Contacts of the helix formed by residues 316 - 339 (chain C) in PDB entry 3RMD
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 316 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C LEU* 3.1 21.6 + - + +
315C SER* 1.3 83.4 - - - +
317C HIS* 1.3 60.9 + - - +
318C GLN* 3.0 11.8 + - - +
319C ARG* 3.1 33.5 + - + +
320C TYR 3.1 15.8 + - - -
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Residues in contact with HIS 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C ASP 5.2 0.2 + - - -
150C ASP* 3.1 40.0 + - - -
151C LEU 3.7 1.6 + - - -
152C LEU* 5.2 0.4 - - - +
159C VAL* 3.1 41.7 - - + +
160C GLU 3.8 13.4 + - - -
161C GLU 5.1 3.4 + - - -
162C TRP* 5.0 1.7 + - - -
188C TYR* 4.5 1.8 - - - -
313C ARG* 3.0 54.9 + - - +
314C GLU 3.7 2.8 + - - +
316C ASN* 1.3 71.8 - - - +
318C GLN* 1.3 65.0 + - - +
320C TYR* 3.5 7.2 - + - +
321C ILE* 3.4 35.1 + - + +
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Residues in contact with GLN 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C GLU 4.2 4.0 + - - -
162C TRP* 3.3 23.1 - - - +
163C SER 2.9 45.0 + - - +
166C ILE* 3.1 38.3 - - + +
176C ASP* 3.2 22.2 - - - +
316C ASN* 3.0 10.4 + - - +
317C HIS* 1.3 82.4 - - - +
319C ARG* 1.3 64.9 + - - +
321C ILE 3.3 4.5 + - - -
322C SER* 2.9 15.8 + - - -
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Residues in contact with ARG 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C GLN* 4.3 12.5 + - - +
174C GLY 5.3 1.4 - - - -
175C GLY 2.8 26.6 + - - +
176C ASP* 3.4 26.9 + - - +
303C LEU* 3.0 50.3 - - - +
304C LYS 5.5 4.7 + - - -
305C TYR* 4.0 26.3 - - + +
312C LEU* 4.5 3.1 - - + -
316C ASN* 3.1 30.1 + - + +
318C GLN* 1.3 79.1 - - - +
320C TYR* 1.3 56.7 + - - +
322C SER* 2.8 6.5 + - - -
323C TYR* 2.7 41.8 + - + +
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Residues in contact with TYR 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C GLU* 3.4 32.2 + - + +
117C VAL 3.9 7.1 + - - -
118C THR* 3.4 9.9 + - - -
134C ASP* 2.5 30.4 + - - -
135C ALA* 4.1 7.2 - - + -
309C ILE* 4.5 12.4 - - + +
312C LEU* 3.2 40.7 - - + +
313C ARG* 3.4 34.1 - - + -
316C ASN 3.1 11.1 + - - +
317C HIS* 3.5 16.2 - + - +
319C ARG* 1.3 79.6 - - - +
321C ILE* 1.3 71.9 + - + +
323C TYR* 3.4 12.0 - + - +
324C ASN* 3.4 15.8 + - - +
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Residues in contact with ILE 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C ASP 4.6 0.2 - - - +
135C ALA* 3.9 19.5 - - + -
148C VAL* 4.2 16.6 - - + -
150C ASP* 3.6 26.2 - - + +
162C TRP* 3.5 35.2 - - + -
188C TYR* 4.3 1.8 - - + -
317C HIS* 3.4 27.8 + - + +
318C GLN 3.3 1.8 + - - +
319C ARG 2.9 1.8 + - - -
320C TYR* 1.3 88.4 - - + +
322C SER* 1.3 68.3 + - - +
323C TYR 3.1 0.9 - - - -
324C ASN* 3.1 6.8 + - + +
325C ILE* 3.0 35.0 + - + +
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Residues in contact with SER 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C TRP* 2.9 11.8 + - - +
176C ASP* 2.5 48.9 + - - -
178C VAL* 3.9 10.4 - - - +
318C GLN 2.9 9.4 + - - -
319C ARG* 2.8 7.9 + - - -
321C ILE* 1.3 75.4 - - - +
323C TYR* 1.3 55.0 + - - +
325C ILE* 3.0 11.0 + - - +
326C ILE* 2.5 40.3 + - - +
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Residues in contact with TYR 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ASP* 5.6 1.1 - - - -
116C GLU* 3.5 27.8 - - - -
302C LYS* 3.1 51.5 - - + -
303C LEU* 5.0 1.3 - - + +
305C TYR* 4.2 28.4 + + - -
309C ILE* 5.6 10.0 - - + +
312C LEU* 4.9 10.8 - - + -
319C ARG* 2.7 29.7 + - + +
320C TYR* 3.4 13.9 - + - +
322C SER* 1.3 73.9 - - - +
324C ASN* 1.3 58.3 + - - +
326C ILE* 3.5 11.2 - - - +
327C ALA* 3.1 28.4 + - + +
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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
----------------------------------------------------------
114C ASP* 3.3 26.3 + - - +
116C GLU* 2.8 41.3 - - + +
135C ALA* 3.6 11.7 - - + +
136C ILE 3.6 7.8 + - - -
137C THR* 2.8 28.0 + - - +
148C VAL* 5.6 1.1 - - - +
320C TYR 3.4 5.3 + - - +
321C ILE* 3.1 13.6 + - + +
323C TYR* 1.3 78.3 - - - +
325C ILE* 1.3 64.4 + - - +
327C ALA* 3.2 15.0 - - - +
328C VAL* 3.4 6.4 + - - +
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Residues in contact with ILE 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C THR* 3.9 22.4 - - + +
146C PHE* 4.4 7.2 - - + -
148C VAL* 3.9 22.4 - - + -
162C TRP* 3.8 29.4 - - + -
178C VAL* 5.1 5.6 - - + -
182C ILE* 3.7 24.0 - - + -
186C ILE* 4.1 13.5 - - + -
321C ILE* 3.2 32.1 - - + +
322C SER* 3.0 7.5 + - - +
324C ASN* 1.3 76.7 - - - +
326C ILE* 1.3 63.0 + - + +
328C VAL* 3.4 5.7 + - - +
329C TYR* 3.1 18.9 + - - +
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Residues in contact with ILE 326 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ASP 4.8 5.8 - - - +
177C GLU 5.8 0.7 - - - +
178C VAL* 5.2 7.1 - - + +
179C PRO* 4.4 19.3 - - + -
182C ILE* 5.5 0.9 - - - -
301C GLY 5.1 0.2 - - - +
302C LYS* 3.3 31.6 - - + +
303C LEU* 4.2 29.4 - - + -
319C ARG* 6.0 0.7 - - - -
322C SER* 2.5 31.1 + - - +
323C TYR* 3.4 10.3 - - - +
325C ILE* 1.3 70.6 - - - +
327C ALA* 1.3 67.0 - - - +
329C TYR* 2.9 9.5 + - + +
330C ARG* 2.8 55.8 + - - +
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Residues in contact with ALA 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ASP* 3.8 21.3 - - - +
116C GLU* 5.2 0.7 - - - +
290C LEU* 3.4 23.6 - - + +
302C LYS* 3.6 12.7 - - - +
323C TYR* 3.1 19.8 + - + +
324C ASN* 3.2 13.9 - - - +
326C ILE* 1.3 78.1 - - - +
328C VAL* 1.3 64.0 + - - +
330C ARG* 3.2 15.0 + - - +
331C VAL* 3.5 3.7 + - - +
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Residues in contact with VAL 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ASN* 3.4 34.3 - - - +
113C PHE 4.5 0.7 - - - -
114C ASP* 3.9 18.2 - - + +
137C THR* 3.6 33.2 - - + +
139C TYR* 4.0 8.5 - - + +
146C PHE* 4.0 19.7 - - + -
324C ASN 3.4 14.6 - - - +
325C ILE 3.6 5.8 - - - +
326C ILE 3.2 0.4 - - - -
327C ALA* 1.3 75.7 - - - +
329C TYR* 1.3 64.0 + - - +
330C ARG 3.2 0.7 + - - -
331C VAL* 3.2 15.8 + - - +
332C LEU* 3.2 12.0 + - + +
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Residues in contact with TYR 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C PHE* 3.9 18.8 - + + -
179C PRO* 3.6 36.1 - - + +
181C GLU* 3.9 20.5 - - + +
182C ILE* 3.3 36.1 - - + -
325C ILE 3.1 10.7 + - - +
326C ILE* 2.9 11.5 + - + +
328C VAL* 1.3 79.7 - - - +
330C ARG* 1.3 54.2 + - - +
332C LEU* 3.0 13.7 + - + +
333C GLN* 2.8 81.8 + - + +
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Residues in contact with ARG 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C PRO* 4.5 13.3 - - - +
290C LEU* 4.2 11.4 - - + -
294C SER* 4.1 22.0 - - - -
298C LEU* 3.8 4.2 - - - +
300C VAL* 3.0 44.7 - - - +
301C GLY 2.6 34.4 + - - +
302C LYS* 3.8 13.5 - - - +
303C LEU* 6.1 2.7 - - - +
326C ILE* 2.8 41.8 + - - +
327C ALA* 3.3 8.7 - - - +
328C VAL 3.2 0.2 + - - -
329C TYR* 1.3 71.0 - - - +
331C VAL* 1.3 55.0 + - - +
333C GLN* 2.9 32.0 + - - +
334C ILE* 2.6 40.6 + - - +
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Residues in contact with VAL 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ASN* 3.3 29.8 - - - +
214C THR* 4.8 0.4 - - - +
215C GLY* 4.5 3.8 - - - +
216C TRP* 4.1 21.8 - - + +
273C TYR* 3.8 36.8 - - + -
290C LEU* 4.0 16.4 - - + -
327C ALA 3.5 13.4 + - - +
328C VAL* 3.2 5.1 + - - +
330C ARG* 1.3 75.6 - - - +
332C LEU* 1.3 54.1 + - - +
334C ILE* 3.0 12.1 + - - +
335C ASP* 2.8 33.7 + - + +
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Residues in contact with LEU 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ASN* 3.7 20.4 - - + +
139C TYR* 3.6 42.0 - - + +
146C PHE* 3.4 41.7 - - + -
328C VAL* 3.2 9.2 + - + +
329C TYR* 3.0 17.0 + - + +
331C VAL* 1.3 80.2 - - - +
333C GLN* 1.3 53.4 + - - +
335C ASP* 3.4 7.7 + - + +
336C ALA* 2.7 30.2 + - - +
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Residues in contact with GLN 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C LEU* 3.4 23.7 - - + +
300C VAL* 6.1 1.8 - - - +
329C TYR* 2.8 69.1 + - + +
330C ARG* 3.3 32.3 + - - +
332C LEU* 1.3 71.1 - - - +
334C ILE* 1.3 67.9 + - - +
336C ALA* 3.1 10.1 + - - +
337C LYS* 3.0 23.4 + - - +
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Residues in contact with ILE 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C TRP* 4.1 6.1 - - + -
273C TYR* 4.2 19.1 - - + -
277C TYR* 4.3 15.7 - - + -
290C LEU* 3.7 30.7 - - + -
293C ILE* 4.1 11.9 - - + -
294C SER* 3.9 18.6 - - - -
297C GLU* 4.5 7.4 - - + -
298C LEU* 3.9 23.1 - - + -
330C ARG 2.6 20.9 + - - +
331C VAL* 3.5 7.4 - - - +
333C GLN* 1.3 72.4 - - - +
335C ASP* 1.3 58.9 + - - +
337C LYS* 3.2 3.6 + - - +
338C ARG* 2.8 39.5 + - + +
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Residues in contact with ASP 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ASN* 6.1 0.7 - - - +
273C TYR* 2.8 38.8 + - + +
331C VAL* 2.8 15.7 + - + +
332C LEU* 3.7 9.9 - - + +
334C ILE* 1.3 69.5 - - - +
336C ALA* 1.3 65.8 + - - +
337C LYS 2.9 1.8 - - - -
339C GLN* 2.5 34.9 + - - -
340C PHE 3.1 14.7 + - - -
341C ILE* 3.3 24.1 + - - +
342C ASN 4.9 0.2 + - - -
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Residues in contact with ALA 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C LEU 2.7 22.8 + - - +
333C GLN* 3.2 12.8 - - - +
335C ASP* 1.3 72.5 - - - +
337C LYS* 1.3 58.4 + - - +
339C GLN* 3.3 22.6 + - - +
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Residues in contact with LYS 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C PHE 5.1 0.8 + - - -
297C GLU* 3.0 56.7 + - + +
298C LEU* 4.6 6.1 - - + -
333C GLN 3.0 10.5 + - - +
334C ILE* 3.5 7.0 - - - +
335C ASP 2.9 1.4 - - - -
336C ALA* 1.3 79.7 - - - +
338C ARG* 1.3 76.9 + - + +
339C GLN* 3.5 7.6 + - - +
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Residues in contact with ARG 338 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C TYR* 4.1 1.6 - - - +
277C TYR* 4.6 1.7 - - + -
280C PHE 4.8 1.0 + - - -
281C SER* 3.5 36.4 + - - +
283C THR* 5.2 1.8 - - - +
296C PHE* 6.1 0.2 - - - -
297C GLU* 3.5 34.9 + - - +
334C ILE* 2.8 34.4 + - + +
337C LYS* 1.3 82.8 - - + +
339C GLN* 1.3 73.2 + - - +
340C PHE* 3.3 48.1 + - + -
343C LEU* 5.7 0.9 - - - +
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Residues in contact with GLN 339 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C ASP* 2.5 29.5 + - - -
336C ALA* 3.3 23.3 + - - +
337C LYS 3.7 11.4 - - - +
338C ARG* 1.3 77.0 - - - +
340C PHE* 1.3 61.8 + - - +
341C ILE 3.5 2.0 - - - -
342C ASN* 3.8 17.9 + - + +
343C LEU* 3.3 21.8 + - - +
550C VAL* 4.4 18.0 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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