Contacts of the helix formed by residues 330 - 342 (chain E) in PDB entry 4Q9U
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 330 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625C GLN* 6.0 3.2 - - - +
220E TYR* 3.2 24.9 + - - -
224E PHE* 3.4 27.5 - - + -
225E CYS* 5.6 2.7 - - + -
232E GLU* 5.4 1.3 - - - +
235E ASP* 3.4 29.0 + - - +
238E ILE* 5.6 1.0 - - - +
239E GLN* 5.4 4.0 - - - +
279E ASP* 3.6 23.9 + - - +
328E PRO 4.0 0.2 + - - -
329E PRO* 1.3 73.3 - - + +
331E LEU* 1.3 63.7 + - - +
333E SER* 3.9 3.3 + - - -
334E ASN* 2.9 20.6 + - - -
565H ARG* 4.6 16.3 - - - +
566H GLN* 5.5 0.2 + - - -
569H ASP* 3.1 29.9 + - - +
572H GLU* 4.0 26.2 + - - +
573H LYS* 3.4 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235E ASP* 3.3 4.6 + - - +
238E ILE* 3.7 26.8 - - + +
242E ILE* 5.4 1.6 - - + -
275E ILE* 5.8 2.9 - - + -
278E MET* 3.7 15.7 - - + -
323E VAL* 5.1 5.8 - - + -
328E PRO* 3.0 58.0 + - + +
329E PRO 3.0 9.7 + - - +
330E ARG* 1.3 72.9 - - - +
332E GLN* 1.3 66.7 + - - +
334E ASN* 2.7 16.2 + - + +
335E ILE* 2.8 32.4 + - + +
363E VAL* 5.9 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 332 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E ASP* 3.9 7.2 + - - +
231E ASP* 3.3 22.4 - - - +
234E LYS* 3.5 31.2 - - + +
235E ASP* 2.3 29.1 + - - +
238E ILE* 5.0 4.4 - - + +
331E LEU* 1.3 72.0 - - - +
333E SER* 1.3 55.0 + - - +
335E ILE* 3.1 17.2 + - + +
336E GLN* 2.8 74.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 333 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224E PHE* 3.8 11.6 - - - -
225E CYS* 2.6 34.0 + - - -
231E ASP* 2.4 41.3 + - - +
235E ASP* 2.9 18.0 + - - -
330E ARG* 4.8 3.1 - - - -
332E GLN* 1.3 72.5 - - - +
334E ASN* 1.3 55.7 + - - +
336E GLN* 4.3 0.8 - - - +
337E TYR* 2.9 27.7 + - - +
340E ARG* 3.9 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 334 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224E PHE* 3.2 14.9 - - - -
278E MET* 3.2 39.0 - - + +
279E ASP* 2.4 32.3 + - - +
287E LYS* 3.8 18.7 + - + +
329E PRO 3.3 2.6 + - - -
330E ARG 2.9 17.7 + - - -
331E LEU* 2.7 15.5 + - + +
333E SER* 1.3 69.2 - - - +
335E ILE* 1.3 65.3 + - + +
337E TYR* 3.0 6.2 + - - +
338E ILE* 2.9 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 335 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238E ILE* 5.6 3.1 - - + -
331E LEU* 2.8 42.3 + - + +
332E GLN* 3.4 25.8 - - + +
334E ASN* 1.3 71.6 - - + +
336E GLN* 1.3 61.6 + - + +
338E ILE* 3.1 20.3 - - - +
339E THR* 2.9 31.1 + - + +
356E PHE* 3.9 6.7 - - + -
360E CYS* 4.2 24.0 - - + -
363E VAL* 4.7 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 336 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E ASP* 4.9 3.6 + - - -
231E ASP* 3.9 3.4 + - - +
332E GLN* 2.8 57.5 + - - +
335E ILE* 1.3 77.6 - - + +
337E TYR* 1.3 58.0 + - - +
338E ILE 2.9 1.8 - - - -
339E THR* 2.5 51.9 + - - +
340E ARG* 2.8 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 337 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216E MET* 3.6 22.0 + - + +
219E LEU* 3.0 26.9 - - + +
220E TYR* 3.7 14.6 - + - +
223E VAL* 3.6 15.0 - - + -
224E PHE* 3.2 46.0 - + + -
282E ARG 3.4 23.9 + - - -
284E PRO* 4.4 9.5 - - + +
287E LYS* 4.3 14.6 - - + -
333E SER 2.9 19.0 + - - +
334E ASN* 3.2 11.0 - - - +
336E GLN* 1.3 74.1 - - - +
338E ILE* 1.3 58.4 + - + +
340E ARG* 3.9 2.1 - - - +
341E PHE* 2.9 53.4 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 338 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E MET* 5.7 2.5 - - - -
284E PRO* 6.0 5.4 - - + -
287E LYS* 4.3 24.2 - - + -
288E LEU* 3.9 24.7 - - + -
291E ILE* 6.3 1.1 - - + -
334E ASN* 2.9 19.0 + - + +
335E ILE* 3.1 15.5 - - - +
337E TYR* 1.3 75.3 - - + +
339E THR* 1.3 60.2 + - - +
342E CYS* 2.5 55.2 + - + +
347E LEU* 5.1 0.2 - - + -
356E PHE* 3.6 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 339 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183E GLN* 3.8 8.3 - - - +
335E ILE* 2.9 24.7 + - + +
336E GLN* 2.5 49.3 + - - +
338E ILE* 1.3 74.5 - - - +
340E ARG* 1.3 68.6 + - - +
342E CYS* 4.4 3.8 + - - +
347E LEU* 5.3 9.1 - - - +
356E PHE* 4.3 17.0 - - + -
360E CYS* 6.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 340 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175E ILE* 3.9 22.4 - - + +
179E SER* 4.4 15.8 - - - -
183E GLN* 3.1 32.1 + - - +
186E TYR* 4.3 2.3 - - - -
223E VAL* 3.1 26.5 + - - +
226E PRO* 3.6 5.1 - - - +
231E ASP* 2.2 46.4 + - - -
333E SER* 4.0 3.8 + - - -
336E GLN* 2.8 39.9 + - - +
337E TYR* 4.1 4.3 - - - +
339E THR* 1.3 84.7 + - - +
341E PHE* 1.3 94.3 + - + +
342E CYS 3.7 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 341 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E GLN 6.2 0.2 - - - -
179E SER* 4.9 13.2 - - - -
182E ALA* 6.0 6.3 - - + -
186E TYR* 3.4 10.3 + - - -
212E GLU* 3.5 15.4 - - - +
216E MET* 3.4 28.9 - - + +
219E LEU* 5.0 4.5 - - + -
223E VAL* 3.2 47.3 - - + -
284E PRO* 3.6 11.6 - - + +
337E TYR* 2.9 47.3 + + - +
340E ARG* 1.3 118.0 - - + +
342E CYS* 1.3 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 342 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183E GLN* 4.6 1.7 + - - -
186E TYR* 2.5 24.0 + - - -
212E GLU* 4.6 2.2 - - - -
284E PRO* 4.7 5.6 - - + -
288E LEU* 3.4 33.2 - - + -
338E ILE* 2.5 40.6 + - + +
339E THR 4.6 2.8 - - - +
340E ARG 4.3 2.4 - - - +
341E PHE* 1.3 71.1 - - - +
343E ASN* 1.3 83.0 + - - +
344E PRO* 3.5 3.6 - - - +
346E ARG* 4.4 3.4 - - - -
347E LEU* 3.5 24.4 - - + +
----------------------------------------------------------
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