Contacts of the helix formed by residues 240 - 255 (chain M) in PDB entry 1PRC
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 GLY 240 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118H ALA* 3.5 12.8 - - - -
120H ARG* 3.7 14.8 - - - -
236H ASP* 4.5 0.4 - - - -
235M GLN* 3.2 18.1 + - - -
239M ARG* 1.3 76.9 - - - +
241M THR* 1.3 69.6 + - - -
242M ALA* 3.1 3.4 - - - -
243M VAL* 3.0 2.6 + - - +
244M GLU* 2.8 21.3 + - - +
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Residues in contact with THR 241 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H SER 3.4 15.1 + - - +
118H ALA* 3.4 4.2 - - - +
236H ASP* 2.6 37.1 + - + +
9L TYR* 3.1 15.7 + - - -
227M PHE* 3.5 33.2 - - + -
240M GLY* 1.3 71.7 - - - -
242M ALA* 1.3 59.4 + - - +
244M GLU* 4.0 7.2 - - - -
245M ARG* 2.5 63.0 + - - +
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Residues in contact with ALA 242 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224M VAL* 3.7 15.7 - - + +
227M PHE* 3.5 33.4 + - + +
229M GLY* 3.6 29.4 - - - -
235M GLN* 3.8 10.5 - - - +
241M THR* 1.3 83.5 - - - +
243M VAL* 1.3 59.1 + - - +
246M ALA* 2.8 27.9 + - - +
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Residues in contact with VAL 243 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H GLU* 5.7 2.2 - - + +
221M ILE* 5.8 1.8 - - + -
224M VAL* 5.9 0.7 - - + -
229M GLY* 5.1 4.3 - - - +
235M GLN* 3.3 42.3 + - + +
239M ARG* 3.6 25.4 - - + -
240M GLY 3.0 4.5 + - - +
242M ALA* 1.3 75.5 - - + +
244M GLU* 1.3 70.7 + - - +
246M ALA* 3.5 5.3 - - + +
247M ALA* 2.7 27.0 + - - +
260M ILE* 3.7 42.2 - - + +
608M MQ7 4.6 6.9 - - + -
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Residues in contact with GLU 244 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H GLU* 4.3 1.0 - - - +
118H ALA* 3.7 24.2 - - - +
119H GLU 5.0 0.7 + - - -
5L PHE* 3.7 30.9 - - + +
8L LYS* 3.2 16.9 + - - -
9L TYR* 2.4 39.4 + - + +
239M ARG* 2.9 39.9 + - + +
240M GLY 2.8 19.8 + - - +
241M THR 3.5 2.2 - - - +
243M VAL* 1.3 80.4 - - - +
245M ARG* 1.3 63.1 + - - +
247M ALA* 3.2 1.2 + - - -
248M LEU* 3.1 26.8 + - - +
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Residues in contact with ARG 245 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H PRO* 2.5 37.2 + - - +
116H SER* 3.0 27.7 + - - +
240H ALA* 3.6 11.5 - - - +
243H ALA* 3.9 3.8 - - - +
9L TYR* 3.9 18.8 - - + -
111L LEU* 2.8 48.3 + - + +
112L GLY* 4.2 0.2 - - - -
113L ILE* 4.0 14.8 - - + -
224M VAL* 4.4 0.9 - - + -
227M PHE* 3.6 39.5 - - - -
241M THR* 2.5 36.5 + - - +
242M ALA 3.7 2.5 - - - +
244M GLU* 1.3 71.3 - - - +
246M ALA* 1.3 67.4 + - - +
247M ALA 3.0 0.3 + - - -
248M LEU* 3.2 2.5 + - - +
249M PHE* 2.9 25.6 + - - +
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Residues in contact with ALA 246 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113L ILE* 5.5 1.6 - - - -
220M THR* 3.5 28.9 - - + -
221M ILE* 5.5 1.3 - - + -
224M VAL* 4.2 15.6 - - + +
242M ALA 2.8 17.5 + - - +
243M VAL* 3.1 5.8 + - + +
245M ARG* 1.3 76.6 - - - +
247M ALA* 1.3 58.4 + - - +
249M PHE* 3.6 8.6 + - - +
250M TRP* 3.1 28.0 - - - -
608M MQ7 4.0 15.0 - - + -
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Residues in contact with ALA 247 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L LEU* 5.3 0.2 - - + -
5L PHE* 4.6 14.1 - - + -
243M VAL 2.7 20.0 + - - +
244M GLU 3.9 2.9 - - - +
246M ALA* 1.3 72.9 - - - +
248M LEU* 1.3 61.0 + - - +
250M TRP 3.4 1.4 + - - -
251M ARG* 2.8 27.5 + - - +
257M ASN* 3.3 28.6 - - - +
258M ALA 3.9 9.9 - - - +
259M THR* 5.6 0.7 - - - -
608M MQ7 4.1 10.5 - - + -
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Residues in contact with LEU 248 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L LEU* 3.5 29.2 - - + -
5L PHE* 3.9 6.1 - - + -
6L GLU* 3.4 38.4 - - + -
9L TYR* 3.3 45.8 - - + -
111L LEU* 4.2 8.5 - - + -
244M GLU 3.1 13.6 + - - +
245M ARG 4.0 2.2 - - - +
247M ALA* 1.3 73.9 - - - +
249M PHE* 1.3 67.0 + - - +
251M ARG* 3.7 6.5 - - - -
252M TRP* 2.8 41.7 + - + +
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Residues in contact with PHE 249 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104L GLU* 3.9 30.3 - - + -
107L ILE* 4.0 15.2 - - + +
108L SER* 3.5 25.6 - - - -
111L LEU* 3.6 19.7 - - + +
113L ILE* 4.2 17.9 - - + -
117L VAL* 3.7 31.6 - - + -
118L PRO* 4.6 0.2 - - + -
220M THR* 5.8 0.9 - - + -
245M ARG 2.9 13.2 + - - +
246M ALA* 4.0 5.2 - - - +
247M ALA 3.2 0.4 - - - -
248M LEU* 1.3 80.4 - - - +
250M TRP* 1.3 106.7 + + - +
252M TRP 4.0 0.5 - - - -
253M THR* 2.9 36.0 + - - -
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Residues in contact with TRP 250 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104L GLU* 4.7 2.2 - - - -
117L VAL* 3.7 21.1 - - + -
606L BPB 3.6 37.5 - - - -
216M ALA* 3.7 26.9 - - + -
220M THR* 2.7 31.4 + - + +
246M ALA 3.1 22.2 + - - -
247M ALA 3.4 6.5 + - - +
249M PHE* 1.3 99.2 - + - +
251M ARG* 1.3 66.7 + - - +
253M THR* 4.5 2.0 - - + -
254M ILE* 3.0 38.2 + - + +
256M PHE 3.1 14.8 - - - +
257M ASN* 4.3 0.2 - - + -
608M MQ7 3.3 55.4 - + + +
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Residues in contact with ARG 251 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H TYR* 3.5 18.2 + - - -
43H LEU* 4.0 13.1 - - - +
617H SO4 3.5 18.3 + - - -
1L ALA 4.0 17.6 + - - -
3L LEU* 3.6 30.8 - - - +
6L GLU* 3.6 22.8 + - - -
10L ARG* 5.5 0.2 - - - +
28L PRO* 3.6 30.4 - - + +
247M ALA 2.8 19.0 + - - +
248M LEU* 3.7 11.2 - - - +
250M TRP* 1.3 78.6 - - - +
252M TRP* 1.3 61.7 + - + +
255M GLY* 2.8 36.8 + - - +
256M PHE* 3.6 9.5 + - - +
257M ASN* 3.3 21.4 + - + +
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Residues in contact with TRP 252 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L GLU* 2.4 33.8 + - - -
9L TYR* 4.0 17.9 - - + -
10L ARG* 3.8 15.5 - - + -
25L TRP* 3.4 33.3 - + - +
28L PRO 3.3 19.7 - - - +
29L TYR* 3.8 2.2 - - - -
30L PHE* 3.1 22.8 + - + -
103L ARG* 2.9 19.9 + - - -
107L ILE* 3.9 24.8 - - + +
110L LYS* 4.0 12.8 - - + -
111L LEU* 3.6 33.9 - - + -
248M LEU* 2.8 39.7 + - + +
249M PHE 4.1 2.7 - - - +
251M ARG* 1.3 85.0 - - + +
253M THR* 1.3 58.7 + - - +
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Residues in contact with THR 253 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L TYR* 3.9 6.1 - - - -
100L TRP* 3.7 24.0 - - + +
103L ARG* 3.4 28.9 + - - +
104L GLU* 3.7 32.6 - - + +
107L ILE* 3.2 16.6 - - - +
606L BPB 4.3 0.4 - - - +
249M PHE* 2.9 24.8 + - - -
250M TRP* 4.0 7.4 - - + -
251M ARG 3.3 0.2 - - - -
252M TRP* 1.3 78.5 - - - +
254M ILE* 1.3 76.0 + - + +
255M GLY 3.5 0.6 + - - -
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Residues in contact with ILE 254 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L TYR* 3.6 12.2 + - - -
100L TRP* 4.4 4.9 - - + -
606L BPB 3.8 30.1 - - - +
250M TRP* 3.0 24.7 + - + +
253M THR* 1.3 93.8 - - + +
255M GLY* 1.3 57.9 + - - +
256M PHE* 3.3 56.9 + - + +
608M MQ7 3.9 49.1 - - + +
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Residues in contact with GLY 255 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617H SO4 4.3 9.5 + - - -
28L PRO* 3.6 24.1 - - - +
29L TYR* 3.6 24.3 - - - -
251M ARG* 2.8 23.9 + - - +
253M THR 3.5 1.6 - - - -
254M ILE* 1.3 77.2 - - - +
256M PHE* 1.3 61.3 + - - +
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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