Contacts of the helix formed by residues 242 - 259 (chain A) in PDB entry 2JBO
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 LYS 242 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A HIS* 3.2 73.4 + - + +
181A ASN* 3.1 30.1 - - - +
182A ILE 4.7 0.2 - - - +
183A ALA* 4.1 6.1 - - + -
214A THR* 3.4 21.1 + - + -
238A GLU* 2.8 35.1 + - - +
241A ASP* 1.3 74.6 - - - +
243A SER* 1.3 63.3 + - - +
244A CYS 3.1 3.8 + - - -
245A ASP* 3.3 10.1 - - - +
246A MET* 3.5 4.8 + - - +
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Residues in contact with SER 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A TYR* 3.3 34.9 + - - +
241A ASP 3.1 0.4 + - - -
242A LYS* 1.3 80.6 - - - +
244A CYS* 1.3 61.6 + - - +
246A MET* 3.4 14.4 + - - +
247A TRP 3.2 9.9 + - - -
310A PRO* 4.0 20.5 - - - +
313A ARG* 2.8 30.4 + - - -
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Residues in contact with CYS 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ARG* 4.0 31.0 - - - -
241A ASP* 3.6 17.4 + - - +
242A LYS 3.1 1.4 - - - -
243A SER* 1.3 77.7 + - - +
245A ASP* 1.3 65.7 + - - +
247A TRP* 2.8 24.2 + - + +
248A SER* 2.9 17.4 + - - +
313A ARG* 4.0 7.9 - - - +
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Residues in contact with ASP 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ILE* 4.2 13.8 - - + +
177A LEU* 5.3 0.2 - - - +
178A HIS* 2.7 29.9 + - + +
183A ALA* 3.7 3.3 - - - -
184A HIS* 3.0 23.3 + - - +
185A ARG* 2.8 29.3 + - - -
187A VAL* 3.8 14.8 - - - +
242A LYS* 3.3 11.7 - - - +
244A CYS* 1.3 77.9 - - - +
246A MET* 1.3 64.2 + - - +
248A SER* 3.3 9.6 + - - -
249A LEU* 3.1 23.7 + - - +
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Residues in contact with MET 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ILE* 4.5 6.3 - - - -
178A HIS* 4.5 4.3 - - + -
242A LYS 3.5 8.5 + - - +
243A SER* 3.4 14.7 + - - +
244A CYS 3.1 0.6 - - - -
245A ASP* 1.3 81.5 - - - +
247A TRP* 1.3 63.6 + - - +
249A LEU* 3.2 26.3 + - + +
250A GLY 3.2 7.6 + - - -
305A LEU* 3.9 28.8 - - + +
313A ARG* 4.1 11.7 - - + -
314A MET 3.1 23.6 - - - +
315A THR* 3.9 4.5 - - - +
316A ILE* 3.6 52.0 - - + +
319A PHE* 4.0 5.2 - - + -
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Residues in contact with TRP 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A SER 3.2 4.9 + - - -
244A CYS* 2.8 17.4 + - + +
246A MET* 1.3 70.3 - - - +
248A SER* 1.3 59.0 + - - +
250A GLY* 2.7 24.6 + - - -
251A VAL* 3.0 26.5 + - + +
263A PHE* 3.8 37.9 - + - -
279A ILE* 4.0 30.7 - - + +
282A GLY* 5.4 0.7 - - - -
305A LEU 3.9 9.0 - - - -
306A LEU* 3.4 47.2 - - + +
307A LYS 4.0 5.6 - - - -
308A THR* 4.4 6.3 - - - -
313A ARG* 3.7 34.2 - - - +
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Residues in contact with SER 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ARG* 5.9 1.6 - - - -
187A VAL* 3.4 40.0 + - - +
244A CYS* 2.9 13.6 + - - -
245A ASP* 3.3 11.8 + - - -
247A TRP* 1.3 82.3 - - - +
249A LEU* 1.3 63.9 + - - +
251A VAL* 3.1 7.7 + - - +
252A ILE* 2.9 29.6 + - - +
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Residues in contact with LEU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A MET* 3.6 26.2 - - + +
170A ILE* 3.4 31.4 - - + -
171A GLY* 4.6 3.4 - - - -
174A ILE* 4.6 13.0 - - + -
187A VAL* 4.7 6.3 - - + -
245A ASP 3.1 8.0 + - - +
246A MET* 3.3 35.2 - - + +
247A TRP 3.1 0.2 - - - -
248A SER* 1.3 80.2 - - - +
250A GLY* 1.3 62.0 + - - +
252A ILE* 3.4 4.4 + - + -
253A MET* 2.9 24.3 + - - +
305A LEU* 4.1 7.6 - - + -
316A ILE* 4.0 16.4 - - + -
319A PHE* 4.1 17.3 - - + -
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Residues in contact with GLY 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A MET 3.2 4.4 + - - -
247A TRP 2.7 15.3 + - - -
249A LEU* 1.3 73.3 - - - +
251A VAL* 1.3 55.6 + - - -
253A MET* 3.2 3.6 + - - +
254A TYR* 2.8 30.3 + - - +
302A ILE* 4.3 5.5 - - - +
305A LEU* 3.6 28.6 - - - +
306A LEU* 3.8 12.8 - - - -
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Residues in contact with VAL 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PRO* 6.4 1.1 - - + -
247A TRP* 3.0 40.9 + - + +
248A SER* 3.1 7.8 + - - +
250A GLY* 1.3 76.8 - - - +
252A ILE* 1.3 64.1 + - + +
254A TYR* 3.1 7.6 + - - +
255A ILE* 3.0 35.4 + - + +
261A PRO* 5.0 3.8 - - + -
262A PRO* 3.8 24.9 - - + -
263A PHE* 5.8 0.7 - - + -
306A LEU* 4.1 9.0 - - + -
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Residues in contact with ILE 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 4.6 10.3 - - + -
147A PHE* 4.4 5.9 - - + -
167A MET* 4.0 15.5 - - + -
170A ILE* 4.1 16.4 - - + -
187A VAL* 3.5 34.1 - - + +
189A PRO* 3.6 24.7 - - + -
192A LEU* 3.6 25.8 - - + -
248A SER 2.9 19.0 + - - +
249A LEU* 3.9 7.9 - - + +
251A VAL* 1.3 76.8 - - + +
253A MET* 1.3 58.5 + - - +
255A ILE* 3.5 7.0 + - + +
256A LEU* 2.9 30.7 + - + +
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Residues in contact with MET 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A MET* 3.7 26.4 - - + -
249A LEU 2.9 18.1 + - - +
250A GLY* 3.5 5.4 - - - +
252A ILE* 1.3 75.5 - - - +
254A TYR* 1.3 68.3 + - - +
256A LEU* 3.1 4.4 + - + +
257A LEU* 3.1 32.1 + - + +
298A VAL* 3.8 24.5 - - + +
301A LEU* 3.9 24.2 - - + -
302A ILE* 3.5 27.1 - - + -
305A LEU* 4.4 10.8 - - - -
319A PHE* 4.9 3.6 - - - -
324A TRP* 3.7 30.1 - - + -
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Residues in contact with TYR 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A GLY 2.8 17.2 + - - +
251A VAL 3.4 8.3 - - - +
253A MET* 1.3 71.0 - - - +
255A ILE* 1.3 56.6 + - - +
257A LEU* 2.9 20.1 + - - +
258A CYS* 3.4 16.3 + - - -
260A TYR* 3.0 48.4 - + - -
262A PRO* 3.4 45.5 + - + +
284A TYR* 4.1 5.2 - + - -
285A GLU 2.6 29.1 + - - -
286A PHE* 3.6 15.7 - + - -
287A PRO* 3.7 7.4 - - - +
291A TRP* 3.4 28.6 - + - -
302A ILE* 3.7 20.0 - - + +
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Residues in contact with ILE 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A PHE* 3.5 36.1 - - + -
189A PRO* 4.8 10.5 - - + -
251A VAL* 3.0 26.5 + - + +
252A ILE* 3.9 4.9 - - - +
254A TYR* 1.3 72.0 - - - +
256A LEU* 1.3 68.1 + - - +
259A GLY* 2.8 28.6 + - - +
260A TYR* 3.7 27.8 - - - +
261A PRO* 3.7 24.7 - - + -
338A THR* 3.6 3.3 - - - +
342A LEU* 4.7 6.5 - - + -
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Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU* 4.7 2.2 - - + -
147A PHE* 3.8 22.9 - - + -
150A ILE* 4.6 7.2 - - + -
158A PHE* 3.5 35.2 - - + -
163A ALA* 4.0 16.6 - - + +
166A ILE* 3.6 37.0 - - + -
167A MET* 3.7 29.6 - - + -
252A ILE* 2.9 19.8 + - + +
253A MET* 3.1 6.5 + - + +
255A ILE* 1.3 76.7 - - - +
257A LEU* 1.3 55.1 + - + +
336A LEU* 4.1 0.6 - - - +
338A THR* 2.6 31.3 + - + +
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Residues in contact with LEU 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A GLU* 4.4 11.0 - - + -
163A ALA* 4.7 4.3 - - + -
253A MET* 3.1 32.0 + - + +
254A TYR 2.9 7.7 + - - +
256A LEU* 1.3 83.1 - - + +
258A CYS* 1.3 59.1 + - - +
290A GLU* 5.3 4.0 - - - +
291A TRP* 4.1 14.6 - - + -
294A VAL* 4.6 14.9 - - + +
298A VAL* 3.8 19.5 - - + -
302A ILE* 3.7 23.6 - - + -
324A TRP* 4.4 20.0 - - + -
336A LEU* 3.7 38.4 - - + +
337A HIS* 4.8 2.1 + - - +
338A THR* 3.7 4.1 + - - -
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Residues in contact with CYS 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A TYR* 3.6 22.4 - - - -
255A ILE 3.3 0.6 + - - -
256A LEU 3.3 0.8 + - - -
257A LEU* 1.3 82.1 - - - +
259A GLY* 1.3 64.3 + - - +
260A TYR* 3.4 47.2 - - + -
290A GLU* 4.1 12.2 - - + +
291A TRP* 3.7 20.6 - - + +
337A HIS* 4.5 1.9 - - - +
338A THR* 3.8 11.5 + - - +
341A VAL* 3.4 28.6 - - - +
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Residues in contact with GLY 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A ILE* 2.8 18.8 + - - -
258A CYS* 1.3 79.2 - - - +
260A TYR* 1.3 64.4 + - - +
261A PRO* 4.8 0.2 - - - +
338A THR* 4.2 7.2 - - - -
341A VAL* 3.8 13.9 - - - +
342A LEU* 3.5 32.9 + - - +
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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