Contacts of the helix formed by residues 308 - 332 (chain C) in PDB entry 1P5Q
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 ASN 308 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLN* 4.2 24.0 + - - +
381A GLN* 2.8 42.0 + - - +
306C PHE 3.8 1.2 + - - -
307C SER* 1.3 83.3 - - - +
309C GLU* 1.3 58.5 + - - +
310C GLU 3.3 0.2 - - - -
311C ALA* 3.6 17.3 - - - +
312C GLN* 2.8 35.0 + - - +
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Residues in contact with GLU 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C SER* 2.3 39.6 + - - +
308C ASN* 1.3 66.4 - - - +
310C GLU* 1.3 85.0 + - + +
312C GLN* 3.1 17.2 + - - +
313C LYS* 3.2 27.1 + - - +
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Residues in contact with GLU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C SER* 3.5 34.6 + - - -
264C GLU* 4.2 14.2 + - - +
267C LEU* 4.0 18.0 - - + +
305C SER 4.5 1.0 - - - +
306C PHE* 3.6 13.1 - - + -
307C SER* 3.0 39.0 + - - +
309C GLU* 1.3 90.0 - - + +
311C ALA* 1.3 55.9 - - - +
313C LYS* 2.7 33.2 + - + +
314C ALA* 2.8 12.5 + - - +
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Residues in contact with ALA 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLN* 4.0 11.9 - - - +
306C PHE* 3.7 24.5 - - + +
308C ASN* 3.6 23.8 + - - +
309C GLU 3.3 0.4 - - - -
310C GLU* 1.3 79.7 - - - +
312C GLN* 1.3 62.6 + - - +
314C ALA* 3.9 3.8 - - - +
315C GLN* 3.0 22.5 + - - +
318C ARG* 4.4 5.4 + - - +
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Residues in contact with GLN 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A GLN* 5.0 7.1 - - - +
308C ASN 2.8 27.3 + - - +
309C GLU* 3.3 9.6 - - - +
310C GLU 3.0 0.4 - - - -
311C ALA* 1.3 77.9 - - - +
313C LYS* 1.3 61.9 + - + +
315C GLN* 3.1 20.4 - - - +
316C ALA* 3.1 8.8 + - - +
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Residues in contact with LYS 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C LEU* 4.1 24.6 - - + +
309C GLU* 3.3 24.2 + - - +
310C GLU* 2.7 17.3 + - - +
312C GLN* 1.3 70.3 - - + +
314C ALA* 1.3 65.7 + - - +
316C ALA* 3.0 9.0 + - - +
317C LEU* 2.9 30.8 + - + +
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Residues in contact with ALA 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C LEU* 3.8 19.2 - - + +
300C LEU* 4.0 4.7 - - + +
306C PHE* 3.6 26.7 - - + -
310C GLU 2.8 14.1 + - - +
311C ALA 4.0 2.0 - - - +
313C LYS* 1.3 72.8 - - - +
315C GLN* 1.3 63.3 + - - +
317C LEU* 3.3 6.5 + - - +
318C ARG* 2.9 49.9 + - - +
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Residues in contact with GLN 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LYS* 3.5 33.7 - - - +
311C ALA 3.0 14.5 + - - +
312C GLN* 3.1 14.6 - - - +
314C ALA* 1.3 77.8 - - - +
316C ALA* 1.3 59.1 + - - +
318C ARG* 3.2 14.3 + - - +
319C LEU* 2.9 30.5 + - + +
348C LEU* 3.0 48.0 + - + +
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Residues in contact with ALA 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C LYS* 5.9 0.7 - - - -
312C GLN 3.1 8.2 + - - +
313C LYS* 3.0 11.7 + - - +
315C GLN* 1.3 81.8 - - - +
317C LEU* 1.3 57.1 + - + +
319C LEU* 3.4 9.9 + - - +
320C ALA* 2.8 30.7 + - - +
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Residues in contact with LEU 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C LEU* 4.3 19.7 - - + +
270C SER* 4.0 36.3 - - - +
271C THR* 4.1 16.4 - - - +
274C LYS* 3.8 31.4 - - + +
296C ILE* 4.4 5.2 - - + -
300C LEU* 3.9 15.3 - - + -
313C LYS* 2.9 18.1 + - + +
314C ALA 3.6 6.5 - - - +
316C ALA* 1.3 74.1 - - + +
318C ARG* 1.3 57.4 + - - +
320C ALA* 2.9 5.4 + - - +
321C SER* 2.6 39.6 + - - -
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Residues in contact with ARG 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C ILE* 4.8 1.6 - - - -
297C VAL* 4.9 13.5 - - + +
300C LEU* 2.5 60.5 + - + +
301C GLU* 4.8 3.0 + - - +
303C GLU 4.2 4.8 + - - -
306C PHE* 4.0 16.4 - - - -
311C ALA* 4.4 5.9 + - - +
314C ALA* 2.9 42.2 + - - +
315C GLN* 3.6 15.2 + - - +
317C LEU* 1.3 73.9 - - - +
319C LEU* 1.3 64.2 + - - +
321C SER* 3.0 9.3 + - - -
322C HIS* 2.8 33.1 + - + +
348C LEU* 3.8 17.3 - - + +
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Residues in contact with LEU 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C GLN* 2.9 15.8 + - + +
316C ALA* 3.5 12.3 - - - +
318C ARG* 1.3 78.5 - - - +
320C ALA* 1.3 58.0 + - - +
322C HIS* 3.2 2.8 + - - +
323C LEU* 3.0 37.5 + - + +
345C ALA* 3.5 39.7 - - + +
348C LEU* 3.7 15.3 - - + +
349C ASP* 3.8 20.4 - - + +
352C ASN* 3.6 28.9 - - - +
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Residues in contact with ALA 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C LYS* 3.5 35.4 - - + +
316C ALA 2.8 20.7 + - - +
317C LEU* 3.6 4.0 - - - +
319C LEU* 1.3 75.7 - - - +
321C SER* 1.3 62.1 + - - +
323C LEU* 3.6 8.5 + - - +
324C ASN* 2.9 34.0 + - - +
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Residues in contact with SER 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C LYS* 6.0 0.2 - - - +
293C TYR* 4.2 16.5 - - - +
296C ILE* 2.8 43.0 - - - +
297C VAL* 3.8 21.3 - - - -
317C LEU 2.6 13.9 + - - -
318C ARG 3.4 8.3 - - - -
320C ALA* 1.3 71.4 - - - +
322C HIS* 1.3 65.6 + - - +
324C ASN* 3.4 1.6 + - - +
325C LEU* 3.1 31.4 + - - +
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Residues in contact with HIS 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C VAL* 3.6 32.0 - - + +
318C ARG* 2.8 30.1 + - + +
319C LEU 3.9 3.1 - - - +
321C SER* 1.3 78.4 - - - +
323C LEU* 1.3 61.5 + - - +
325C LEU* 3.6 12.2 + - + +
326C ALA* 3.2 18.4 + - - +
341C SER* 3.7 31.5 + - - +
344C LYS* 3.6 54.1 + - + +
345C ALA* 3.9 10.1 - - + -
348C LEU* 4.5 7.2 - - + -
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Residues in contact with LEU 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C LEU* 3.0 27.2 + - + +
320C ALA* 3.6 7.6 + - - +
322C HIS* 1.3 77.9 - - - +
324C ASN* 1.3 63.3 + - - +
326C ALA* 3.3 8.4 - - + +
327C MET 3.3 9.0 + - - -
342C CYS* 5.6 1.6 - - - -
345C ALA* 3.3 24.7 - - + -
352C ASN* 3.5 28.3 - - - +
354C LYS* 4.3 16.2 - - + -
355C GLY* 3.7 28.0 - - - +
358C ARG* 2.8 29.4 + - - +
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Residues in contact with ASN 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C LYS* 4.9 8.9 - - - +
293C TYR* 3.3 48.0 + - + -
320C ALA* 2.9 27.1 + - - +
321C SER 4.0 1.1 - - - +
323C LEU* 1.3 76.3 - - - +
325C LEU* 1.3 68.0 + - - +
326C ALA 3.1 1.3 - - - -
327C MET* 2.8 29.6 + - + +
328C CYS* 2.8 26.3 + - - -
358C ARG* 4.4 2.1 + - - -
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Residues in contact with LEU 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C LEU* 3.3 39.5 - - + +
293C TYR* 3.6 26.7 - - + -
294C LYS* 4.2 17.5 - - + +
297C VAL* 4.6 9.2 - - + -
321C SER 3.1 23.2 + - - +
322C HIS* 3.8 17.7 - - + +
324C ASN* 1.3 74.1 - - - +
326C ALA* 1.3 65.1 + - - +
327C MET 3.0 0.3 + - - -
328C CYS* 3.0 2.7 + - - +
329C HIS* 2.7 35.9 + - + +
341C SER* 3.6 15.9 - - - +
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Residues in contact with ALA 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322C HIS 3.2 12.5 + - - +
323C LEU* 3.3 13.7 - - + +
324C ASN 3.1 0.4 - - - -
325C LEU* 1.3 79.8 - - - +
327C MET* 1.3 55.5 + - - +
329C HIS 3.6 0.2 + - - -
330C LEU* 3.0 35.8 + - - +
338C ALA* 3.8 13.8 - - + +
341C SER* 3.8 9.1 - - - -
342C CYS* 3.7 30.5 - - - +
358C ARG* 4.3 9.6 - - + -
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Residues in contact with MET 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C PHE* 3.9 42.0 - - + -
293C TYR* 5.3 3.1 - - - +
323C LEU 3.3 1.6 + - - -
324C ASN* 2.8 37.9 + - + +
326C ALA* 1.3 77.3 - - - +
328C CYS* 1.3 58.8 + - - +
330C LEU* 3.1 10.1 + - + +
331C LYS* 2.8 36.4 + - + +
358C ARG* 3.4 38.8 - - - +
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Residues in contact with CYS 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C PHE* 3.9 16.2 - - - -
286C TYR* 4.3 18.6 - - + +
289C ALA* 3.6 27.6 - - - -
290C LEU* 3.9 20.6 - - + -
293C TYR* 4.3 10.3 - - - -
324C ASN* 2.8 26.3 + - - -
325C LEU* 3.7 5.8 - - - +
327C MET* 1.3 73.0 - - - +
329C HIS* 1.3 63.2 + - - +
331C LYS* 3.2 2.9 + - - +
332C LEU* 2.9 30.1 + - - +
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Residues in contact with HIS 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C LEU* 3.6 32.9 - - + +
294C LYS* 5.2 11.4 - - - -
325C LEU* 2.7 31.5 + - - +
328C CYS* 1.3 71.9 - - - +
330C LEU* 1.3 51.1 + - - +
332C LEU* 2.9 7.6 + - - +
333C GLN 2.6 31.4 + - - -
334C ALA* 2.7 34.6 + - - +
337C ALA* 3.2 32.0 - - + +
338C ALA* 3.5 9.4 - - - +
341C SER* 3.7 21.1 + - - -
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Residues in contact with LEU 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C ALA 3.0 24.0 + - - +
327C MET* 3.4 7.6 - - + +
329C HIS* 1.3 79.9 - - - +
331C LYS* 1.3 60.1 + - + +
333C GLN* 3.0 21.2 + - - +
335C PHE* 3.5 39.0 - - + -
338C ALA* 3.7 13.5 - - + -
358C ARG* 3.8 37.0 - - + +
361C GLU* 4.4 11.2 - - + -
362C ALA* 4.0 15.3 - - - +
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Residues in contact with LYS 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C PHE* 4.1 15.5 - - + -
286C TYR* 3.5 50.3 - - + +
327C MET* 2.8 23.1 + - + +
328C CYS 3.9 2.9 - - - +
330C LEU* 1.3 78.3 - - + +
332C LEU* 1.3 59.7 + - - +
333C GLN* 3.3 9.3 - - - +
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Residues in contact with LEU 332 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C TYR* 3.7 31.6 - - + -
287C LYS* 4.2 26.7 - - + +
290C LEU* 3.6 31.9 - - + -
328C CYS 2.9 21.1 + - - +
329C HIS* 2.9 10.5 + - - +
331C LYS* 1.3 76.4 - - - +
333C GLN* 1.3 79.4 + - - +
334C ALA* 3.4 7.0 + - + +
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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