ILE* 3.0 35.5 + - + +
335A ILE* 3.3 7.2 + - + +
337A TYR* 1.3 75.9 - - + +
339A THR* 1.3 60.9 + - - +
342A LEU* 3.3 14.6 - - + +
343A GLN 3.1 7.8 + - - -
344A ASN* 3.1 44.3 + - + +
347A LEU* 4.0 18.8 - - + -
348A ALA* 3.6 17.9 - - + +
351A MET* 3.8 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ILE* 3.1 14.6 + - - +
336A PRO* 3.8 6.7 - - - +
338A ILE* 1.3 78.4 - - - +
340A ASN* 1.3 70.1 + - - +
343A GLN* 3.2 21.3 - - - +
344A ASN 3.9 5.9 + - - +
345A PRO* 4.8 8.4 - - + +
348A ALA* 3.0 25.5 - - - +
359A GLY 5.1 1.9 + - - -
362A GLU 4.8 3.4 - - - +
363A LEU* 3.7 43.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A PRO* 2.9 38.7 + - - +
339A THR* 1.3 88.1 - - - +
341A VAL* 1.3 65.5 + - + +
343A GLN* 3.4 23.4 + - - +
363A LEU 5.1 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 5.3 6.3 - - + +
337A TYR* 2.8 63.5 + - + +
340A ASN* 1.3 77.3 - - + +
342A LEU* 1.3 64.2 + - + +
343A GLN* 3.3 10.4 + - - +
----------------------------------------------------------
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