Contacts of the helix formed by residues 236 - 251 (chain A) in PDB entry 6V3O
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 THR 236 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A GLN 3.6 3.2 + - - -
235A PRO* 1.3 74.3 - - - +
237A PRO* 1.3 73.4 - - - +
238A GLN* 2.9 28.2 + - + +
239A ASP* 3.0 39.8 + - - +
240A GLU* 2.9 21.8 + - - +
242A ARG* 4.8 1.1 - - - +
298A ARG* 4.1 2.7 - - - +
303A VAL* 5.5 0.2 - - - +
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Residues in contact with PRO 237 (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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236A THR* 1.3 91.8 - - - +
238A GLN* 1.3 57.5 + - - +
240A GLU* 3.5 14.2 + - + +
241A MET* 2.9 28.8 + - - +
289A MET* 4.7 4.0 - - + +
290A GLY* 4.7 8.2 + - - +
298A ARG* 3.7 52.5 - - + +
299A VAL* 4.1 16.8 - - + -
303A VAL* 3.8 22.4 - - + -
307A VAL* 4.5 3.5 - - - +
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Residues in contact with GLN 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A THR* 2.9 24.0 + - + -
237A PRO* 1.3 73.1 - - - +
239A ASP* 1.3 58.0 + - - +
241A MET* 3.3 4.9 + - - +
242A ARG* 2.9 49.5 + - - +
303A VAL* 3.6 31.7 - - - +
306A ASP* 3.1 40.0 + - + +
307A VAL* 4.3 12.8 - - + -
310A LEU* 4.3 12.7 - - + +
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Residues in contact with ASP 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A PRO* 4.3 3.7 - - + +
236A THR* 3.0 33.5 + - + +
238A GLN* 1.3 74.2 - - - +
240A GLU* 1.3 54.7 + - - +
242A ARG* 2.5 37.0 + - - +
243A TYR* 2.7 61.3 + - + +
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Residues in contact with GLU 240 (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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176A ALA* 3.4 27.2 - - + +
177A HIS 5.0 5.1 - - - +
235A PRO* 3.9 19.0 - - + +
236A THR 2.9 19.7 + - - +
237A PRO* 3.6 8.7 - - - +
239A ASP* 1.3 74.3 - - - +
241A MET* 1.3 62.1 + - - +
243A TYR* 3.2 17.7 - - + +
244A GLY* 3.0 19.6 + - - -
289A MET* 4.2 17.7 - - + +
298A ARG* 3.7 19.3 + - - -
758A SER* 3.6 21.0 + - - -
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Residues in contact with MET 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A PRO 2.9 15.1 + - - +
238A GLN 3.4 6.7 - - - +
239A ASP 3.1 0.2 - - - -
240A GLU* 1.3 73.8 - - - +
242A ARG* 1.3 69.3 + - - +
244A GLY* 3.1 10.0 + - - -
245A MET* 3.2 42.1 + - + +
287A SER* 5.3 1.8 - - - +
289A MET* 3.9 27.3 - - + +
307A VAL* 3.3 46.4 - - + +
310A LEU* 4.2 19.7 - - + -
311A ALA* 3.6 26.9 - - + +
314A MET* 4.4 3.4 - - - +
451A VAL* 5.6 2.0 - - + -
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Residues in contact with ARG 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A THR* 4.8 1.0 - - - +
238A GLN* 2.9 27.4 + - - +
239A ASP* 2.5 54.3 + - - +
241A MET* 1.3 82.7 - - - +
243A TYR* 1.3 66.8 + - + +
244A GLY 3.3 0.3 + - - -
245A MET* 3.3 14.1 + - - +
246A SER* 3.5 10.7 + - - -
310A LEU* 4.2 30.8 - - + +
314A MET* 4.9 12.0 - - + +
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Residues in contact with TYR 243 (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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177A HIS* 6.3 0.7 - - + -
180A GLN 4.5 5.2 - - - +
181A SER* 3.5 43.4 + - - -
182A ALA* 3.5 25.0 - - + +
183A ARG* 4.8 9.9 - - + -
235A PRO* 3.8 31.6 - - + +
239A ASP* 2.7 39.1 + - + +
240A GLU* 3.2 20.8 + - + +
242A ARG* 1.3 77.0 - - + +
244A GLY* 1.3 56.6 + - - +
246A SER* 2.5 25.5 + - - -
247A TYR* 4.3 4.9 - - - -
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Residues in contact with GLY 244 (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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174A PHE* 3.8 24.5 - - - -
240A GLU 3.0 10.5 + - - -
241A MET 3.1 3.7 + - - -
243A TYR* 1.3 77.1 - - - +
245A MET* 1.3 68.0 + - - +
246A SER 3.4 0.5 + - - -
247A TYR* 3.8 12.0 + - - +
248A ILE* 4.2 2.4 - - - +
289A MET* 3.9 18.2 - - - -
677A ILE* 5.8 3.6 - - - -
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Residues in contact with MET 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PHE* 5.4 4.5 - - + -
241A MET* 3.2 35.4 + - + +
242A ARG 3.3 2.6 + - - +
244A GLY* 1.3 80.7 - - - +
246A SER* 1.3 58.8 + - - +
247A TYR 3.2 0.4 - - - -
248A ILE* 3.1 15.3 + - + +
249A HIS* 3.0 33.4 + - + -
287A SER* 4.3 13.7 - - - +
289A MET* 4.5 4.3 - - + -
311A ALA* 5.6 1.3 - - - -
314A MET* 3.4 32.3 - - + +
450A LEU* 4.2 20.6 - - + -
451A VAL* 3.6 41.1 - - + -
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Residues in contact with SER 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ALA 2.9 18.4 + - - -
183A ARG* 5.0 0.2 - - - -
184A ARG* 3.7 29.2 - - - +
187A LEU* 3.8 10.9 - - - +
242A ARG 3.5 8.3 + - - -
243A TYR 2.5 25.4 + - - -
245A MET* 1.3 78.8 - - - +
247A TYR* 1.3 64.3 + - - +
249A HIS* 3.3 4.2 + - - +
250A GLU* 2.9 33.6 + - - +
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Residues in contact with TYR 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PHE* 4.4 7.6 - - + -
182A ALA* 3.8 26.5 - - + +
187A LEU* 3.8 22.2 - - + +
243A TYR 4.3 5.4 - - - -
244A GLY* 3.8 9.8 + - - +
245A MET 3.2 0.2 - - - -
246A SER* 1.3 82.7 + - - +
248A ILE* 1.3 66.1 + - - +
250A GLU* 4.4 2.2 - - + +
251A THR* 3.1 21.4 + - - -
252A VAL* 3.2 11.8 + - + +
677A ILE* 3.6 32.1 - - + -
678A GLU* 2.8 50.3 + - - +
681A PHE* 4.1 24.5 - - + -
682A GLY* 4.1 6.7 - - - -
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Residues in contact with ILE 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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174A PHE* 4.5 13.9 - - + -
244A GLY 4.2 5.4 - - - +
245A MET* 3.1 29.4 + - + +
247A TYR* 1.3 79.2 - - - +
249A HIS* 1.3 62.9 + - - +
252A VAL* 3.6 13.0 + - + -
253A TRP* 3.0 35.9 + - + +
285A PHE* 4.4 20.6 - - + -
318A LEU* 5.1 0.7 - - + -
446A PHE* 4.2 24.0 - - + -
450A LEU* 4.1 26.9 - - + -
451A VAL* 4.3 20.6 - - + -
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Residues in contact with HIS 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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184A ARG* 3.4 51.4 + - - +
245A MET* 3.0 32.2 + - + +
246A SER* 3.5 5.6 - - - +
248A ILE* 1.3 79.3 - - - +
250A GLU* 1.3 62.8 + - - +
251A THR 3.6 0.2 + - - -
253A TRP* 4.2 9.1 - - - +
254A LYS* 4.6 10.4 + - - -
314A MET* 3.5 41.5 - - + +
317A ASN* 5.8 2.7 - - + -
318A LEU* 3.6 44.5 - - + +
450A LEU* 4.8 3.2 - - + +
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Residues in contact with GLU 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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184A ARG* 2.8 37.1 + - + +
187A LEU* 4.0 28.7 - - + -
188A GLN* 3.0 35.1 + - - +
246A SER 2.9 20.4 + - - +
247A TYR* 4.5 1.8 - - + +
248A ILE 3.3 0.2 - - - -
249A HIS* 1.3 77.4 - - - +
251A THR* 1.3 68.3 + - - +
254A LYS* 5.8 1.6 + - - -
682A GLY 6.1 0.2 - - - +
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Residues in contact with THR 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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247A TYR* 3.1 7.1 + - - -
249A HIS 3.4 1.4 - - - -
250A GLU* 1.3 89.1 + - - +
252A VAL* 1.3 64.4 + - + +
253A TRP 3.4 1.6 - - - -
254A LYS* 3.9 5.1 + - - +
255A GLY* 3.0 23.2 + - - -
681A PHE 3.2 28.7 + - - +
682A GLY 3.7 11.3 + - - -
683A GLU 4.5 3.8 - - - +
684A GLU* 4.5 12.5 + - - +
687A CYS* 3.3 30.7 - - + -
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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
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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