Contacts of the helix formed by residues 302 - 321 (chain X) in PDB entry 1M6E
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 TYR 302 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297X VAL 4.6 4.5 - - - +
298X GLU* 5.0 1.1 - - - -
300X GLU 2.8 3.4 + - - -
301X GLY* 1.3 78.3 - - - +
303X ASN* 1.3 59.8 + - - +
304X VAL 3.2 0.7 - - - -
305X ALA* 2.7 15.0 + - + +
306X ARG* 2.6 80.9 + - + +
333X LYS* 3.7 37.1 - - + +
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Residues in contact with ASN 303 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X ASN* 5.3 1.9 + - - +
286X SER* 3.7 24.6 - - - +
287X CYS* 3.1 25.0 - - - +
290X ASP* 4.4 11.0 + - - +
298X GLU* 3.5 17.5 + - - +
299X GLU 3.8 9.6 - - - +
301X GLY 3.0 4.9 + - - -
302X TYR* 1.3 82.7 - - - +
304X VAL* 1.3 59.6 + - - +
306X ARG* 4.3 21.7 - - - +
307X CYS* 3.5 19.6 + - - +
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Residues in contact with VAL 304 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225X ILE* 4.1 10.5 - - + -
284X TRP* 3.5 51.8 - - + +
286X SER* 3.3 24.2 - - - +
300X GLU* 2.9 33.3 + - + +
303X ASN* 1.3 77.1 - - - +
305X ALA* 1.3 59.8 + - - +
307X CYS* 3.8 2.7 - - + +
308X MET* 3.3 26.3 + - + +
336X ILE* 4.1 13.4 - - + +
347X PHE* 5.6 3.8 - - + -
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Residues in contact with ALA 305 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300X GLU 3.6 1.6 + - - -
302X TYR* 2.7 19.9 + - + +
304X VAL* 1.3 76.5 - - - +
306X ARG* 1.3 53.5 + - + +
307X CYS 3.0 1.3 - - - -
308X MET* 2.8 7.6 + - - +
309X ARG* 2.6 38.8 + - - +
329X PHE* 4.5 8.5 - - + +
332X TYR* 4.9 6.1 - - + -
333X LYS* 4.1 20.0 - - + +
336X ILE* 3.9 19.5 - - + +
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Residues in contact with ARG 306 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16X ASN* 4.1 23.6 - - - +
17X SER* 5.0 0.5 + - - -
20X MET* 4.4 11.9 + - - +
21X ASN* 3.0 39.1 + - - +
302X TYR* 2.6 74.2 + - + +
303X ASN* 4.3 13.5 - - - +
305X ALA* 1.3 72.4 - - + +
307X CYS* 1.3 55.8 + - - +
309X ARG* 3.5 14.5 - - - +
310X ALA* 2.9 28.9 + - - +
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Residues in contact with CYS 307 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21X ASN* 3.6 22.4 - - + +
24X ILE* 5.6 4.3 - - - -
25X GLN* 3.6 25.4 - - - -
286X SER* 4.6 9.4 - - - +
303X ASN 3.5 18.9 + - - +
304X VAL* 3.8 7.4 - - - +
305X ALA 3.0 0.4 - - - -
306X ARG* 1.3 75.1 - - - +
308X MET* 1.3 63.6 + - - +
309X ARG 2.9 4.0 - - - -
310X ALA* 3.3 2.3 + - - +
311X VAL* 2.8 43.0 + - - +
347X PHE* 6.4 1.1 - - - -
2000X SAL 5.1 7.4 - - - -
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Residues in contact with MET 308 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225X ILE* 3.7 18.2 - - + -
226X TRP* 3.3 46.9 - - + -
304X VAL* 3.3 18.5 + - + +
305X ALA 2.8 2.9 + - - +
307X CYS* 1.3 81.7 - - - +
309X ARG* 1.3 57.4 + - - +
311X VAL* 3.8 7.2 - - + -
312X ALA* 3.2 27.1 + - + +
329X PHE* 3.8 6.9 - - - -
332X TYR* 3.5 38.9 - - + +
347X PHE* 5.8 1.1 - - + -
2000X SAL 3.5 35.9 - - + -
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Residues in contact with ARG 309 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16X ASN 5.5 0.2 - - - -
17X SER* 4.2 17.6 + - - -
305X ALA 2.6 18.8 + - - +
306X ARG* 3.5 15.5 - - - +
307X CYS 2.9 0.2 - - - -
308X MET* 1.3 72.0 - - - +
310X ALA* 1.3 57.3 + - - +
311X VAL 2.9 4.9 - - - -
313X GLU* 2.7 54.5 + - + +
325X ILE* 3.6 23.0 + - - +
326X GLU* 4.9 7.5 + - - +
329X PHE* 3.4 54.7 - - + +
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Residues in contact with ALA 310 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X LYS* 3.2 9.2 - - - +
11X GLY* 2.9 28.2 + - - +
17X SER* 3.9 14.1 - - - -
18X TYR* 3.3 41.5 - - + +
21X ASN* 4.4 3.8 - - + -
306X ARG 2.9 17.2 + - - +
307X CYS 3.8 3.8 - - - +
309X ARG* 1.3 76.9 - - - +
311X VAL* 1.3 59.5 + - - +
313X GLU* 4.7 0.9 - - - -
314X PRO* 4.5 1.7 - - - +
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Residues in contact with VAL 311 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8X HIS* 5.8 0.5 + - - +
9X MET 4.3 4.0 - - - +
10X LYS* 3.5 28.5 + - + -
18X TYR* 4.3 9.9 - - + -
21X ASN 5.8 0.2 - - - +
25X GLN* 5.1 0.4 - - - +
151X TRP* 4.2 7.4 - - + -
226X TRP* 4.9 0.9 - - + -
307X CYS* 2.8 37.8 + - - +
308X MET* 4.1 13.0 - - + -
309X ARG 2.9 0.4 - - - -
310X ALA* 1.3 82.4 - - - +
312X ALA* 1.3 60.7 + - + +
313X GLU 3.9 0.2 - - - -
314X PRO* 4.5 2.7 - - - +
315X LEU* 4.5 8.5 - - - +
2000X SAL 3.6 52.7 - - + +
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Residues in contact with ALA 312 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226X TRP* 4.0 31.0 - - + -
229X LEU* 5.5 1.1 - - + -
308X MET* 3.2 17.2 + - + +
311X VAL* 1.3 77.4 - - - +
313X GLU* 1.3 69.6 + - - +
314X PRO* 2.9 5.9 - - - -
315X LEU* 3.0 23.7 + - + +
316X LEU* 3.1 24.8 + - + +
329X PHE* 5.0 0.4 - - + -
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Residues in contact with GLU 313 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X GLY* 5.4 6.5 - - - -
309X ARG* 2.7 50.6 + - + +
310X ALA* 5.2 0.4 - - - -
312X ALA* 1.3 71.3 - - - +
314X PRO* 1.4 61.8 - - + +
316X LEU* 3.7 2.7 - - - +
317X LEU* 2.8 49.2 + - - +
322X GLU* 5.5 1.7 - - - +
325X ILE* 4.0 37.6 - - + +
329X PHE* 4.3 10.4 - - + -
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Residues in contact with PRO 314 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X LEU* 3.7 9.5 - - - +
8X HIS* 5.0 1.3 - - + -
9X MET* 3.5 54.7 - - + +
11X GLY* 4.6 10.5 - - - +
309X ARG 4.3 1.6 - - - +
310X ALA 4.5 3.6 - - - +
311X VAL 4.5 1.8 - - - +
312X ALA* 3.2 8.7 - - - +
313X GLU* 1.4 98.0 - - + +
315X LEU* 1.3 65.0 + - + +
316X LEU 3.2 1.3 - - - -
317X LEU* 4.1 8.2 - - + +
318X ASP* 3.0 27.0 + - - +
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Residues in contact with LEU 315 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X ARG* 3.0 32.6 + - - +
7X LEU* 3.6 11.4 - - + +
8X HIS* 3.5 32.3 - - + +
9X MET 6.0 0.2 - - - +
151X TRP* 3.8 29.6 - - + -
226X TRP* 5.0 4.9 - - + -
251X ASN* 4.4 7.6 - - - +
253X PRO* 5.3 5.8 - - + -
254X GLN* 4.1 8.7 - - - +
311X VAL 4.5 2.7 - - - +
312X ALA* 3.0 26.5 + - + +
314X PRO* 1.3 77.7 - - + +
316X LEU* 1.3 64.4 + - + +
318X ASP* 3.7 2.8 + - - +
319X HIS* 3.2 22.0 + - - +
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Residues in contact with LEU 316 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229X LEU* 4.4 27.8 - - + -
233X LEU* 4.6 8.5 - - + -
251X ASN* 3.9 23.3 - - - +
312X ALA* 3.1 17.0 + - + +
313X GLU* 3.7 4.3 - - - +
315X LEU* 1.3 76.2 - - + +
317X LEU* 1.3 54.2 + - - +
318X ASP 2.9 4.0 - - - -
319X HIS* 2.5 24.5 + - - -
320X PHE* 2.6 38.3 + - + -
321X GLY 4.7 0.2 - - - -
324X ILE* 6.4 1.1 - - + -
325X ILE* 5.3 6.5 - - + -
328X VAL* 4.8 9.9 - - + -
329X PHE* 3.6 37.0 - - + -
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Residues in contact with LEU 317 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313X GLU* 2.8 35.5 + - - +
314X PRO* 4.1 6.3 - - + +
316X LEU* 1.3 72.4 - - - +
318X ASP* 1.3 57.9 + - - +
321X GLY* 3.0 24.7 + - - +
322X GLU* 3.0 53.4 - - + +
325X ILE* 3.0 24.8 - - + +
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Residues in contact with ASP 318 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2X ASP* 3.7 5.9 - - - +
7X LEU* 2.8 39.7 - - + +
314X PRO 3.0 18.6 + - - +
315X LEU 3.9 2.0 - - - +
316X LEU 2.9 1.2 - - - -
317X LEU* 1.3 80.5 - - + +
319X HIS* 1.3 58.1 + - - +
321X GLY 4.8 0.4 - - - -
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Residues in contact with HIS 319 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2X ASP* 3.7 26.0 + - - +
247X MET* 3.1 36.6 + - - +
250X PHE* 3.6 24.6 - + + +
251X ASN* 3.3 25.4 + - + +
315X LEU 3.2 15.0 + - - +
316X LEU 2.5 11.1 + - - +
318X ASP* 1.3 75.0 - - - +
320X PHE* 1.3 85.4 + + + +
321X GLY 4.0 0.2 - - - -
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Residues in contact with PHE 320 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233X LEU* 4.5 10.5 - - + -
242X ILE* 3.8 19.2 - - - +
243X GLU* 3.6 26.5 - - + -
247X MET* 3.6 29.0 - - + +
248X ASP* 3.7 30.5 - - - -
251X ASN* 3.6 27.6 - - + -
316X LEU* 2.6 39.8 + - + +
319X HIS* 1.3 98.7 - + + +
321X GLY* 1.3 60.8 + - - +
324X ILE* 3.2 21.3 - - + +
325X ILE* 6.4 0.2 - - + -
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Residues in contact with GLY 321 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317X LEU* 3.0 27.1 + - - -
318X ASP 4.8 0.2 - - - -
320X PHE* 1.3 82.5 - - - +
322X GLU* 1.3 64.8 + - - -
323X ALA* 3.4 3.6 + - - -
324X ILE* 3.6 7.8 + - - +
325X ILE* 3.6 12.1 - - - +
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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