Contacts of the helix formed by residues 321 - 342 (chain G) in PDB entry 3Q2K
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 ASP 321 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G LEU 3.1 15.7 - - - +
128G VAL* 3.8 5.7 - - - +
318G PRO* 3.7 29.0 + - + +
319G GLU 4.0 1.0 - - - -
320G THR* 1.3 77.9 - - - +
322G GLY* 1.3 64.7 + - - +
323G ARG* 3.0 15.3 + - - +
324G GLU* 3.0 22.6 + - - +
325G GLY 3.2 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 322 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G MET* 3.5 10.8 - - - +
116G VAL* 3.9 8.3 - - - -
126G LEU* 3.0 39.0 + - - +
128G VAL* 4.2 6.1 - - - -
321G ASP* 1.3 76.1 - - - +
323G ARG* 1.3 63.8 + - - +
325G GLY 3.3 1.6 + - - -
326G LEU* 3.0 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 323 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179F GLU* 2.7 41.1 + - - -
180F TRP* 3.4 24.3 - - - +
116G VAL* 3.5 19.4 - - + +
120G ASP* 3.2 37.8 + - - -
321G ASP* 3.0 13.1 + - - +
322G GLY* 1.3 77.7 - - - +
324G GLU* 1.3 57.5 + - - +
326G LEU* 3.0 22.0 + - + +
327G GLN* 2.5 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 324 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G ARG* 2.9 54.0 + - - +
194G ASP* 4.6 1.2 - - - +
197G ASP* 5.0 4.5 - - - +
198G TRP* 4.1 10.9 - - - +
319G GLU 3.9 10.3 - - - +
320G THR* 3.9 5.6 - - + -
321G ASP* 3.0 27.3 + - - +
323G ARG* 1.3 74.9 - - - +
325G GLY* 1.3 66.9 + - - +
327G GLN* 3.2 29.5 + - - +
328G SER* 3.9 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 325 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G MET* 3.4 16.9 - - - +
128G VAL* 4.1 17.9 - - - -
130G LYS* 5.4 3.1 - - - -
320G THR* 4.5 3.2 - - - +
321G ASP 3.2 9.4 + - - -
322G GLY 3.3 4.2 + - - -
324G GLU* 1.3 79.3 - - - +
326G LEU* 1.3 53.3 + - - +
327G GLN 3.0 2.1 + - - -
328G SER* 3.2 11.0 + - - -
329G LEU* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 326 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179F GLU* 6.0 1.3 - - - +
105G MET* 3.4 10.1 - - - -
109G TRP* 3.5 27.2 - - + -
112G GLY 3.8 29.2 - - - +
113G LYS* 4.0 16.8 - - + +
116G VAL* 3.9 19.1 - - + -
322G GLY 3.0 14.3 + - - +
323G ARG* 3.0 24.4 + - + +
325G GLY* 1.3 74.7 - - - +
327G GLN* 1.3 57.6 + - - +
329G LEU* 3.4 7.2 - - + -
330G ALA* 2.7 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 327 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218F GLU* 4.8 10.8 - - - +
133G ARG* 5.7 2.2 - - - +
194G ASP* 5.8 0.7 - - - +
197G ASP* 3.1 41.0 - - + +
323G ARG* 2.5 33.5 + - - +
324G GLU* 3.2 24.1 + - - +
325G GLY 3.0 0.4 - - - -
326G LEU* 1.3 81.0 - - - +
328G SER* 1.3 66.8 + - - +
330G ALA* 3.4 4.7 + - - +
331G LEU* 3.2 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 328 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G LYS* 4.0 19.4 + - - -
190G SER 4.5 3.6 - - - -
193G VAL* 4.1 10.1 - - - -
194G ASP* 3.8 36.0 + - - +
197G ASP* 5.5 1.3 - - - +
324G GLU 3.9 1.0 + - - -
325G GLY* 3.2 13.7 + - - -
327G GLN* 1.3 81.3 - - - +
329G LEU* 1.3 62.9 + - - +
331G LEU* 3.7 4.5 - - - +
332G LEU* 2.9 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 329 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G PRO* 5.4 1.8 - - + -
105G MET* 4.3 8.3 - - + -
106G ALA* 3.5 35.2 - - + +
107G THR 4.8 4.0 - - - -
108G ARG 3.9 7.9 - - - +
109G TRP* 4.0 18.2 - - + -
112G GLY* 3.8 28.9 - - - -
186G MET* 4.7 13.0 - - + -
325G GLY 3.0 18.4 + - - +
326G LEU* 3.1 11.6 + - + +
327G GLN 3.1 0.4 - - - -
328G SER* 1.3 79.3 + - - +
330G ALA* 1.3 58.1 + - - +
332G LEU* 3.3 9.9 + - + +
333G THR* 2.9 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 330 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G TRP* 3.6 23.7 - - + -
326G LEU 2.7 21.1 + - - +
327G GLN* 3.7 6.1 - - - +
329G LEU* 1.3 73.6 - - - +
331G LEU* 1.3 56.6 + - - +
333G THR* 3.0 3.3 + - - -
334G ALA* 2.9 26.5 + - - +
347G LEU* 4.1 13.0 - - + +
348G PRO* 6.4 0.2 - - + -
349G LEU* 3.5 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193G VAL* 3.9 20.4 - - + +
196G LEU* 4.1 22.2 - - + -
197G ASP* 4.6 10.3 - - + -
203G VAL* 3.9 26.9 - - + -
206G VAL* 3.8 29.4 - - + -
227G LEU* 5.0 3.1 - - + -
327G GLN 3.2 14.9 + - - +
328G SER* 3.7 7.6 - - - +
330G ALA* 1.3 78.1 - - - +
332G LEU* 1.3 58.0 + - - +
334G ALA* 3.1 3.9 + - + +
335G ILE* 2.8 37.4 + - + +
347G LEU* 3.9 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 332 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G PRO* 4.5 9.6 - - + -
130G LYS* 6.0 0.2 - - - +
185G PHE* 3.6 34.8 - - + +
186G MET* 4.0 39.3 - - + +
190G SER* 4.1 16.2 - - - -
193G VAL* 3.8 26.0 - - + -
328G SER* 2.9 25.5 + - - +
329G LEU* 3.6 11.2 - - + +
331G LEU* 1.3 77.0 - - - +
333G THR* 1.3 58.3 + - - +
335G ILE* 3.3 6.4 + - + +
336G TYR* 3.0 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 333 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G THR 5.6 1.0 + - - -
109G TRP* 3.6 27.6 + - + +
186G MET* 5.6 2.2 - - - +
329G LEU* 2.9 27.3 + - - +
330G ALA 3.5 4.5 - - - -
331G LEU 3.0 0.2 - - - -
332G LEU* 1.3 80.3 - - - +
334G ALA* 1.3 57.5 + - - +
336G TYR* 3.3 6.6 + - - +
337G ARG* 2.8 63.0 + - + +
349G LEU* 3.8 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 334 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206G VAL* 3.7 17.3 - - + -
330G ALA 2.9 16.0 + - - +
331G LEU* 3.1 5.8 + - - +
333G THR* 1.3 77.6 - - - +
335G ILE* 1.3 63.5 + - - +
337G ARG* 4.4 1.3 - - - +
338G SER* 2.9 27.0 + - - -
345G ILE* 3.6 31.0 - - + +
347G LEU* 4.1 17.7 - - + -
349G LEU* 4.5 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 335 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G PHE* 4.2 36.8 - - + -
193G VAL* 4.3 16.8 - - + -
196G LEU* 5.6 1.1 - - + -
206G VAL* 4.1 17.0 - - + -
208G ALA* 3.6 19.0 - - + +
210G THR* 4.8 2.9 - - + -
225G ALA* 3.9 24.2 - - + -
227G LEU* 5.3 3.6 - - + -
237G ILE* 4.8 3.4 - - + -
331G LEU* 2.8 26.6 + - + +
332G LEU* 3.6 7.4 - - + +
333G THR 3.1 0.2 - - - -
334G ALA* 1.3 79.4 - - - +
336G TYR* 1.3 68.9 + - + +
339G ALA* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 336 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178G TRP* 3.7 27.6 - + + -
182G GLY* 4.5 0.9 - - - -
183G GLY 3.0 16.6 + - - -
185G PHE* 3.8 15.0 - + + -
186G MET* 3.0 49.4 + - + +
210G THR* 5.0 6.3 - - + -
220G GLU* 2.5 40.4 + - - -
332G LEU* 3.0 20.7 + - + +
333G THR* 3.8 5.2 - - - +
335G ILE* 1.3 82.8 - - + +
337G ARG* 1.3 65.4 + - + +
339G ALA* 3.5 3.6 + - + +
340G ARG* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 337 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C ASP* 4.9 13.5 + - - +
109G TRP* 4.1 19.6 - - - +
333G THR* 2.8 47.2 + - + +
334G ALA* 4.5 0.4 - - - +
336G TYR* 1.3 73.2 - - + +
338G SER* 1.3 54.2 + - - +
340G ARG* 3.2 21.4 + - - +
341G ASP* 2.7 45.1 + - - +
345G ILE* 3.8 28.7 - - + +
349G LEU* 3.7 24.3 - - - +
350G ASP* 5.1 6.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 338 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206G VAL* 4.3 4.7 - - - -
207G TYR* 3.3 11.2 - - - -
208G ALA 2.8 30.1 + - - +
334G ALA 2.9 18.4 + - - -
335G ILE 3.7 1.6 - - - -
337G ARG* 1.3 78.8 - - - +
339G ALA* 1.3 58.0 + - - +
341G ASP 4.6 0.2 - - - +
342G GLY* 2.7 31.4 + - - -
343G VAL 2.7 27.1 + - - +
345G ILE* 3.6 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 339 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208G ALA 3.3 15.0 + - - +
209G TYR* 4.6 1.1 - - - +
210G THR* 3.6 45.7 + - + +
335G ILE 2.9 17.7 + - - +
336G TYR* 3.9 5.6 - - + +
338G SER* 1.3 80.9 + - - +
340G ARG* 1.3 61.1 + - - +
342G GLY* 4.1 3.1 + - - -
228H ARG* 5.7 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 340 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C ARG* 3.1 20.4 + - - -
346C PRO* 3.3 31.2 - - + +
347C LEU 3.8 14.4 - - - +
348C PRO* 3.2 35.1 + - + +
349C LEU* 4.2 1.0 - - - +
350C ASP* 2.8 44.0 + - - +
336G TYR 3.0 16.5 + - - +
337G ARG* 3.7 20.6 - - - +
339G ALA* 1.3 78.0 - - - +
341G ASP* 1.3 92.4 + - - +
342G GLY 3.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 341 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C ARG* 3.7 13.3 + - - +
346C PRO* 3.4 14.9 - - - +
337G ARG* 2.7 26.8 + - - +
340G ARG* 1.3 115.2 + - - +
342G GLY* 1.3 61.8 + - - +
343G VAL* 3.3 23.3 + - + +
345G ILE* 4.9 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 342 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C ARG* 4.4 3.8 - - - +
207G TYR* 3.5 27.5 + - - -
208G ALA 5.7 0.2 - - - -
338G SER 2.7 19.4 + - - -
339G ALA 4.1 3.6 + - - -
340G ARG 3.5 2.6 + - - -
341G ASP* 1.3 75.1 - - - +
343G VAL* 1.3 60.4 + - - +
344H ARG* 4.3 22.2 + - - +
----------------------------------------------------------
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