Contacts of the helix formed by residues 310 - 321 (chain E) in PDB entry 6IWQ
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 TRP 310 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193E ARG* 2.5 23.5 - - - +
211E VAL* 4.5 8.5 - - + -
230E VAL* 4.2 8.5 - - + -
233E ARG 3.5 12.7 + - - -
234E THR* 3.0 38.7 - - + +
298E ILE* 3.6 42.4 - - + -
300E LEU* 4.5 9.2 - - + -
306E VAL* 3.3 34.1 - - + +
307E ALA 3.3 16.4 - - - +
308E VAL 3.2 0.2 + - - -
309E ASN* 1.3 76.2 - - - +
311E TYR* 1.3 78.1 + + + +
313E PRO* 3.3 2.1 - - - +
314E LEU* 3.2 28.7 - - + +
328E PRO* 6.1 0.4 - - + -
436E SER* 2.4 31.1 + - - +
437E ARG 4.0 10.1 - - - +
438E VAL* 4.7 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 311 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E PHE* 6.0 0.4 - + - -
206E LEU* 4.1 11.2 - - + -
207E LEU 2.5 27.2 + - - -
208E THR 3.6 0.5 - - - -
209E SER* 2.9 32.2 + - - -
211E VAL* 6.1 0.4 - - + -
233E ARG 5.2 0.2 - - - +
234E THR* 4.9 5.2 - - + -
235E PRO* 4.4 18.6 - - + -
238E TYR* 3.3 43.0 - + + +
239E LEU* 5.6 2.2 - - + -
298E ILE* 3.5 16.8 - - + -
309E ASN* 3.3 1.4 - - - +
310E TRP* 1.3 105.4 - + + +
312E ALA* 1.3 62.8 + - + +
314E LEU* 3.3 1.7 + - - -
315E VAL* 2.9 58.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 312 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E PHE* 3.9 24.4 - - + -
202E TYR* 4.0 17.9 - - + -
206E LEU* 3.7 22.6 - - + +
309E ASN* 3.7 14.5 + - - +
311E TYR* 1.3 75.6 - - - +
313E PRO* 1.3 66.9 - - + +
316E ALA* 3.0 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 313 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202E TYR* 3.4 31.9 - - + +
309E ASN* 3.2 30.3 - - - +
310E TRP 3.3 9.2 - - - +
312E ALA* 1.3 95.6 - - + +
314E LEU* 1.3 54.4 + - - +
317E PRO* 3.1 22.9 - - - +
381E PRO* 5.0 1.7 - - - +
433E VAL* 3.5 28.4 - - + +
435E CYS* 3.8 22.0 - - + +
436E SER* 4.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 314 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298E ILE* 4.0 16.6 - - + -
310E TRP* 3.2 43.9 + - + +
311E TYR 3.3 2.9 + - - +
313E PRO* 1.3 81.5 - - - +
315E VAL* 1.3 63.5 + - + +
317E PRO* 3.4 4.0 - - - +
318E ILE* 4.4 2.9 - - - +
326E THR* 3.2 53.9 + - + +
327E VAL* 4.6 0.4 - - - -
328E PRO* 3.5 42.4 - - + -
392E PHE 5.7 0.4 - - - -
393E ALA* 4.0 21.3 - - + +
433E VAL* 4.3 0.4 - - - -
436E SER* 3.5 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 315 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206E LEU* 4.4 4.3 - - + -
207E LEU* 3.8 25.1 - - + +
209E SER* 4.2 0.7 - - - +
296E VAL* 4.1 22.0 - - + -
298E ILE* 4.2 11.9 - - + -
311E TYR* 2.9 51.2 + - + +
312E ALA 4.6 0.7 - - - +
314E LEU* 1.3 83.0 - - + +
316E ALA* 1.3 63.9 + - - +
317E PRO 3.4 0.4 - - - -
318E ILE* 3.3 9.3 + - + +
319E SER* 2.7 34.3 + - - +
393E ALA* 5.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 316 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E TYR* 3.7 29.6 - - + +
124E ASP* 5.2 1.7 - - - +
125E PRO* 4.8 7.4 - - + -
202E TYR* 4.1 15.0 - - + -
206E LEU* 3.7 10.9 - - + +
312E ALA 3.0 19.7 + - - +
313E PRO 4.4 0.9 - - - +
315E VAL* 1.3 76.3 - - - +
317E PRO* 1.3 68.6 - - + +
319E SER* 3.1 11.9 + - - -
320E LYS* 3.2 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 317 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E ASP* 5.4 4.5 - - - +
313E PRO 3.1 26.7 - - - +
314E LEU 3.4 4.3 - - - +
316E ALA* 1.3 85.7 - - + +
318E ILE* 1.3 60.1 + - - +
320E LYS* 3.6 4.3 + - + +
321E ASP 3.1 18.4 + - - +
324E ILE* 3.3 32.3 - - + +
326E THR* 3.3 21.1 - - - +
381E PRO* 4.5 11.9 - - + -
431E LEU* 4.2 11.2 - - + -
433E VAL* 4.3 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 318 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E GLN* 4.6 0.3 - - - +
120E PHE* 5.0 0.3 - - - -
207E LEU* 4.6 4.6 - - + +
296E VAL* 4.3 16.2 - - + -
314E LEU 4.4 5.8 - - - +
315E VAL* 3.3 10.9 + - + +
316E ALA 3.3 0.8 - - - -
317E PRO* 1.3 73.4 - - - +
319E SER* 1.3 59.2 + - - +
321E ASP 2.3 34.3 - - - +
322E ARG* 3.4 5.2 + - - +
324E ILE 3.6 19.7 - - - +
326E THR* 4.0 15.3 - - - +
393E ALA* 3.4 43.7 - - + +
394E ILE* 4.1 5.6 - - - +
395E GLU* 3.8 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 319 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E GLN* 2.9 22.9 + - - -
120E PHE* 3.0 16.8 - - - -
122E TYR* 3.6 22.0 - - - +
206E LEU* 3.8 3.3 - - - -
207E LEU* 2.4 44.6 + - - +
315E VAL 2.7 18.6 + - - -
316E ALA* 3.1 9.8 + - - -
318E ILE* 1.3 75.3 - - - +
320E LYS* 1.3 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 320 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E GLN* 2.9 21.7 + - - +
122E TYR* 3.1 39.5 + - + +
123E HIS* 4.6 5.1 + - - +
124E ASP* 3.6 48.9 + - - +
316E ALA 3.2 6.2 + - - +
317E PRO* 4.2 5.6 - - + +
319E SER* 1.3 77.7 - - - +
321E ASP* 1.3 61.8 + - + +
324E ILE* 5.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 321 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E GLN* 4.0 7.1 - - - +
317E PRO 3.1 3.0 + - - +
318E ILE* 2.3 31.2 - - - +
320E LYS* 1.3 83.3 - - + +
322E ARG* 1.3 69.2 + - - +
323E THR* 3.2 25.7 + - - +
324E ILE* 3.6 32.4 + - + +
429E LYS* 5.0 5.7 - - - +
----------------------------------------------------------
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