Contacts of the helix formed by residues 242 - 254 (chain O) in PDB entry 6FF7
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 ILE 242 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240O THR 3.6 5.1 + - - +
241O VAL* 1.3 72.9 - - - +
243O SER* 1.3 62.3 + - - +
244O ASN 3.3 2.5 - - - -
245O TRP* 4.0 8.7 + - + +
246O ILE* 3.7 20.1 + - - +
268O ALA 6.2 0.2 - - - +
272O ASP* 5.8 7.4 - - + -
278O LEU* 5.4 12.2 - - + +
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Residues in contact with SER 243 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816 C 4.7 22.2 - - - -
836 A 5.8 4.9 - - - -
241O VAL* 3.5 5.3 - - - +
242O ILE* 1.3 77.6 - - - +
244O ASN* 1.3 58.8 + - - +
246O ILE* 3.5 3.7 + - - +
247O LYS* 3.0 32.1 + - - +
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Residues in contact with ASN 244 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231O PHE* 5.4 5.2 - - + +
234O ASN* 4.8 19.3 - - + +
235O ILE* 5.0 14.6 - - + +
238O ASN 6.0 0.9 - - - +
241O VAL 4.5 7.8 + - - +
242O ILE* 3.3 1.0 - - - +
243O SER* 1.3 79.8 - - - +
245O TRP* 1.3 58.4 + - - +
247O LYS* 3.9 2.9 - - - +
248O TYR* 3.0 30.7 + - - +
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Residues in contact with TRP 245 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235O ILE* 5.5 9.0 - - + +
241O VAL 5.4 0.4 + - - -
242O ILE* 4.0 10.9 + - + +
244O ASN* 1.3 77.5 - - - +
246O ILE* 1.3 59.1 + - - +
248O TYR* 3.4 6.5 + - - +
249O ALA* 2.9 30.5 + - - +
264O ILE* 5.4 4.0 - - + +
268O ALA* 4.0 26.5 - - + -
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Residues in contact with ILE 246 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242O ILE 3.7 14.5 + - - +
243O SER* 3.5 4.1 + - - +
244O ASN 3.3 0.6 - - - -
245O TRP* 1.3 76.7 - - - +
247O LYS* 1.3 61.1 + - - +
249O ALA* 3.8 4.6 - - - +
250O GLN* 2.9 30.1 + - - +
278O LEU* 5.9 7.0 - - + -
281O LYS* 5.5 11.4 - - + -
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Residues in contact with LYS 247 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816 C 5.4 13.9 - - - +
243O SER 3.0 18.3 + - - +
244O ASN* 4.2 3.4 - - - +
246O ILE* 1.3 76.1 - - - +
248O TYR* 1.3 59.3 + - - +
250O GLN* 3.8 4.2 - - - +
251O TRP* 3.0 28.4 + - - +
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Residues in contact with TYR 248 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231O PHE* 4.3 22.7 - - + -
244O ASN 3.0 18.5 + - - +
245O TRP* 3.7 6.3 - - - +
247O LYS* 1.3 76.6 - - - +
249O ALA* 1.3 57.9 + - - +
251O TRP* 3.2 9.2 + - - +
252O GLU* 3.0 24.6 + - - +
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Residues in contact with ALA 249 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245O TRP 2.9 19.2 + - - +
246O ILE* 4.1 5.4 - - - +
248O TYR* 1.3 76.5 - - - +
250O GLN* 1.3 58.1 + - - +
252O GLU* 3.3 8.0 + - - +
253O GLU* 2.9 24.3 + - - +
261O ALA* 4.5 21.5 - - + +
264O ILE* 4.8 15.3 - - + -
265O TYR* 5.5 4.3 - - + +
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Residues in contact with GLN 250 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246O ILE 2.9 18.8 + - - +
247O LYS* 4.2 4.5 - - - +
249O ALA* 1.3 73.7 - - - +
251O TRP* 1.3 59.6 + - - +
253O GLU* 3.5 11.0 - - + +
254O SER* 2.9 26.5 + - - -
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Residues in contact with TRP 251 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247O LYS 3.0 15.6 + - - +
248O TYR* 3.2 12.5 + - - +
250O GLN* 1.3 76.6 - - - +
252O GLU* 1.3 60.7 + - - +
254O SER* 3.4 20.1 + - - -
255O LEU* 3.8 4.3 + - - +
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Residues in contact with GLU 252 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248O TYR 3.0 12.9 + - - +
249O ALA* 3.3 8.7 + - - +
250O GLN 3.3 0.2 - - - -
251O TRP* 1.3 74.4 - - - +
253O GLU* 1.3 64.2 + - - +
255O LEU* 3.1 22.6 + - + +
256O LYS 3.8 2.4 + - - -
258O ILE* 4.5 16.2 - - + +
261O ALA* 4.6 15.5 - - + +
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Residues in contact with GLU 253 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249O ALA 2.9 17.0 + - - +
250O GLN* 3.2 14.1 + - + +
252O GLU* 1.3 74.6 - - - +
254O SER* 1.3 58.7 + - - +
256O LYS* 3.1 22.1 + - - +
258O ILE* 5.8 2.5 - - - -
261O ALA* 5.5 2.4 - - + +
285O MET* 5.9 7.2 - - + -
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Residues in contact with SER 254 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250O GLN 2.9 12.3 + - - -
251O TRP* 3.5 15.0 - - - -
252O GLU 3.2 0.4 - - - -
253O GLU* 1.3 77.6 - - - +
255O LEU* 1.3 59.0 + - - +
256O LYS* 3.2 3.5 + - - +
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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
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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