Contacts of the helix formed by residues 316 - 332 (chain a) in PDB entry 4IL6
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 THR 316 (chain a).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302a PHE* 4.7 4.1 + - - +
305a SER* 6.2 0.9 - - - -
306a VAL* 3.6 24.2 - - + +
314a ILE 4.0 2.7 - - - +
315a ASN* 1.3 77.7 - - - +
317a TRP* 1.3 59.5 + - - +
318a ALA* 3.2 23.9 + - - +
319a ASP* 2.8 30.4 + - - +
320a ILE 3.3 8.1 + - - -
63d LEU* 3.7 10.7 - - - +
64d ALA* 3.4 23.3 - - + +
71d CYS* 3.6 20.0 - - - -
75d THR* 4.3 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 317 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316a THR* 1.3 74.4 - - - +
318a ALA* 1.3 62.3 + - - +
320a ILE* 3.3 18.0 + - + +
321a ILE* 3.1 27.2 + - - +
61d HIS* 3.5 39.0 - + - -
63d LEU* 3.6 14.3 - - + +
64d ALA 5.5 0.9 - - - -
65d SER* 5.1 5.8 - - - -
75d THR 4.3 10.4 + - - +
77d ALA* 3.7 14.6 - - + +
79d SER* 3.1 20.5 + - - -
168d PHE* 5.8 1.1 - + - -
172d SER* 3.6 16.6 - - - -
176d ALA* 3.8 10.5 - - + -
177d ALA* 3.7 38.5 - - + +
180d ARG* 3.3 51.3 - - + +
333d ASP* 3.9 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 318 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191a ASN* 5.8 1.2 + - - -
194a MET* 4.7 7.6 - - + -
302a PHE* 4.0 25.1 - - + +
303a ASN* 3.7 6.0 - - - +
316a THR* 3.0 14.1 + - - +
317a TRP* 1.3 79.2 - - - +
319a ASP* 1.3 56.2 + - - +
321a ILE* 3.4 16.0 - - - +
322a ASN* 3.0 24.3 + - - +
75d THR* 3.8 21.2 - - + +
176d ALA* 4.3 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 319 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302a PHE 4.4 1.7 - - - +
303a ASN* 3.4 9.0 - - - +
304a HIS* 2.9 41.7 + - + -
305a SER 5.1 0.7 + - - -
306a VAL 5.7 0.5 + - - -
314a ILE 4.2 2.6 - - - +
315a ASN* 3.3 32.8 - - - +
316a THR* 2.8 35.9 + - - +
318a ALA* 1.3 75.8 - - - +
320a ILE* 1.3 64.2 + - - +
322a ASN* 3.2 10.1 + - - +
323a ARG* 3.1 26.3 + - - +
332d GLN* 4.9 2.0 + - - +
137v TYR 5.3 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 320 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315a ASN* 5.2 2.0 - - + +
316a THR 3.3 11.1 + - - +
317a TRP* 3.3 25.7 + - + +
319a ASP* 1.3 75.4 - - - +
321a ILE* 1.3 64.6 + - - +
323a ARG* 3.1 15.9 + - + +
324a ALA* 3.2 12.6 + - - +
63d LEU* 4.0 20.0 - - + -
180d ARG* 3.6 15.9 - - + -
329d MET* 4.0 7.1 - - + +
332d GLN* 3.8 43.1 - - + +
333d ASP* 3.3 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 321 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187a GLN* 3.7 9.2 - - - +
191a ASN* 3.6 16.6 - - - +
193a LEU* 5.8 0.2 - - + -
194a MET* 4.2 11.9 - - + -
317a TRP 3.1 18.0 + - - +
318a ALA* 3.4 10.8 - - - +
320a ILE* 1.3 74.2 - - - +
322a ASN* 1.3 59.2 + - - +
324a ALA* 3.1 5.9 + - - +
325a ASN* 2.8 47.4 + - - +
176d ALA* 3.6 36.8 - - + +
179d PHE* 3.7 20.4 - - + -
180d ARG* 4.1 15.7 - - - +
183d LEU* 4.0 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 322 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191a ASN* 6.0 0.6 + - - +
303a ASN* 3.3 37.3 + - - +
304a HIS* 5.8 0.4 + - - -
318a ALA 3.0 7.6 + - - +
319a ASP* 3.2 12.5 + - - +
321a ILE* 1.3 77.4 - - - +
323a ARG* 1.3 56.6 + - - +
325a ASN* 3.4 8.6 + - - +
326a LEU* 2.9 31.4 + - - +
411c ALA 3.8 1.9 - - - +
412c THR* 3.0 46.6 + - - +
414c ILE* 5.2 0.2 - - - +
137v TYR* 4.1 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 323 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319a ASP 3.1 18.9 + - - +
320a ILE* 3.1 10.3 + - + +
322a ASN* 1.3 73.2 - - - +
324a ALA* 1.3 66.2 + - - +
326a LEU* 3.3 13.0 + - - +
327a GLY 3.2 16.6 + - - -
327d ALA 5.3 0.4 + - - -
328d TRP* 2.8 65.0 + - - +
329d MET* 3.7 11.4 - - - +
331d PRO* 5.6 4.9 - - - +
332d GLN* 3.5 35.2 + - + +
346d LEU* 5.3 5.7 - - - +
134v LYS 3.5 12.1 + - - -
135v VAL 2.9 28.3 + - - -
136v TYR 4.1 0.2 - - - -
137v TYR* 3.0 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320a ILE 3.2 5.6 + - - +
321a ILE* 3.1 8.8 + - - +
323a ARG* 1.3 74.6 - - - +
325a ASN* 1.3 65.3 + - - +
327a GLY* 3.2 11.1 + - - -
328a MET* 3.2 32.8 + - + +
183d LEU* 4.0 16.4 - - + -
325d ILE* 3.8 12.0 - - + +
329d MET* 3.8 30.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 325 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187a GLN* 3.0 51.8 + - - +
188a ALA* 3.6 8.4 + - - +
191a ASN* 3.4 21.2 + - - +
321a ILE* 2.8 23.6 + - - +
322a ASN* 3.5 13.8 + - - +
324a ALA* 1.3 76.6 - - - +
326a LEU* 1.3 55.9 + - - +
328a MET* 3.3 14.8 + - - +
329a GLU* 2.9 28.4 + - - +
411c ALA* 5.2 2.2 + - - +
412c THR* 3.7 16.7 - - + +
183d LEU* 3.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 326 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322a ASN* 2.9 22.1 + - - +
323a ARG* 3.3 30.5 - - - +
325a ASN* 1.3 73.6 - - - +
327a GLY* 1.3 60.1 + - - +
329a GLU* 3.1 6.9 + - - +
330a VAL* 2.9 36.4 + - - +
412c THR* 3.7 27.8 - - + +
328d TRP* 3.7 14.1 - - + -
134v LYS* 3.6 53.8 - - + +
137v TYR* 4.1 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 327 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323a ARG 3.2 8.7 + - - -
324a ALA 3.2 4.1 + - - -
326a LEU* 1.3 76.9 - - - +
328a MET* 1.3 60.7 + - - +
330a VAL* 3.5 1.1 - - - +
331a MET* 3.3 30.8 + - - +
321d LEU 4.4 0.2 - - - +
324d GLY* 3.3 34.2 - - - -
325d ILE* 3.8 0.7 - - - -
328d TRP* 3.7 13.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 328 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184a ILE* 3.4 42.0 - - + +
185a VAL* 5.6 0.7 - - - -
187a GLN* 4.1 4.7 - - + -
188a ALA* 3.5 20.2 - - + -
324a ALA* 3.2 24.4 + - + +
325a ASN* 3.4 21.1 - - - +
327a GLY* 1.3 74.1 - - - +
329a GLU* 1.3 63.5 + - - +
331a MET 3.4 0.7 + - - -
332a HIS* 3.0 29.0 + - - +
407a CLA 5.9 0.2 - - - -
183d LEU* 3.8 29.8 - - + -
186d GLN* 6.4 0.2 - - + -
321d LEU* 3.6 13.1 - - + +
325d ILE* 3.6 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 329 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188a ALA* 3.7 14.4 - - + +
189a GLU* 6.1 2.0 - - + -
325a ASN 2.9 17.4 + - - +
326a LEU* 3.5 9.0 - - - +
328a MET* 1.3 75.6 - - - +
330a VAL* 1.3 62.5 + - - +
332a HIS* 2.6 35.1 + - + -
342a ASP* 5.6 4.9 - - + +
410c VAL* 4.3 10.4 - - - +
412c THR* 2.5 37.2 + - + +
352d LEU* 3.4 17.0 - - + +
134v LYS* 2.6 35.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 330 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326a LEU* 2.9 25.6 + - - +
327a GLY* 3.5 7.6 - - - +
329a GLU* 1.3 73.7 - - - +
331a MET* 1.3 58.6 + - + +
332a HIS 4.5 1.7 - - - +
328d TRP* 3.5 42.8 - - + +
347d PRO 3.5 12.3 - - - +
348d ARG* 4.2 9.2 - - + +
349d GLY* 2.8 31.4 + - - -
352d LEU* 3.4 35.6 - - - +
134v LYS* 4.0 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 331 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327a GLY 3.3 18.8 + - - +
328a MET 4.1 1.3 - - - +
329a GLU 3.2 0.6 - - - -
330a VAL* 1.3 78.6 - - - +
332a HIS* 1.3 65.6 + - - +
333a GLU 3.5 0.3 + - - -
334a ARG* 3.5 27.0 + - + +
383b PHE* 4.7 10.3 - - + -
320d LEU* 3.3 63.9 - - + +
321d LEU* 4.2 4.4 - - - +
323d GLU* 5.1 2.0 - - - +
324d GLY* 3.4 13.5 - - - +
347d PRO* 3.4 44.4 - - + +
348d ARG* 3.5 9.4 - - - -
349d GLY 4.4 0.4 - - - +
157o LEU* 5.3 2.5 - - + -
168o TYR* 5.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 332 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185a VAL* 3.8 17.3 - - + -
188a ALA* 6.0 0.7 - - + -
189a GLU* 2.8 8.7 + - + -
328a MET 3.0 14.9 + - - +
329a GLU* 2.6 38.7 + - + +
330a VAL 4.5 1.6 - - - +
331a MET* 1.3 75.2 - - - +
333a GLU* 1.3 84.5 + - - +
334a ARG* 3.2 1.9 + - - -
337a HIS* 3.5 9.8 + + - -
342a ASP* 3.1 10.5 - - - -
403a OER 2.1 48.9 + - - -
405a CL 3.7 8.5 - - + -
321d LEU* 3.5 19.3 - - + +
352d LEU* 3.7 13.1 - - + +
----------------------------------------------------------
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