Contacts of the helix formed by residues 315 - 327 (chain L) 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 L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218L HIS* 5.8 1.3 - - - -
310L ASP* 3.0 46.2 + - - +
311L ASN* 5.4 4.0 - - - +
313L ILE* 3.2 5.5 + - - +
314L PRO* 1.3 75.0 + - - +
316L VAL* 1.3 58.0 + - - +
317L LYS* 3.8 18.6 - - + +
318L ASP* 2.7 38.9 + - - +
319L ILE* 3.2 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 316 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218L HIS* 3.9 35.3 - - + +
221L GLU* 4.1 18.6 - - + +
222L ALA* 3.8 21.5 - - + +
225L VAL* 5.2 4.5 - - + -
314L PRO 4.5 0.2 + - - -
315L GLN* 1.3 73.4 + - - +
317L LYS* 1.3 63.1 + - - +
318L ASP 3.1 0.2 + - - -
319L ILE* 3.3 8.9 + - - +
320L ILE* 3.1 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 317 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315L GLN* 3.8 15.6 + - + +
316L VAL* 1.3 75.0 - - - +
318L ASP* 1.3 68.8 + - - +
320L ILE* 3.6 10.2 + - - +
321L PHE* 2.9 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 318 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351I ALA* 2.9 33.1 - - + +
352I ASN* 3.2 23.6 + - - +
355I ILE* 3.7 14.1 - - - +
295L VAL* 3.9 9.0 - - + +
313L ILE 4.0 1.6 - - - +
315L GLN* 2.7 36.1 + - - +
317L LYS* 1.3 80.6 - - - +
319L ILE* 1.3 66.5 + - - +
321L PHE* 4.2 4.6 - - - +
322L ALA* 3.0 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 319 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209L VAL* 4.6 2.7 - - + -
215L PRO* 5.8 0.2 - - + -
218L HIS* 3.9 35.7 - - + +
219L CYS* 4.2 9.2 - - - +
222L ALA* 4.2 12.3 - - + -
260L VAL* 5.2 1.6 - - + -
262L VAL* 3.7 45.8 - - + -
295L VAL* 4.1 10.8 - - + -
314L PRO* 4.7 5.6 - - + -
315L GLN 3.2 13.7 + - - +
316L VAL* 4.0 5.6 - - - +
318L ASP* 1.3 77.9 - - - +
320L ILE* 1.3 62.9 + - - +
322L ALA* 3.2 2.8 + - - +
323L ILE* 3.0 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 320 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222L ALA* 3.7 16.4 - - + -
225L VAL* 3.7 30.7 - - + -
226L LEU* 3.9 30.5 - - + -
316L VAL* 3.1 33.9 + - + +
317L LYS* 3.8 8.5 - - - +
319L ILE* 1.3 74.4 - - - +
321L PHE* 1.3 62.6 + - - +
323L ILE* 3.0 8.6 + - - +
324L LYS* 2.9 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 321 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352I ASN* 4.0 13.9 - - - +
354I TRP* 3.8 31.4 - + + -
355I ILE* 6.1 1.6 - - + -
317L LYS 2.9 22.7 + - - +
318L ASP* 4.0 8.5 - - - +
319L ILE 3.4 0.2 - - - -
320L ILE* 1.3 73.4 - - - +
322L ALA* 1.3 61.8 + - - +
324L LYS* 4.3 6.5 - - - +
325L LYS* 3.2 53.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 322 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352I ASN* 4.1 5.6 - - - +
354I TRP* 4.3 18.4 - - + -
260L VAL* 4.1 6.3 - - + +
293L VAL* 4.1 10.0 - - + +
295L VAL* 3.3 33.9 - - + -
318L ASP 3.0 10.8 + - - +
319L ILE 3.8 2.7 - - - +
320L ILE 3.1 0.2 - - - -
321L PHE* 1.3 75.0 - - - +
323L ILE* 1.3 66.3 + - - +
325L LYS* 3.6 1.9 - - - +
326L THR* 3.1 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 323 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207L ILE* 3.9 33.0 - - + -
209L VAL* 3.7 26.7 - - + -
222L ALA* 5.4 2.9 - - + -
226L LEU* 3.7 33.0 - - + -
231L VAL* 4.7 1.3 - - + -
233L CYS* 4.0 5.2 - - - -
260L VAL* 4.4 12.1 - - + -
319L ILE* 3.0 26.6 + - + +
320L ILE* 3.0 7.1 + - - +
322L ALA* 1.3 76.0 - - - +
324L LYS* 1.3 66.0 + - - +
326L THR* 2.9 12.0 + - - -
327L LEU* 3.0 24.6 + - + +
329L ILE* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 324 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225L VAL* 6.3 0.2 - - - +
226L LEU* 4.5 10.5 - - + +
229L GLU* 3.2 32.1 + - - -
320L ILE* 2.9 37.5 + - + +
321L PHE* 4.3 6.3 - - + +
323L ILE* 1.3 73.0 - - - +
325L LYS* 1.3 54.0 + - - +
327L LEU 3.5 0.2 + - - -
328L ASN* 2.8 14.2 + - - -
329L ILE* 2.8 73.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 325 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354I TRP* 3.1 51.2 - - + +
321L PHE* 3.2 44.4 + - + +
322L ALA 3.6 5.6 - - - +
324L LYS* 1.3 78.2 - - - +
326L THR* 1.3 57.9 + - - +
328L ASN* 3.1 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 326 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354I TRP* 5.1 1.1 - - - -
207L ILE* 3.9 16.2 - - + -
258L HIS* 3.5 30.3 + - + -
259L LEU 4.5 7.9 - - - +
260L VAL* 4.3 4.0 - - - -
290L ALA* 3.6 21.1 - - + +
291L PRO* 4.0 10.6 + - - +
293L VAL* 3.2 31.4 - - - +
322L ALA 3.1 9.1 + - - -
323L ILE 2.9 11.9 + - - -
325L LYS* 1.3 71.8 - - - +
327L LEU* 1.3 57.2 + - - +
328L ASN* 3.1 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 327 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206L HIS* 3.5 31.4 - - + +
207L ILE* 4.2 8.7 - - + -
231L VAL* 3.7 30.1 - - + -
258L HIS* 3.3 33.9 - - + +
323L ILE* 3.0 23.3 + - + +
326L THR* 1.3 73.8 - - - +
328L ASN* 1.3 70.1 + - - +
329L ILE* 3.0 30.4 - - + +
----------------------------------------------------------
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