Contacts of the helix formed by residues 240 - 258 (chain A) in PDB entry 2Z7S
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 SER 240 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ILE* 3.7 18.1 - - - +
232A GLU* 5.5 2.7 + - - +
239A HIS* 1.3 78.5 - - - +
241A HIS* 1.3 81.3 + - - +
242A SER* 3.1 19.5 + - - -
243A ALA* 3.2 18.0 + - - +
301A PRO* 5.5 1.7 - - - +
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Residues in contact with HIS 241 (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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179A HIS* 3.7 36.7 - - + +
184A ILE* 4.3 7.5 - - + +
240A SER* 1.3 93.8 + - - +
242A SER* 1.3 77.2 + - - +
244A ASP* 2.9 23.8 + - - +
245A TRP* 3.5 13.3 + - - -
306A GLY 4.2 19.0 + - - -
307A SER* 4.9 6.1 - - - -
311A GLY* 6.4 0.2 - - - -
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Residues in contact with SER 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A GLU* 4.2 0.9 - - - -
240A SER* 3.1 12.0 + - - -
241A HIS* 1.3 90.7 + - - +
243A ALA* 1.3 62.5 - - - +
245A TRP* 3.0 21.3 + - - +
246A TRP 3.2 4.9 + - - -
301A PRO* 3.2 19.6 + - - +
304A ARG* 3.0 29.1 + - - +
305A LEU 6.0 0.2 - - - -
306A GLY 6.1 0.2 - - - -
307A SER* 2.9 26.4 + - - -
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ALA* 3.8 8.5 - - + +
232A GLU* 3.5 18.6 + - - +
233A VAL* 3.9 13.2 - - + -
239A HIS* 3.3 27.1 - - + +
240A SER* 3.2 17.3 + - - +
241A HIS 3.1 0.2 - - - -
242A SER* 1.3 77.9 - - - +
244A ASP* 1.3 62.7 + - - +
246A TRP* 3.2 6.1 + - - +
247A SER* 3.2 23.9 + - - -
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Residues in contact with ASP 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 4.0 9.2 - - + -
179A HIS* 2.7 31.5 + - + +
184A ILE* 3.5 15.4 - - - +
185A TYR* 2.8 53.3 + - - +
186A ARG* 3.8 2.8 + - - +
188A LEU* 3.8 5.3 - - + +
239A HIS* 4.6 1.4 + - - -
241A HIS 2.9 10.0 + - - +
243A ALA* 1.3 79.6 - - - +
245A TRP* 1.3 57.1 + - - +
247A SER* 3.2 9.5 + - - -
248A TYR* 2.8 27.8 + - - +
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Residues in contact with TRP 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ALA* 3.9 23.1 - - + -
175A LEU* 3.7 13.7 - - + -
176A ASP* 4.5 2.5 - - - -
179A HIS* 3.4 29.1 + + - -
241A HIS* 3.5 24.1 + + - -
242A SER* 3.0 11.9 + - - +
244A ASP* 1.3 73.4 - - - +
246A TRP* 1.3 60.3 + - - +
248A TYR* 3.2 48.8 - + + +
249A GLY* 2.9 20.8 + - - -
296A LEU* 3.6 19.4 - - + +
304A ARG* 4.5 3.6 - - - -
305A LEU 3.9 16.8 - - - +
306A GLY* 4.1 23.8 + - - -
312A ALA* 4.0 27.5 - - + +
315A ILE* 4.3 20.6 - - + -
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Residues in contact with TRP 246 (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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227A GLU 5.2 0.8 + - - -
228A TYR 4.0 1.5 - - - -
229A MET 3.3 13.1 + - - -
230A ALA* 3.4 27.4 - - + -
231A PRO* 3.5 29.8 - - + -
242A SER 3.2 4.0 + - - -
243A ALA 3.2 9.5 + - - +
244A ASP 3.2 0.6 - - - -
245A TRP* 1.3 75.8 - - - +
247A SER* 1.3 60.0 + - - +
249A GLY* 2.8 18.2 + - - -
250A VAL* 2.9 28.9 + - + +
262A PHE* 3.4 33.5 - + - -
274A ILE* 3.9 11.4 - - + +
277A ALA* 4.3 13.5 - - + -
296A LEU 3.7 24.2 - - - -
297A PHE* 3.6 38.6 - + - -
298A LYS 3.8 16.4 - - - -
299A ARG 4.3 1.1 - - - -
304A ARG* 3.8 11.4 - - - +
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Residues in contact with SER 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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185A TYR 5.7 0.2 - - - -
186A ARG 5.1 5.1 + - - -
188A LEU* 3.9 28.6 + - - +
228A TYR* 2.6 33.6 + - - +
229A MET* 4.8 0.2 - - - -
230A ALA 4.7 1.4 + - - -
243A ALA 3.2 11.9 + - - -
244A ASP* 3.2 10.9 + - - -
246A TRP* 1.3 79.7 - - - +
248A TYR* 1.3 57.2 + - - +
250A VAL* 3.1 7.1 + - - +
251A LEU* 2.9 27.9 + - - +
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Residues in contact with TYR 248 (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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168A LEU* 2.6 43.8 + - + +
171A LEU* 3.6 30.5 - - + -
172A ALA* 3.6 8.2 - - - +
175A LEU* 4.1 3.6 - - + -
188A LEU* 4.1 11.2 - - + +
244A ASP 2.8 14.4 + - - +
245A TRP* 3.2 42.0 - + + +
247A SER* 1.3 76.6 - - - +
249A GLY* 1.3 61.9 + - - +
251A LEU* 3.4 4.8 + - - +
252A MET* 3.1 20.6 + - - +
296A LEU* 3.7 21.5 - - + -
315A ILE* 3.7 12.9 - - + +
321A TYR* 2.5 32.2 + - - -
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Residues in contact with GLY 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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245A TRP 2.9 8.2 + - - -
246A TRP 2.8 9.8 + - - -
248A TYR* 1.3 77.5 - - - +
250A VAL* 1.3 60.5 + - - +
252A MET* 3.3 5.4 + - - +
253A PHE 3.0 18.4 + - - -
293A LEU* 3.5 4.2 - - - +
296A LEU* 3.6 26.2 - - - -
297A PHE* 3.3 18.9 - - - -
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Residues in contact with VAL 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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227A GLU 3.7 21.8 - - - +
228A TYR* 3.5 31.6 - - + -
246A TRP* 2.9 41.0 + - + +
247A SER* 3.1 9.2 + - - +
249A GLY* 1.3 76.4 - - - +
251A LEU* 1.3 57.5 + - - +
253A PHE* 3.2 2.6 + - - +
254A GLU* 2.8 28.4 + - - +
260A LEU* 3.9 11.2 - - + -
261A PRO* 3.9 13.6 - - + +
262A PHE* 5.2 0.9 - - + -
297A PHE* 3.7 14.6 - - + -
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Residues in contact with LEU 251 (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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149A LEU* 4.8 0.9 - - + -
167A TYR* 6.5 0.2 - - + -
168A LEU* 4.0 7.4 - - + -
171A LEU* 3.2 36.3 - - + -
188A LEU* 4.0 6.7 - - + -
190A PRO* 3.7 35.9 - - + -
193A ILE* 3.3 18.6 - - + -
228A TYR* 3.5 14.3 - - + +
247A SER 2.9 12.1 + - - +
248A TYR 3.6 6.3 - - - +
249A GLY 3.3 0.2 - - - -
250A VAL* 1.3 75.0 - - - +
252A MET* 1.3 58.7 + - - +
254A GLU* 3.3 1.5 + - - +
255A MET* 2.9 63.1 + - + +
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Residues in contact with MET 252 (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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164A VAL* 4.3 0.4 - - + -
168A LEU* 3.4 30.9 - - + +
248A TYR* 3.1 11.5 + - + +
249A GLY 3.4 8.1 - - - +
251A LEU* 1.3 78.0 - - - +
253A PHE* 1.3 63.0 + - - +
255A MET* 3.9 4.6 - - - +
256A LEU* 2.9 49.3 + - + +
289A ALA* 3.5 37.5 - - + +
292A LEU* 3.5 36.3 - - + -
293A LEU* 3.6 15.0 - - + -
296A LEU* 4.4 6.7 - - - -
320A PHE* 4.0 10.1 - - + -
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Residues in contact with PHE 253 (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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249A GLY 3.0 13.8 + - - +
250A VAL 3.5 7.0 - - - +
252A MET* 1.3 76.5 - - - +
254A GLU* 1.3 56.3 + - - +
256A LEU* 3.2 4.1 + - - -
257A THR* 2.9 58.6 + - + +
259A SER* 3.1 26.9 - - - -
260A LEU 3.8 3.6 - - - -
261A PRO* 3.4 40.8 - - + -
279A LEU* 4.1 26.0 - - + -
280A GLY 4.3 1.8 - - - -
281A MET* 4.8 1.8 - - - -
282A PRO* 3.9 28.9 - - + -
293A LEU* 3.9 27.8 - - + +
297A PHE* 4.4 1.1 - - + -
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Residues in contact with GLU 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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150A PHE* 5.1 10.1 - - - -
153A LEU* 3.7 21.3 - - + +
190A PRO* 3.6 12.9 - - - +
228A TYR* 2.4 34.3 + - - +
250A VAL 2.8 18.4 + - - +
251A LEU* 3.8 2.4 - - - +
253A PHE* 1.3 74.4 - - - +
255A MET* 1.3 56.8 + - - +
258A GLY* 2.8 36.9 + - - +
259A SER* 3.1 21.9 + - - +
260A LEU* 3.8 25.9 + - + +
261A PRO* 4.9 0.2 - - - +
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Residues in contact with MET 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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149A LEU* 3.9 26.5 - - + -
153A LEU* 4.1 16.2 - - + -
158A MET* 3.5 4.9 - - - -
159A PHE* 2.9 53.1 + - + +
164A VAL* 3.8 20.6 - - + -
167A TYR* 4.3 11.7 - - + -
168A LEU* 3.3 39.3 - - + -
190A PRO* 5.7 0.4 - - + -
251A LEU* 2.9 38.2 + - + +
252A MET 3.9 0.9 - - - +
254A GLU* 1.3 76.8 - - - +
256A LEU* 1.3 60.1 + - - +
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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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158A MET* 3.7 10.0 - - - +
159A PHE 4.2 7.5 - - - +
161A GLU* 3.7 33.2 - - + +
164A VAL* 3.5 29.2 - - + -
252A MET* 2.9 51.6 + - + +
253A PHE* 3.8 3.4 - - - +
255A MET* 1.3 79.0 - - - +
257A THR* 1.3 59.9 + - + +
284A PHE* 3.3 20.6 - - - -
285A LEU* 3.9 18.8 - - + -
289A ALA* 4.2 13.9 - - + -
293A LEU* 4.6 7.6 - - + -
320A PHE* 5.2 1.3 - - + -
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Residues in contact with THR 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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157A VAL* 4.4 1.4 - - - +
158A MET* 4.2 13.5 - - - +
253A PHE* 2.9 34.6 + - + +
256A LEU* 1.3 85.2 - - + +
258A GLY* 1.3 59.2 + - - +
259A SER* 2.9 31.3 + - - -
282A PRO* 3.9 27.8 - - + -
284A PHE* 3.9 15.4 - - + -
285A LEU* 4.4 6.7 - - + -
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Residues in contact with GLY 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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153A LEU* 4.9 2.2 - - - -
157A VAL* 3.0 32.5 + - - +
158A MET* 4.0 1.8 - - - +
254A GLU* 2.8 25.1 + - - +
256A LEU 3.7 1.0 - - - -
257A THR* 1.3 78.0 - - - +
259A SER* 1.3 60.2 + - - +
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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