Contacts of the helix formed by residues 242 - 257 (chain M) in PDB entry 1JH0
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 242 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115H VAL* 3.6 5.8 - - - -
117H ARG* 3.6 22.4 - - - -
231H ASP* 3.9 0.4 - - - -
237M GLN* 2.8 21.6 + - - -
240M ASP 3.2 1.0 + - - -
241M ARG* 1.3 78.6 - - - +
243M THR* 1.3 63.4 + - - -
244M ALA 2.9 6.8 + - - -
245M ALA 3.0 10.6 + - - -
246M GLU* 3.4 11.4 + - - +
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Residues in contact with THR 243 (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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113H SER 3.2 14.8 + - - +
115H VAL* 3.2 15.0 - - - +
231H ASP* 3.0 35.2 + - - +
235H GLY 5.4 0.2 - - - +
9L TYR* 3.1 14.1 + - - -
229M PHE* 3.5 34.5 - - + -
242M GLY* 1.3 70.0 - - - -
244M ALA* 1.3 60.7 + - - +
246M GLU* 3.7 1.4 - - - +
247M ARG* 2.9 56.9 + - - +
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Residues in contact with ALA 244 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226M VAL* 4.0 14.1 - - + +
229M PHE* 3.6 29.6 - - + +
231M GLY* 4.0 18.4 - - - -
237M GLN* 3.4 24.2 - - - +
242M GLY 2.9 0.2 - - - -
243M THR* 1.3 82.0 - - - +
245M ALA* 1.3 58.3 + - - +
248M ALA* 3.1 28.5 + - - +
262M MET* 4.6 2.0 - - + -
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Residues in contact with ALA 245 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5L PHE* 5.2 0.5 - - - -
237M GLN* 3.4 12.3 + - - +
241M ARG* 4.1 15.0 - - + -
242M GLY 3.0 5.9 + - - +
244M ALA* 1.3 76.6 - - - +
246M GLU* 1.3 59.4 + - - +
248M ALA* 3.7 5.1 - - - +
249M ALA* 3.1 27.2 + - - +
262M MET* 3.2 42.6 - - + +
857M U10 3.7 4.6 - - - +
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Residues in contact with GLU 246 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H GLU* 4.6 0.2 - - - +
115H VAL* 3.6 18.6 - - - +
5L PHE* 3.2 33.8 - - + +
8L LYS* 3.2 13.1 + - - -
9L TYR* 2.6 41.7 + - + +
241M ARG* 2.9 43.9 + - - +
242M GLY 3.4 10.7 + - - +
243M THR 3.7 2.0 - - - +
244M ALA 3.3 0.6 - - - -
245M ALA* 1.3 75.1 - - - +
247M ARG* 1.3 61.2 + - - +
249M ALA* 3.1 3.6 + - - +
250M LEU* 2.8 34.2 + - - +
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Residues in contact with ARG 247 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H PRO* 2.7 34.0 + - - +
113H SER 2.5 35.3 + - - +
235H GLY* 3.9 4.0 - - - -
238H ALA* 4.3 1.6 - - - +
9L TYR* 3.8 20.9 - - + -
111L LEU* 3.1 42.1 + - + +
112L GLY* 4.5 0.6 - - - -
113L ILE* 4.1 14.4 - - + -
226M VAL* 4.6 2.9 - - + -
229M PHE* 3.1 43.2 - - - -
243M THR* 2.9 30.3 + - - +
244M ALA 4.2 2.0 - - - +
246M GLU* 1.3 74.4 - - - +
248M ALA* 1.3 63.2 + - - +
250M LEU* 4.3 5.6 - - - -
251M PHE* 2.9 23.9 + - - +
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Residues in contact with ALA 248 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113L ILE* 6.1 0.7 - - - -
222M THR* 3.9 17.7 - - + +
223M ILE* 6.5 0.4 - - + -
226M VAL* 4.3 11.8 - - + +
244M ALA 3.1 20.9 + - - +
245M ALA* 3.7 8.5 - - - +
246M GLU 3.1 0.2 - - - -
247M ARG* 1.3 79.9 - - - +
249M ALA* 1.3 61.7 + - - +
251M PHE* 3.4 7.6 + - - +
252M TRP* 3.4 23.8 + - - -
262M MET* 5.5 1.8 - - + -
857M U10 3.8 24.7 - - - +
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Residues in contact with ALA 249 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L LEU* 5.2 0.7 - - + -
5L PHE* 4.3 16.4 - - + -
245M ALA 3.1 18.0 + - - +
246M GLU 3.1 4.7 + - - +
248M ALA* 1.3 77.7 - - - +
250M LEU* 1.3 58.0 + - - +
252M TRP* 3.4 1.9 + - - -
253M ARG* 3.0 21.7 + - - +
259M ASN* 3.2 25.8 - - - +
260M ALA 3.8 18.6 - - - +
857M U10 3.6 10.9 - - - -
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Residues in contact with LEU 250 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L LEU* 4.1 13.9 - - + -
5L PHE* 4.0 10.1 - - + -
6L GLU* 3.3 42.2 - - + +
9L TYR* 3.2 49.8 - - + -
111L LEU* 3.9 12.3 - - + -
246M GLU 2.8 19.8 + - - +
247M ARG* 3.8 4.0 - - - +
249M ALA* 1.3 72.0 - - - +
251M PHE* 1.3 63.6 + - - +
253M ARG* 3.7 4.3 - - - -
254M TRP* 3.1 43.8 + - + +
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Residues in contact with PHE 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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104L GLU* 3.5 45.5 - - + -
107L ILE* 3.5 18.9 - - + +
108L CYS* 3.9 17.7 - - - -
111L LEU* 3.5 12.1 - - + +
113L ILE* 4.2 14.6 - - + -
117L ILE* 3.7 17.9 - - + -
222M THR* 6.2 0.7 - - + -
247M ARG 2.9 16.2 + - - +
248M ALA* 3.8 5.2 - - - +
249M ALA 3.3 0.4 - - - -
250M LEU* 1.3 78.0 - - - +
252M TRP* 1.3 108.2 + + - +
254M TRP* 4.0 1.7 - - - +
255M THR* 2.9 45.3 + - - -
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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
----------------------------------------------------------
104L GLU* 3.9 2.2 - - - -
117L ILE* 3.4 33.0 - - + -
855L BPH 3.6 37.5 - - - -
218M MET* 3.8 28.3 - - + -
222M THR* 3.0 28.1 + - + +
248M ALA 3.4 20.4 - - - -
249M ALA 3.4 4.8 + - - +
250M LEU 3.2 0.2 - - - -
251M PHE* 1.3 96.7 - + - +
253M ARG* 1.3 63.5 + - - +
255M THR* 3.8 7.0 - - + -
256M MET* 3.0 37.4 + - + +
258M PHE 3.1 17.8 - - - +
857M U10 3.3 45.8 - + + +
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Residues in contact with ARG 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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40H TYR* 3.7 18.9 + - - -
42H LEU* 3.9 26.3 - - - +
1L ALA* 4.3 11.3 + - - +
3L LEU* 3.5 17.0 - - - +
6L GLU* 3.5 27.9 + - - -
28L PRO* 3.7 29.7 - - + +
249M ALA 3.0 10.7 + - - +
250M LEU* 4.0 9.4 - - - +
251M PHE 3.4 0.4 - - - -
252M TRP* 1.3 75.1 - - - +
254M TRP* 1.3 63.1 + - + +
257M GLY* 2.7 44.9 + - - +
258M PHE* 3.8 14.3 + - - +
259M ASN* 3.0 29.6 + - - +
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Residues in contact with TRP 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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6L GLU* 3.3 22.0 + - + -
9L TYR* 3.8 27.8 - - + -
10L ARG* 3.9 15.4 - - + +
25L TRP* 3.4 36.2 - + - +
28L PRO 3.3 18.2 - - - -
29L PHE* 3.4 3.1 - - - -
30L TYR* 2.9 34.8 + - + +
103L ARG* 2.9 10.4 + - - -
107L ILE* 3.8 24.2 - - + -
110L LYS* 3.6 24.5 - - + -
111L LEU* 3.8 26.9 - - + -
250M LEU* 3.1 33.2 + - + +
251M PHE 4.0 2.5 - - - +
253M ARG* 1.3 84.5 - - + +
255M THR* 1.3 57.6 + - - +
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Residues in contact with THR 255 (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 PHE* 3.7 6.6 - - - -
100L TRP* 3.5 30.5 - - + +
103L ARG* 2.8 32.1 + - - +
104L GLU* 4.0 19.4 - - + +
107L ILE* 3.3 16.7 - - - +
855L BPH 4.1 6.1 - - - +
251M PHE* 2.9 34.9 + - - -
252M TRP* 4.0 12.1 - - + -
253M ARG 3.2 0.4 - - - -
254M TRP* 1.3 75.7 - - - +
256M MET* 1.3 62.5 + - + +
257M GLY 3.5 0.2 - - - -
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Residues in contact with MET 256 (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 PHE* 3.5 12.3 - - - -
100L TRP* 4.7 0.7 - - + -
855L BPH 3.3 30.1 - - - +
252M TRP* 3.0 22.3 + - + +
255M THR* 1.3 79.3 - - + +
257M GLY* 1.3 56.7 + - - +
258M PHE* 3.0 60.5 + - + +
857M U10 3.7 75.3 - - + +
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Residues in contact with GLY 257 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L PRO* 3.6 26.6 - - - +
29L PHE* 3.3 22.4 - - - -
253M ARG* 2.7 34.9 + - - -
255M THR 3.5 0.4 - - - -
256M MET* 1.3 70.2 - - - +
258M PHE* 1.3 59.5 + - - +
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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