Contacts of the helix formed by residues 309 - 330 (chain F) in PDB entry 1I43
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 309 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266F HIS* 4.5 4.3 - - - -
306F GLY 3.3 11.1 + - - -
307F MET 3.0 0.2 - - - -
308F LYS* 1.3 84.1 - - - +
310F LEU* 1.3 63.4 + - - +
311F HIS* 3.5 8.1 - - - -
312F LEU* 3.2 13.8 + - + -
313F ARG* 2.9 37.4 + - - +
266G HIS* 4.2 8.2 + - - +
309G THR* 4.1 14.6 + - - +
313G ARG* 3.8 25.8 - - + -
392G CYS* 3.8 19.7 - - - -
428G VAL* 5.1 0.4 - - + -
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Residues in contact with LEU 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F ALA* 4.3 4.3 - - + -
126F LEU* 4.0 24.2 - - + -
241F THR* 4.7 4.9 - - + -
242F PRO* 4.7 3.4 - - + -
243F LEU* 3.6 20.9 - - + -
262F PHE* 3.6 18.6 - - + +
263F LEU* 3.9 26.7 - - + +
307F MET* 3.2 23.0 + - + +
308F LYS 3.6 0.2 - - - -
309F THR* 1.3 74.6 - - - +
311F HIS* 1.3 67.4 + - - +
313F ARG* 2.9 29.1 + - - +
314F VAL* 2.8 40.9 + - + +
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Residues in contact with HIS 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F ASP* 5.7 0.2 - - + -
58F GLY* 3.3 37.7 + - - +
61F ALA* 4.9 2.8 - - + +
62F ILE* 3.9 8.4 - - + +
243F LEU* 3.3 22.1 - - + +
308F LYS 3.5 14.5 - - - -
309F THR* 4.1 0.7 - - - -
310F LEU* 1.3 79.0 + - - +
312F LEU* 1.3 83.3 + - + +
314F VAL* 4.1 0.4 - - - +
315F GLN* 3.1 38.6 + - - +
316G GLN* 5.2 1.8 - - - -
428G VAL* 3.2 46.2 + - + +
429G GLU 5.4 0.7 - - - -
430G ASP* 4.7 9.9 - - - +
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Residues in contact with LEU 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309F THR* 3.2 14.3 + - + +
310F LEU 3.0 0.4 + - - -
311F HIS* 1.3 109.5 - - + +
313F ARG* 1.3 66.3 + - - +
315F GLN* 3.6 12.8 - - - +
316F GLN* 3.4 14.7 + - - +
312G LEU* 3.8 26.2 - - + +
313G ARG* 3.6 30.1 - - + +
316G GLN* 4.1 26.9 - - + +
428G VAL* 3.5 25.8 - - + -
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Residues in contact with ARG 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262F PHE* 2.8 25.6 + - - +
263F LEU 3.5 7.5 + - - -
264F GLY 4.6 0.4 - - - -
265F GLY* 3.2 19.0 - - - -
266F HIS* 4.4 3.4 - - - -
306F GLY 2.9 22.4 + - - -
309F THR* 2.9 24.8 + - - +
310F LEU* 2.9 35.1 + - - +
312F LEU* 1.3 74.1 - - - +
314F VAL* 1.3 66.9 + - - +
316F GLN* 3.0 6.6 + - - +
317F GLN* 2.9 35.5 + - - +
390F GLY 4.2 6.6 + - - -
391F GLY 6.1 0.2 - - - -
392F CYS* 4.0 15.3 - - - +
428F VAL* 4.2 7.2 - - + -
309G THR* 3.9 30.1 - - + -
312G LEU* 3.8 13.7 - - + -
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Residues in contact with VAL 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F THR* 4.2 15.9 - - + +
243F LEU* 3.5 28.0 - - + -
244F ASN* 4.1 15.3 - - - +
262F PHE* 5.3 9.9 - - + -
310F LEU* 2.8 39.9 + - + +
311F HIS 4.2 0.2 - - - +
313F ARG* 1.3 72.4 - - + +
315F GLN* 1.3 64.0 + - - +
317F GLN* 3.2 8.8 + - + -
318F ASN* 2.8 45.7 + - - +
359F GLY* 6.1 0.2 - - - -
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Residues in contact with GLN 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311F HIS* 3.1 31.1 + - - +
312F LEU* 3.6 13.8 - - - +
314F VAL* 1.3 80.2 - - - +
316F GLN* 1.3 62.9 + - - +
318F ASN* 3.4 8.9 + - - +
319F SER* 3.3 23.1 + - - -
316G GLN* 5.4 4.0 + - - +
430G ASP* 5.4 5.1 + - - -
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Residues in contact with GLN 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312F LEU 3.4 8.2 + - - +
313F ARG 3.0 9.2 + - - +
315F GLN* 1.3 79.2 - - - +
317F GLN* 1.3 64.2 + - - +
319F SER* 3.2 8.6 + - - -
320F THR* 3.1 31.3 + - - +
427F GLY 5.0 0.2 - - - +
428F VAL* 3.3 38.8 + - + +
429F GLU 3.4 12.9 + - - -
430F ASP* 4.6 7.3 + - - +
431F PHE* 4.7 3.4 - - - +
311G HIS* 5.1 2.6 + - - -
312G LEU* 4.1 21.2 - - + +
315G GLN* 5.4 6.2 + - - +
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Residues in contact with GLN 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262F PHE* 3.5 26.7 - - + -
313F ARG* 2.9 32.9 + - - +
314F VAL* 3.7 6.3 + - + +
316F GLN* 1.3 74.8 - - - +
318F ASN* 1.3 64.0 + - - +
320F THR* 4.1 3.5 - - - +
321F ALA* 2.9 28.4 + - - +
360F GLY* 3.7 16.1 - - - +
390F GLY* 3.4 23.7 + - - +
391F GLY 4.2 5.1 + - - -
425F SER* 5.4 0.2 + - - -
426F PHE* 2.6 30.7 + - - +
427F GLY 3.3 20.0 + - - +
428F VAL* 4.4 6.7 - - + -
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Residues in contact with ASN 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244F ASN* 2.8 33.9 + - - +
314F VAL* 2.8 30.6 + - - +
315F GLN* 3.5 8.7 - - - +
317F GLN* 1.3 72.5 - - - +
319F SER* 1.3 63.8 + - - +
322F LEU* 3.2 19.1 + - - +
339F TYR* 3.5 7.8 + - - -
356F THR 5.1 0.4 + - - -
357F GLY* 3.6 9.4 - - - -
358F PHE 4.1 4.9 - - - +
359F GLY* 3.0 34.2 + - - -
360F GLY 4.2 0.2 + - - -
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Residues in contact with SER 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315F GLN 3.3 11.3 + - - -
316F GLN* 3.2 11.0 + - - -
317F GLN 3.2 0.8 - - - -
318F ASN* 1.3 73.2 - - - +
320F THR* 1.3 70.2 + - - +
321F ALA 3.0 0.9 - - - -
322F LEU* 2.9 17.8 + - - +
323F ARG* 3.0 38.0 + - - +
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Residues in contact with THR 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F GLN* 3.1 28.7 + - - +
317F GLN* 4.1 3.8 - - - -
319F SER* 1.3 78.1 - - - +
321F ALA* 1.3 63.7 + - - +
323F ARG* 4.1 3.1 + - - +
324F MET* 2.9 32.0 + - + +
426F PHE* 3.6 30.7 - - + -
427F GLY 5.4 1.7 + - - -
429F GLU 4.7 2.8 + - - -
431F PHE* 3.9 33.6 - - + +
434F LEU* 3.8 18.2 - - + -
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Residues in contact with ALA 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317F GLN 2.9 20.2 + - - +
318F ASN 3.7 0.2 - - - +
319F SER 2.9 0.6 + - - -
320F THR* 1.3 78.8 - - - +
322F LEU* 1.3 51.6 + - - +
324F MET* 3.6 1.9 - - - +
325F ALA* 2.7 35.2 + - - +
339F TYR* 3.5 11.4 - - + +
359F GLY 3.1 22.4 - - - +
360F GLY* 3.6 14.8 - - - +
362F VAL* 3.8 8.8 - - + +
426F PHE* 3.8 12.9 - - + -
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Residues in contact with LEU 322 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318F ASN 3.2 10.1 + - - +
319F SER* 2.9 12.7 + - - +
321F ALA* 1.3 74.5 - - - +
323F ARG* 1.3 68.7 + - + +
325F ALA* 2.7 15.4 + - - +
326F GLU* 3.1 26.1 + - - +
339F TYR* 3.5 31.1 + - + +
341F GLY* 4.0 21.3 - - - +
342F LEU* 4.5 7.9 - - + -
358F PHE* 4.9 11.2 - - + -
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Residues in contact with ARG 323 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F SER* 3.0 34.7 + - - +
320F THR* 4.1 3.0 + - - +
322F LEU* 1.3 80.8 - - + +
324F MET* 1.3 61.9 + - - +
326F GLU* 3.4 14.9 + - - +
327F ILE* 3.2 28.5 + - + +
431F PHE* 3.0 58.9 - - + +
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Residues in contact with MET 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320F THR* 2.9 24.9 + - + +
321F ALA 3.6 1.1 - - - +
323F ARG* 1.3 74.6 - - - +
325F ALA* 1.3 66.3 + - - +
327F ILE* 4.4 13.9 - - + -
328F LEU* 2.9 44.4 + - + +
426F PHE* 3.5 28.5 - - + -
431F PHE* 3.4 25.1 - - + -
434F LEU* 5.6 0.2 - - + -
435F LYS* 3.7 27.6 - - + +
438F ILE* 3.4 31.9 - - + -
439F LEU* 5.8 1.6 - - + -
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Residues in contact with ALA 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321F ALA 2.7 13.2 + - - +
322F LEU 2.7 15.7 + - - +
324F MET* 1.3 72.7 - - - +
326F GLU* 1.3 56.3 + - - +
328F LEU* 3.2 5.2 + - - +
329F GLU* 2.8 28.8 + - - +
337F VAL* 3.9 10.4 - - + +
339F TYR* 3.9 31.9 - - + -
342F LEU* 3.9 16.4 - - + -
362F VAL* 4.4 8.3 - - + +
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Residues in contact with GLU 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322F LEU* 3.1 26.6 + - + +
323F ARG* 3.6 12.7 - - - +
325F ALA* 1.3 72.4 - - - +
327F ILE* 1.3 68.7 + - + +
329F GLU* 2.8 17.3 + - - +
330F ALA* 3.0 14.5 + - - +
342F LEU* 3.8 20.5 - - + +
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Residues in contact with ILE 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323F ARG* 3.2 14.0 + - + +
324F MET* 3.8 17.0 - - + +
326F GLU* 1.3 79.5 - - + +
328F LEU* 1.3 64.6 + - + +
330F ALA* 3.3 6.6 + - - +
331F HIS* 3.1 21.9 + - + +
431F PHE* 4.0 14.1 - - + -
435F LYS* 3.7 32.8 - - + +
439F LEU* 4.3 26.2 - - + -
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Residues in contact with LEU 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324F MET* 2.9 37.2 + - + +
325F ALA 3.3 4.5 - - - +
327F ILE* 1.3 79.3 - - + +
329F GLU* 1.3 62.3 + - - +
331F HIS* 3.0 13.9 + - + +
334F VAL* 3.2 38.6 - - + +
337F VAL* 3.8 11.2 - - + -
362F VAL* 4.3 13.5 - - + -
364F PHE* 3.6 39.9 - - + -
426F PHE* 4.9 6.3 - - + -
438F ILE* 4.0 24.0 - - + -
439F LEU* 6.2 1.6 - - + -
442F LEU* 4.3 8.7 - - + -
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Residues in contact with GLU 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325F ALA 2.8 12.2 + - - +
326F GLU* 2.8 14.8 + - - +
328F LEU* 1.3 73.7 - - - +
330F ALA* 1.3 60.6 + - + +
331F HIS 3.2 6.3 + - - +
334F VAL* 4.5 5.5 - - - +
336F HIS* 5.6 1.4 + - - -
337F VAL* 3.6 23.8 + - + +
342F LEU* 3.7 23.3 - - + +
343F GLN 5.3 0.7 + - - -
344F SER* 2.7 31.6 + - - -
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Residues in contact with ALA 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326F GLU 3.0 13.7 + - - +
327F ILE* 3.7 6.7 - - - +
329F GLU* 1.3 74.9 - - + +
331F HIS* 1.3 61.9 + - - +
332F PRO* 3.6 5.5 - - - +
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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) + - + + + + + -
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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