Contacts of the helix formed by residues 307 - 320 (chain E) in PDB entry 6G2T
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 GLY 307 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218E VAL* 3.9 15.2 - - - +
220E LEU* 5.5 6.1 - - - -
305E TYR 3.7 0.2 + - - -
306E PRO* 1.3 73.3 - - - +
308E ILE* 1.3 64.4 + - - +
309E ALA* 3.3 2.6 - - - +
310E ASP* 3.3 20.5 + - - +
311E ARG* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 308 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218E VAL* 3.3 26.7 - - + -
260E LEU* 5.6 5.4 - - + -
261E PHE* 4.4 6.9 - - + -
273E ILE* 5.0 7.2 - - + -
298E LEU* 3.9 20.6 - - + -
302E THR 3.4 22.4 - - - +
303E THR* 3.4 27.6 - - + +
305E TYR* 3.2 30.2 + - + +
306E PRO 3.2 1.4 - - - -
307E GLY* 1.3 78.0 - - - +
309E ALA* 1.3 59.3 + - - +
311E ARG* 3.4 1.4 + - - +
312E MET* 3.0 44.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 309 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298E LEU* 4.0 11.8 - - + +
307E GLY* 4.5 0.6 - - - +
308E ILE* 1.3 79.5 - - - +
310E ASP* 1.3 62.7 + - - +
312E MET* 3.8 3.2 - - - +
313E GLN* 3.0 31.7 + - - +
328E ILE* 4.1 14.3 - - + +
330E ALA* 4.0 26.2 - - + -
334E ARG* 5.9 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 310 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220E LEU* 4.9 21.5 - - + +
307E GLY* 3.3 18.9 + - - +
308E ILE 3.3 0.6 - - - -
309E ALA* 1.3 80.8 - - - +
311E ARG* 1.3 62.7 + - - +
313E GLN* 3.5 14.7 + - - +
314E LYS* 3.4 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 311 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218E VAL* 3.4 29.4 - - + -
219E ALA 3.3 20.3 + - - +
220E LEU* 3.4 17.2 + - - +
221E ASP* 3.8 1.8 + - - +
222E PHE* 3.4 21.8 - - - +
223E GLU* 5.4 2.6 + - - -
258E GLU* 2.8 34.4 + - - -
261E PHE* 3.4 20.6 - - + +
262E GLN* 5.3 5.5 - - - +
307E GLY 2.9 15.2 + - - +
308E ILE 4.0 1.8 - - - +
310E ASP* 1.3 73.6 - - - +
312E MET* 1.3 65.7 + - - +
314E LYS* 3.1 37.1 - - - +
315E GLU* 2.9 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 312 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E MET* 5.2 4.5 - - + -
261E PHE* 3.4 26.0 - - + -
273E ILE* 3.5 22.7 - - + +
274E HIS* 3.8 30.1 - - + +
277E THR* 4.4 7.0 - - - +
296E THR* 5.9 2.5 - - + -
298E LEU* 5.0 15.5 - - + -
308E ILE* 3.0 34.8 + - + +
309E ALA* 3.8 6.3 - - - +
311E ARG* 1.3 77.8 - - - +
313E GLN* 1.3 57.6 + - - +
315E GLU* 4.5 2.7 - - - -
316E ILE* 2.8 50.8 + - + +
328E ILE* 3.7 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 313 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309E ALA 3.0 18.8 + - - +
310E ASP* 3.7 14.7 - - - +
311E ARG 3.3 0.4 - - - -
312E MET* 1.3 76.7 - - - +
314E LYS* 1.3 61.3 + - - +
316E ILE* 4.2 0.7 - - - +
317E THR* 2.7 34.4 + - - +
326E ILE* 4.0 24.6 + - + +
327E LYS* 5.8 0.2 - - - -
328E ILE* 3.4 22.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 314 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220E LEU* 2.8 31.4 - - + +
221E ASP* 4.8 5.8 - - - +
310E ASP 3.4 7.7 + - - +
311E ARG* 3.1 33.2 - - - +
313E GLN* 1.3 79.2 - - - +
315E GLU* 1.3 81.4 + - - +
317E THR* 3.5 4.7 + - - -
318E ALA* 3.0 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 315 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E PHE* 3.0 19.0 - - - -
274E HIS* 3.0 48.0 + - + +
278E PHE* 4.8 0.9 - - - -
311E ARG* 2.9 53.3 + - - +
312E MET* 3.8 2.6 - - - +
314E LYS* 1.3 96.3 + - - +
316E ILE* 1.3 63.2 + - - +
318E ALA* 3.5 4.6 + - - +
319E LEU* 3.3 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 316 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E HIS* 4.5 10.5 - - + +
277E THR* 4.8 15.0 - - + -
278E PHE* 3.1 29.6 - - + -
281E ILE* 5.8 2.5 - - + -
293E TYR* 4.1 17.5 - - + +
296E THR* 4.9 9.9 - - + +
312E MET* 2.8 43.2 + - + +
313E GLN 4.3 0.2 - - - +
315E GLU* 1.3 70.1 - - - +
317E THR* 1.3 61.2 + - - +
320E ALA* 2.9 35.2 + - - +
326E ILE* 3.8 21.1 - - + -
328E ILE* 3.7 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 317 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313E GLN* 2.7 28.4 + - - +
314E LYS* 3.8 5.6 - - - -
316E ILE* 1.3 77.9 - - - +
318E ALA* 1.3 57.5 + - - +
320E ALA* 2.8 22.7 - - - +
321E PRO 4.6 2.9 - - - +
322E SER* 5.0 10.0 + - - -
324E MET 5.7 1.6 - - - +
325E LYS* 6.4 0.2 - - - -
326E ILE* 3.3 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 318 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314E LYS 3.0 18.3 + - - +
315E GLU* 3.8 7.0 - - - +
316E ILE 3.3 0.2 - - - -
317E THR* 1.3 79.5 - - - +
319E LEU* 1.3 67.7 + - + +
320E ALA 3.6 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E HIS* 4.2 18.4 - - + +
275E GLU* 4.8 12.3 - - + +
278E PHE* 3.4 38.7 - - + -
315E GLU 3.3 11.6 + - - +
318E ALA* 1.3 80.2 - - + +
320E ALA* 1.3 62.0 + - - +
321E PRO* 4.1 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 320 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E PHE* 3.5 6.6 - - + -
293E TYR* 3.4 32.1 - - + -
316E ILE 2.9 21.4 + - - +
317E THR 2.8 17.6 - - - +
318E ALA 3.6 3.8 - - - +
319E LEU* 1.3 80.4 - - - +
321E PRO* 1.3 76.9 - - + +
322E SER 3.6 0.9 + - - -
324E MET* 6.4 0.2 - - + -
326E ILE* 4.3 6.3 - - + -
----------------------------------------------------------
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