Contacts of the helix formed by residues 315 - 327 (chain R) in PDB entry 3EXG
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 GLN 315 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214R ARG* 6.0 2.0 + - - +
218R HIS* 5.6 6.3 + - - -
310R ASP* 2.6 43.7 + - + +
311R ASN* 5.3 2.9 - - - -
313R ILE* 3.5 18.7 + - - +
314R PRO* 1.3 76.8 + - - +
316R VAL* 1.3 56.7 + - - +
317R LYS* 2.6 31.7 + - + +
318R ASP* 2.6 35.2 + - - +
319R ILE* 3.2 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 316 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218R HIS* 3.7 21.2 - - + +
221R GLU* 3.6 45.3 - - + +
222R ALA* 3.8 21.1 - - + +
225R VAL* 4.8 4.7 - - + -
314R PRO 4.4 0.2 + - - -
315R GLN* 1.3 72.9 + - - +
317R LYS* 1.3 59.8 + - + +
319R ILE* 3.5 14.8 - - - +
320R ILE* 3.1 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 317 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311R ASN* 5.3 6.5 + - - -
315R GLN* 2.6 19.5 + - + +
316R VAL* 1.3 80.1 - - + +
318R ASP* 1.3 73.6 + - - +
320R ILE* 3.7 10.1 - - + +
321R PHE* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 318 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295R VAL* 4.5 8.7 - - + +
311R ASN* 5.9 2.1 - - - -
313R ILE 4.5 1.0 - - - +
314R PRO* 4.0 0.5 - - - +
315R GLN* 2.6 41.5 + - - +
317R LYS* 1.3 89.2 - - - +
319R ILE* 1.3 62.2 + - - +
321R PHE* 4.4 2.0 - - - -
322R ALA* 3.4 15.4 + - - +
351S ALA* 3.2 30.6 - - + +
352S ASN* 3.3 25.2 + - - +
355S ILE* 3.9 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 319 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209R VAL* 4.9 1.8 - - + -
215R PRO* 5.5 0.7 - - + -
218R HIS* 3.7 39.0 - - + +
219R CYS* 4.1 9.0 - - - +
222R ALA* 4.1 15.0 - - + -
260R VAL* 5.5 0.9 - - + -
262R VAL* 4.1 39.0 - - + -
295R VAL* 4.5 15.7 - - + +
314R PRO* 4.7 6.3 - - + +
315R GLN 3.6 9.0 - - - +
316R VAL* 3.5 12.1 - - - +
318R ASP* 1.3 74.0 - - - +
320R ILE* 1.3 66.4 - - - +
322R ALA* 3.4 2.8 + - - +
323R ILE* 3.3 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 320 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222R ALA* 3.6 17.5 - - + +
225R VAL* 3.6 42.8 - - + -
226R LEU* 4.2 14.6 - - + -
316R VAL* 3.1 27.3 + - + +
317R LYS* 3.7 9.4 + - + +
318R ASP 3.3 0.2 - - - -
319R ILE* 1.3 72.1 - - - +
321R PHE* 1.3 70.7 + - - +
322R ALA 2.8 1.6 + - - -
323R ILE* 3.2 7.1 + - - +
324R LYS* 3.0 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 321 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317R LYS 3.1 18.3 + - - +
318R ASP* 3.8 6.3 - - - +
319R ILE 3.4 0.6 - - - -
320R ILE* 1.3 80.0 - - - +
322R ALA* 1.3 57.8 + - - +
324R LYS* 3.5 6.8 + - + +
325R LYS* 2.8 60.0 + - + +
352S ASN* 3.9 17.0 - - - +
354S TRP* 3.9 28.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 322 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260R VAL* 4.6 3.8 - - + -
293R VAL* 4.4 8.8 - - + +
295R VAL* 3.8 22.7 - - + -
318R ASP 3.4 14.9 + - - +
319R ILE 4.0 2.7 - - - +
320R ILE 3.0 1.0 - - - -
321R PHE* 1.3 77.3 - - - +
323R ILE* 1.3 61.2 + - - +
325R LYS* 3.3 8.7 + - - +
326R THR* 2.9 31.4 + - - -
352S ASN* 4.5 4.5 - - + +
354S TRP* 3.9 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 323 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207R ILE* 3.5 31.2 - - + -
209R VAL* 3.7 27.1 - - + -
219R CYS 6.1 0.2 - - - +
222R ALA* 5.2 4.5 - - + -
226R LEU* 3.6 31.6 - - + -
231R VAL* 4.9 0.2 - - + -
233R CYS* 3.9 6.3 - - - -
260R VAL* 4.4 11.4 - - + -
319R ILE* 3.3 27.1 - - + +
320R ILE* 3.7 6.3 - - - +
322R ALA* 1.3 75.3 - - - +
324R LYS* 1.3 59.2 + - - +
326R THR* 3.0 3.6 + - - -
327R LEU* 2.9 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 324 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225R VAL* 6.1 0.6 - - - +
226R LEU* 4.1 11.8 - - + +
229R GLU* 2.8 41.8 + - - -
320R ILE* 3.0 33.7 + - + +
321R PHE* 3.6 6.5 - - + +
323R ILE* 1.3 78.9 - - - +
325R LYS* 1.3 63.1 + - - +
327R LEU 3.4 0.2 + - - -
328R ASN* 3.1 17.3 + - - -
329R ILE* 3.2 52.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 325 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321R PHE* 2.8 47.9 + - + +
322R ALA* 3.4 7.2 - - - +
324R LYS* 1.3 77.0 - - - +
326R THR* 1.3 54.8 + - - +
328R ASN* 3.2 24.5 + - - +
329R ILE 5.0 1.3 - - - -
354S TRP* 3.1 54.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 326 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207R ILE* 4.2 10.5 - - + -
258R HIS* 3.5 41.3 + - + -
259R LEU 4.6 5.6 - - - +
260R VAL* 3.8 2.8 - - - +
290R ALA* 3.7 20.4 - - + +
291R PRO 4.2 12.1 + - - +
293R VAL* 3.6 22.3 - - - +
322R ALA 2.9 13.8 + - - -
323R ILE 3.0 7.4 + - - -
325R LYS* 1.3 73.3 - - - +
327R LEU* 1.3 58.1 + - - +
328R ASN* 2.8 12.5 + - - +
354S TRP* 5.2 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 327 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206R HIS* 3.6 28.3 - - + +
207R ILE* 4.0 15.5 - - + -
231R VAL* 3.7 30.5 - - + -
258R HIS* 3.8 26.0 - - + +
323R ILE* 2.9 31.2 + - + +
326R THR* 1.3 73.4 - - - +
328R ASN* 1.3 70.2 + - - +
329R ILE* 2.8 34.5 + - + +
----------------------------------------------------------
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