Contacts of the helix formed by residues 316 - 335 (chain B) in PDB entry 1NOY
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 ARG 316 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B ASP* 3.3 13.1 + - - -
171B GLY 5.6 0.6 - - - -
172B GLY 2.9 29.1 + - - -
173B ASP* 2.8 32.9 + - - +
300B LEU* 3.2 35.0 - - - +
301B PRO 3.4 22.2 + - - -
302B TYR* 4.9 3.5 + - - +
303B ASP* 5.7 3.7 - - - +
309B LEU* 4.5 7.6 - - + -
313B ASN* 3.6 31.7 + - - +
314B HIS 2.5 10.1 + - - -
315B GLN* 1.3 71.8 - - - +
317B TYR* 1.3 65.3 + - - +
319B SER* 3.2 2.1 + - - -
320B TYR* 2.8 51.8 + - + +
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Residues in contact with TYR 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU* 3.8 30.0 + - + +
115B VAL 3.8 0.7 + - - -
116B THR* 2.7 13.2 + - - -
131B ASP* 2.6 42.2 + - + -
132B ALA* 5.0 0.4 - - + -
307B ASN 5.0 3.1 - - - -
309B LEU* 3.5 34.1 - - + +
310B ARG* 3.6 26.5 - - + -
313B ASN 3.4 14.0 + - - +
314B HIS* 3.9 15.0 - + - -
315B GLN 4.3 0.2 - - - +
316B ARG* 1.3 76.6 - - - +
318B ILE* 1.3 71.5 + - + +
320B TYR* 2.9 27.1 + - + +
321B ASN* 3.1 6.6 + - - +
5S T 3.6 17.1 + - - -
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Residues in contact with ILE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ASP 4.7 0.2 - - - +
132B ALA* 3.4 31.6 - - + -
145B VAL* 3.7 25.8 - - + -
147B ASP* 3.4 34.5 - - + +
159B TRP* 3.6 32.1 - - + +
185B TYR* 4.6 0.7 - - + -
314B HIS* 3.8 19.7 - - + +
315B GLN 3.5 1.0 + - - +
316B ARG 3.4 0.4 - - - -
317B TYR* 1.3 83.5 - - + +
319B SER* 1.3 66.7 + - - +
321B ASN* 3.0 13.9 + - + +
322B ILE* 3.0 22.2 + - + +
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Residues in contact with SER 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B TRP* 2.9 24.7 + - - +
164B ALA* 3.0 9.2 - - - +
173B ASP* 2.9 30.1 + - - -
175B VAL* 3.7 15.7 - - - +
315B GLN 3.0 9.8 + - - -
316B ARG 3.2 5.4 + - - -
318B ILE* 1.3 76.9 - - - +
320B TYR* 1.3 59.9 + - - +
322B ILE* 3.4 10.5 + - - +
323B ILE* 2.9 33.5 + - - +
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Residues in contact with TYR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU* 5.1 3.8 - - - +
173B ASP* 5.6 3.4 - - + -
299B LYS* 3.4 46.9 - - + +
300B LEU* 2.5 31.5 + - + -
301B PRO 3.5 13.0 + - - -
302B TYR* 4.3 9.5 + + - -
309B LEU* 3.7 31.0 - - + -
316B ARG* 2.8 37.0 + - + -
317B TYR 3.0 12.1 - - - +
319B SER* 1.3 76.2 - - - +
321B ASN* 1.3 63.6 + - - +
323B ILE* 3.0 9.6 + - + +
324B ASP* 2.9 29.9 + - - +
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Residues in contact with ASN 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASP* 2.8 24.1 + - - +
114B GLU* 3.3 38.1 + - + +
132B ALA* 3.9 6.0 - - + +
133B ILE 3.7 9.7 - - - +
134B THR* 2.6 40.4 + - - +
145B VAL* 5.0 2.2 - - - +
317B TYR 3.1 3.9 + - - +
318B ILE* 3.0 16.1 + - - +
320B TYR* 1.3 78.4 - - - +
322B ILE* 1.3 60.8 + - - +
324B ASP* 3.4 2.9 + - - +
325B VAL* 3.2 22.7 + - - +
2000B ZN 4.5 2.7 - - - -
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Residues in contact with ILE 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B THR* 3.9 24.0 - - + +
143B PHE* 4.7 6.7 - - + -
145B VAL* 4.6 7.0 - - + -
159B TRP* 5.0 7.2 - - + -
175B VAL* 4.5 11.7 - - + -
179B ILE* 3.1 35.4 - - + -
180B LEU* 4.7 4.3 - - + -
183B VAL* 3.3 28.3 - - + -
318B ILE* 3.0 25.5 + - + +
319B SER* 3.6 13.9 - - - +
321B ASN* 1.3 71.2 - - - +
323B ILE* 1.3 68.1 + - - +
325B VAL* 3.0 4.2 + - - +
326B GLU* 3.0 20.3 + - - +
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Residues in contact with ILE 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASP* 6.2 1.6 - - + -
174B GLU 5.0 5.2 - - - +
175B VAL* 4.2 35.7 - - + +
176B PRO* 5.2 4.0 - - + -
179B ILE* 5.1 7.1 - - + +
298B GLY 5.0 6.7 - - - +
299B LYS* 3.4 45.3 - - + -
300B LEU 5.6 1.1 - - - +
319B SER 2.9 17.2 + - - +
320B TYR* 3.4 10.5 - - + +
322B ILE* 1.3 79.7 - - - +
324B ASP* 1.3 59.4 + - - +
326B GLU* 3.2 7.1 + - - +
327B SER* 3.1 29.3 + - - +
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Residues in contact with ASP 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASP* 4.2 10.6 - - - +
287B LEU* 3.5 26.1 - - + +
288B GLU* 3.6 9.6 - - - +
299B LYS* 2.8 36.6 + - - +
320B TYR 2.9 11.9 + - - +
321B ASN 3.8 4.9 - - - +
323B ILE* 1.3 73.8 - - - +
325B VAL* 1.3 64.0 + - - +
327B SER* 2.7 23.1 + - - -
328B VAL* 3.6 7.6 + - - +
2000B ZN 2.6 30.2 - - - -
5S T 3.9 3.5 + - - -
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Residues in contact with VAL 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASN* 3.2 28.0 - - - +
111B CYS 4.2 1.6 - - - -
112B ASP* 3.2 40.2 - - + +
134B THR* 3.8 23.6 - - + +
136B TYR* 3.8 32.5 - - + +
143B PHE* 4.3 3.8 - - + -
321B ASN 3.2 9.1 + - - +
322B ILE 3.0 7.6 + - - +
324B ASP* 1.3 77.0 - - - +
326B GLU* 1.3 63.4 + - - +
328B VAL* 3.7 7.5 + - - +
329B GLN* 3.9 6.1 + - - +
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Residues in contact with GLU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B PHE* 3.5 34.5 - - + -
179B ILE* 3.7 32.8 - - + +
182B ARG* 4.3 8.6 + - - +
322B ILE 3.0 10.0 + - - +
323B ILE 3.2 7.9 + - - +
325B VAL* 1.3 76.9 - - - +
327B SER* 1.3 67.6 + - - +
329B GLN* 2.9 9.7 + - + +
330B ALA* 2.9 30.6 + - - +
333B LYS* 3.9 20.3 + - - -
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Residues in contact with SER 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B LEU* 3.6 12.4 - - - +
291B ALA* 3.9 25.6 - - - +
295B THR* 5.5 2.7 - - - -
323B ILE* 3.1 12.8 + - - +
324B ASP* 2.7 30.0 + - - -
326B GLU* 1.3 79.1 + - - +
328B VAL* 1.3 54.2 + - - +
330B ALA* 3.3 10.2 - - - +
331B ILE* 2.8 37.4 + - - +
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASN* 3.8 31.9 - - + +
112B ASP* 6.0 1.1 - - - +
211B THR* 4.9 2.0 - - + -
212B GLY* 4.4 19.1 - - - +
213B TRP* 4.5 17.7 - - + +
270B TYR* 4.1 32.1 - - + -
287B LEU* 4.6 5.6 - - + -
324B ASP 3.6 13.2 + - - +
325B VAL* 3.9 1.6 - - - +
326B GLU 3.1 0.8 + - - -
327B SER* 1.3 77.5 + - - +
329B GLN* 1.3 66.4 + - - +
331B ILE* 3.2 9.7 + - - +
332B ASP* 2.9 22.8 + - + +
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Residues in contact with GLN 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ARG* 5.0 6.1 + - - -
108B VAL* 4.4 19.1 + - - +
110B ASN* 2.8 32.5 - - - +
136B TYR* 3.1 38.8 - - + -
138B SER* 5.1 1.8 - - - -
143B PHE* 5.6 0.9 - - + -
211B THR* 5.5 1.2 - - - +
325B VAL 4.1 6.5 - - - +
326B GLU* 2.9 13.8 + - + +
328B VAL* 1.3 81.7 - - - +
330B ALA* 1.3 57.0 + - - +
332B ASP* 3.3 12.8 + - - +
333B LYS* 2.9 47.5 + - - +
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Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B THR* 3.5 21.5 - - + -
326B GLU* 2.9 25.1 + - - +
327B SER* 3.1 13.4 + - - +
329B GLN* 1.3 75.5 - - - +
331B ILE* 1.3 64.4 + - - +
333B LYS* 3.4 14.1 + - - +
334B ILE* 3.0 27.4 + - - +
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Residues in contact with ILE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TRP* 4.0 15.7 - - + -
270B TYR* 3.9 21.3 - - + -
274B TYR* 4.3 12.3 - - + -
287B LEU* 4.0 17.9 - - + -
290B VAL* 3.7 21.5 - - + -
291B ALA* 4.1 11.4 - - - +
294B GLU* 4.3 19.5 - - + -
295B THR* 4.6 2.7 - - + -
327B SER 2.8 23.6 + - - +
328B VAL* 3.5 5.8 - - - +
330B ALA* 1.3 70.5 - - - +
332B ASP* 1.3 59.4 + - - +
334B ILE* 2.9 16.4 + - - +
335B ARG* 2.8 37.9 + - + +
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Residues in contact with ASP 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ARG* 2.8 34.1 + - - -
270B TYR* 2.6 32.7 + - + +
328B VAL* 2.9 13.1 + - + +
329B GLN* 3.6 15.8 - - - +
331B ILE* 1.3 78.0 - - - +
333B LYS* 1.3 59.9 + - - +
336B GLY* 2.6 30.7 + - - +
337B PHE 3.0 20.3 + - - -
338B ILE* 3.3 20.3 + - - +
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Residues in contact with LYS 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B ARG* 5.8 6.7 - - - +
326B GLU* 3.9 19.8 + - - -
329B GLN* 2.9 39.6 + - - +
330B ALA* 3.8 10.4 - - - +
331B ILE 3.3 0.4 - - - -
332B ASP* 1.3 74.0 - - - +
334B ILE* 1.3 61.3 + - + +
336B GLY* 4.9 0.3 + - - -
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Residues in contact with ILE 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B GLU* 3.6 56.5 - - + +
295B THR* 3.9 11.2 - - + -
330B ALA 3.0 17.5 - - - +
331B ILE* 2.9 6.8 + - - +
333B LYS* 1.3 82.2 - - + +
335B ARG* 1.3 66.1 + - - +
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Residues in contact with ARG 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A HIS* 4.5 13.1 + - - -
56A ALA* 5.0 5.4 - - - +
270B TYR* 4.3 3.1 - - - +
274B TYR* 4.3 2.9 - - + -
277B PHE 5.7 0.4 + - - -
278B ALA* 3.1 33.2 + - - +
280B THR* 3.2 24.5 - - - +
293B HIS* 5.4 0.8 - - - -
294B GLU* 3.3 31.9 + - - +
331B ILE* 2.8 28.7 + - + +
334B ILE* 1.3 81.1 - - - +
336B GLY* 1.3 62.9 + - - +
337B PHE* 3.4 45.6 + - + -
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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
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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