Contacts of the helix formed by residues 232 - 247 (chain A) in PDB entry 6AF6
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 ALA 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A PHE* 6.1 2.0 - - + -
228A GLY* 5.4 0.2 - - - -
229A MET* 3.2 43.2 + - + +
230A GLU 3.2 1.2 - - - +
231A GLY* 1.3 74.6 - - - +
233A GLY* 1.3 63.1 + - - +
234A GLY 3.3 2.5 - - - -
235A ALA* 3.1 13.7 + - + +
236A ILE* 3.0 31.1 + - + +
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Residues in contact with GLY 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A TYR* 3.5 5.5 - - - -
183A VAL* 2.7 33.1 + - - -
184A SER* 3.8 13.6 - - - +
185A ALA* 4.0 3.8 - - - -
229A MET 4.6 0.4 + - - -
232A ALA* 1.3 75.8 - - - +
234A GLY* 1.3 54.4 + - - +
236A ILE* 3.2 8.0 + - - +
237A PHE* 2.7 36.6 + - - +
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Residues in contact with GLY 234 (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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137A TYR* 3.5 19.1 + - - -
180A PHE* 3.3 35.0 + - - -
183A VAL* 3.8 12.3 + - - +
231A GLY 4.6 0.2 + - - -
232A ALA 3.3 0.4 - - - -
233A GLY* 1.3 75.2 - - - +
235A ALA* 1.3 56.1 + - - +
237A PHE* 3.8 0.8 - - - +
238A HIS* 2.9 30.8 + - - +
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Residues in contact with ALA 235 (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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103A PHE* 4.6 8.0 - - + -
180A PHE* 3.5 18.7 - - + -
232A ALA* 3.1 16.5 + - + +
234A GLY* 1.3 76.5 - - - +
236A ILE* 1.3 59.7 + - + +
238A HIS* 3.6 6.0 - - - +
239A ASP* 3.0 28.8 + - - +
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Residues in contact with ILE 236 (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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99A PRO* 3.8 21.7 - - + +
103A PHE* 3.5 47.7 - - + -
169A ILE* 6.1 0.4 - - + -
171A TYR* 3.7 17.5 - - + +
185A ALA* 4.2 11.2 - - + -
227A ILE* 3.4 30.5 - - + +
228A GLY* 4.2 5.2 - - - -
232A ALA* 3.0 24.2 + - + +
233A GLY* 3.6 6.5 - - - +
235A ALA* 1.3 75.6 - - + +
237A PHE* 1.3 67.5 + - - +
239A ASP* 3.3 2.3 + - - +
240A SER* 2.9 22.2 + - - -
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Residues in contact with PHE 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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125A ASN* 4.3 4.9 - - - -
127A ALA* 3.4 25.8 - - + -
136A ILE* 4.0 11.4 - - + -
137A TYR* 3.7 24.5 - + + +
139A MET* 5.9 1.8 - - + -
171A TYR* 3.6 36.1 - + + -
233A GLY 2.7 20.5 + - - +
234A GLY* 3.8 5.4 - - - +
236A ILE* 1.3 73.0 - - - +
238A HIS* 1.3 63.6 + - - +
240A SER* 3.0 6.9 + - - -
241A MET* 2.9 50.4 + - + +
505A PRO* 4.2 3.1 - - - -
506A PRO* 3.3 47.6 - - + -
507A GLY* 4.2 3.6 - - - -
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Residues in contact with HIS 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TYR* 4.0 9.0 + - - +
180A PHE* 4.6 7.1 - + + -
234A GLY 2.9 18.6 + - - +
235A ALA* 3.6 9.0 - - - +
237A PHE* 1.3 77.9 - - - +
239A ASP* 1.3 66.0 + - + +
241A MET* 3.1 13.2 + - - +
242A ILE* 3.2 24.9 + - + +
245A LYS* 6.1 0.2 - - - -
315A GLU* 2.8 38.9 + - + +
374A ILE* 5.8 0.7 - - + -
377A ARG* 5.1 4.7 - - - -
507A GLY* 3.7 24.4 + - - +
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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
----------------------------------------------------------
98A ILE* 4.8 1.7 - - - +
99A PRO* 5.5 1.7 - - - +
102A ARG* 2.9 45.8 + - - -
103A PHE* 3.7 17.0 - - + -
235A ALA 3.0 17.9 + - - +
236A ILE 3.8 4.0 - - - +
238A HIS* 1.3 75.8 - - + +
240A SER* 1.3 67.0 + - - +
242A ILE* 3.2 18.1 + - - +
243A TRP* 3.4 20.5 + - - -
308A HIS* 5.7 2.4 + - - -
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Residues in contact with SER 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A CYS 3.6 20.4 - - - +
95A ALA* 4.2 5.0 + - - +
98A ILE* 5.8 0.4 - - - -
99A PRO* 4.0 22.2 - - - -
125A ASN* 5.0 0.3 + - - -
171A TYR* 4.1 5.5 + - - -
236A ILE 2.9 15.0 + - - -
237A PHE* 3.0 18.0 + - - -
239A ASP* 1.3 80.4 + - - +
241A MET* 1.3 72.8 + - - +
243A TRP* 3.3 7.5 + - - +
244A ALA* 2.9 27.0 + - - +
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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
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95A ALA* 4.2 13.7 - - + -
125A ASN* 4.4 2.0 - - - +
237A PHE* 2.9 47.5 + - + +
238A HIS 3.1 7.6 + - - +
240A SER* 1.3 97.1 + - - +
242A ILE* 1.3 57.4 + - + +
244A ALA* 4.1 3.6 - - + -
245A LYS* 2.7 41.3 + - - +
365A SER* 3.5 31.6 - - - +
505A PRO* 3.6 35.9 - - - +
506A PRO* 4.1 3.8 - - + -
507A GLY 3.8 19.3 - - - +
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Residues in contact with ILE 242 (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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238A HIS* 3.2 24.9 + - + +
239A ASP* 3.5 14.6 - - - +
240A SER 3.2 0.4 - - - -
241A MET* 1.3 77.2 - - + +
243A TRP* 1.3 56.1 + - + +
245A LYS* 3.7 20.1 - - - +
246A GLY* 2.7 34.7 + - - -
308A HIS* 4.7 14.1 - - + -
315A GLU* 3.9 32.8 - - + +
318A ILE* 3.4 31.7 - - + +
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Residues in contact with TRP 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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54A PRO* 3.8 37.0 - - + -
65A GLY* 4.5 1.3 - - - -
66A ALA* 4.0 26.0 - - + -
69A THR* 4.2 8.5 - - + -
94A CYS* 3.6 17.7 - - + +
98A ILE* 3.5 37.8 - - + +
102A ARG* 4.0 15.2 - - - +
239A ASP* 3.4 22.9 + - - -
240A SER* 3.3 7.4 + - - +
242A ILE* 1.3 79.3 - - + +
244A ALA* 1.3 61.9 + - - +
246A GLY* 5.0 0.2 - - - -
247A CYS* 2.9 61.7 + - + +
248A LEU 3.3 5.4 + - - -
308A HIS* 3.9 30.1 + + - -
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Residues in contact with ALA 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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94A CYS* 3.7 18.3 - - + +
95A ALA 5.4 0.4 - - - +
240A SER 2.9 16.7 + - - +
241A MET* 3.7 13.9 - - + +
243A TRP* 1.3 77.5 - - - +
245A LYS* 1.3 61.7 + - - +
248A LEU* 2.9 31.8 + - + +
249A SER* 3.6 2.9 + - - -
365A SER* 3.3 24.4 - - - +
505A PRO* 4.7 9.9 - - + -
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Residues in contact with LYS 245 (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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241A MET 2.7 27.1 + - - +
242A ILE* 4.2 20.3 - - - +
244A ALA* 1.3 74.3 - - - +
246A GLY* 1.3 59.4 + - - +
249A SER* 2.6 27.5 + - - -
301A LEU* 4.9 1.6 - - - +
315A GLU* 5.2 1.8 + - - +
318A ILE* 3.6 16.3 - - + +
319A ALA* 4.5 5.5 - - - +
321A SER* 5.4 0.2 - - - -
322A LYS* 3.8 24.3 + - + +
365A SER* 3.5 31.2 + - - +
371A GLN* 2.9 35.3 + - - +
374A ILE* 3.5 21.2 - - - +
507A GLY 4.1 10.3 + - - -
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Residues in contact with GLY 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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242A ILE 2.7 22.6 + - - -
245A LYS* 1.3 75.6 - - - +
247A CYS* 1.3 63.3 + - - +
250A ALA 4.5 1.2 + - - -
301A LEU* 2.8 34.5 - - - +
305A CYS* 3.8 8.1 - - - -
318A ILE* 3.6 21.3 - - - +
321A SER* 6.0 0.2 - - - -
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Residues in contact with CYS 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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66A ALA* 3.7 31.2 - - - -
69A THR* 4.0 19.3 - - + -
70A ALA* 4.3 7.6 - - - +
73A ILE* 3.7 12.8 - - + +
94A CYS* 4.6 3.4 - - - -
243A TRP* 2.9 45.3 + - + +
246A GLY* 1.3 79.1 - - - +
248A LEU* 1.3 65.7 + - - +
249A SER 3.1 1.8 - - - -
250A ALA* 3.1 21.8 - - - +
305A CYS* 4.5 2.9 - - - -
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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