Contacts of the helix formed by residues 328 - 338 (chain A) in PDB entry 5JQE
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 328 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A TRP* 3.5 45.1 - - + +
248A ASP* 3.7 14.8 + - - -
254A TYR* 2.6 48.3 + - + -
255A GLY* 5.8 1.8 - - - -
256A VAL* 3.3 24.8 - - + +
326A ASP* 3.0 29.7 + - - +
327A PRO* 1.3 80.1 - - + +
329A ILE* 1.3 65.8 + - - +
331A ALA* 3.2 2.9 + - - +
332A THR* 3.1 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A TRP* 4.3 15.3 - - + -
306A ASN* 5.3 3.1 - - - +
310A PRO* 6.0 3.1 - - + -
312A GLY* 3.2 25.8 - - - +
313A ALA* 3.8 15.9 - - + +
320A GLU* 3.5 18.8 - - - +
323A LEU* 3.7 43.5 - - + +
326A ASP* 3.2 19.6 + - + +
328A ARG* 1.3 77.9 - - - +
330A ALA* 1.3 59.9 + - - +
332A THR* 3.3 7.0 + - - -
333A MET* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLU* 5.1 0.2 - - - -
324A ALA* 3.4 34.9 + - + +
326A ASP 3.0 8.6 + - - +
327A PRO* 4.0 8.1 - - + +
328A ARG 3.2 0.2 - - - -
329A ILE* 1.3 78.3 - - - +
331A ALA* 1.3 54.5 + - - +
333A MET* 3.9 5.5 - - - +
334A GLU* 3.2 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A SER* 3.6 2.7 - - - +
256A VAL* 3.5 31.9 - - + +
257A THR* 3.7 20.4 - - - +
258A VAL* 5.3 1.8 - - + +
327A PRO 3.5 4.2 + - - +
328A ARG 3.2 8.0 + - - +
329A ILE 3.2 0.6 - - - -
330A ALA* 1.3 77.6 - - - +
332A THR* 1.3 66.3 + - - +
333A MET 3.0 1.1 - - - -
334A GLU* 3.0 5.7 + - - +
335A ASN* 2.8 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL* 5.0 4.7 - - - +
123A GLU 5.1 0.2 - - - -
124A ALA* 3.7 23.4 + - - +
126A SER* 3.2 21.8 - - - +
239A ASN 5.7 0.2 - - - +
240A GLY 5.4 0.4 - - - -
241A PRO* 3.8 20.4 - - + +
244A TRP* 3.5 32.5 - - + +
313A ALA* 4.2 13.5 + - - +
328A ARG 3.1 10.1 + - - +
329A ILE* 3.3 11.1 + - - -
331A ALA* 1.3 74.0 - - - +
333A MET* 1.3 61.3 + - - +
335A ASN* 4.8 1.1 - - - +
336A ALA* 3.3 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TYR* 3.5 37.7 - - + +
104A PHE* 3.7 26.2 - - + -
122A VAL* 4.7 8.1 - - + -
313A ALA* 4.0 14.6 - - + +
314A VAL 5.0 1.6 - - - +
320A GLU* 3.9 20.9 - - + +
329A ILE 3.2 19.4 + - - +
330A ALA* 3.9 6.3 - - - +
331A ALA 3.0 0.6 - - - -
332A THR* 1.3 76.5 + - - +
334A GLU* 1.3 64.4 + - - +
336A ALA* 3.2 7.9 + - - +
337A GLN* 3.1 50.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A VAL* 3.3 36.0 - - + +
330A ALA 3.2 16.5 + - - +
331A ALA* 3.0 6.4 + - - +
333A MET* 1.3 79.0 - - - +
335A ASN* 1.3 61.9 + - - +
337A GLN* 3.2 19.2 + - - +
338A LYS* 3.2 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ALA* 4.4 4.7 - - + -
125A LEU 3.4 19.8 + - - +
126A SER* 3.9 3.2 + - - +
257A THR 3.9 1.9 - - - +
258A VAL* 3.4 25.9 - - - +
259A LEU* 3.1 50.5 - - - +
267A SER 5.1 2.4 + - - -
269A PRO* 3.6 14.2 - - + +
331A ALA 2.8 24.4 + - - +
332A THR 4.4 0.2 - - - +
334A GLU* 1.3 75.7 - - - +
336A ALA* 1.3 57.4 + - - +
338A LYS* 3.3 7.2 + - - +
339A GLY* 2.9 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PHE* 4.3 13.9 - - + -
122A VAL* 3.4 31.2 - - + -
124A ALA* 3.9 5.5 - - + +
271A VAL* 3.3 26.8 - - + +
332A THR 3.3 15.5 + - - +
333A MET* 3.2 12.5 + - - +
335A ASN* 1.3 78.7 - - - +
337A GLN* 1.3 61.7 + - - +
339A GLY* 3.2 9.2 + - - -
341A ILE* 5.8 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TYR* 4.3 12.0 - - - -
103A PRO* 6.1 0.2 - - - +
104A PHE* 3.7 19.9 - - + +
333A MET* 3.1 40.0 + - + +
334A GLU* 3.2 21.9 + - - +
336A ALA* 1.3 73.5 - - - +
338A LYS* 1.3 60.4 + - + +
339A GLY 3.0 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A VAL* 3.4 29.5 - - + +
259A LEU 5.4 0.6 + - - -
261A THR* 5.2 7.1 - - - +
266A PRO* 3.7 39.5 - - + +
267A SER 4.4 6.5 - - - +
268A LYS* 3.3 28.9 - - - +
334A GLU* 3.2 36.5 + - + +
335A ASN* 3.3 4.9 + - - +
337A GLN* 1.3 75.6 - - + +
339A GLY* 1.3 57.8 + - - +
----------------------------------------------------------
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