Contacts of the helix formed by residues 253 - 266 (chain F) in PDB entry 5IJ7
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 253 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250F ARG* 4.0 14.4 + - - -
251F ILE 3.4 0.4 - - - -
252F ASN* 1.3 84.1 + - - +
254F LYS* 1.3 77.1 + - - +
255F ARG* 3.8 7.4 + - - +
256F MET* 3.1 29.5 + - - +
257F MET* 2.8 28.8 + - - +
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Residues in contact with LYS 254 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252F ASN 3.9 0.6 + - - -
253F SER* 1.3 88.0 - - - +
255F ARG* 1.3 66.5 + - + +
257F MET* 4.1 13.5 - - + +
258F ASN* 2.9 40.3 + - - +
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Residues in contact with ARG 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253F SER* 4.0 7.6 - - - +
254F LYS* 1.3 82.4 - - + +
256F MET* 1.3 59.3 + - + +
258F ASN* 3.6 4.9 + - - +
259F ALA* 3.1 28.2 + - - +
278F GLN* 2.7 52.6 + - - +
279F LYS 3.6 25.1 + - - +
280F ILE* 3.6 27.1 - - + +
281F HIS 5.3 0.6 - - - +
590T GLU* 4.0 23.3 + - - -
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Residues in contact with MET 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203F LEU* 3.6 31.2 - - + -
212F VAL* 4.1 7.9 - - + -
213F ALA* 3.9 27.4 - - + -
215F PHE* 3.9 11.7 - - + -
250F ARG 3.7 13.9 - - - +
251F ILE* 3.6 26.5 - - + +
253F SER* 3.1 18.0 + - - +
255F ARG* 1.3 79.5 - - + +
257F MET* 1.4 64.2 + - - +
259F ALA* 3.3 2.6 + - - +
260F ILE* 3.1 31.1 + - + +
278F GLN* 4.5 9.0 - - - -
280F ILE* 3.9 21.8 - - + -
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Residues in contact with MET 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251F ILE 3.9 4.0 - - - +
252F ASN* 3.2 38.4 - - - +
253F SER 2.8 22.3 + - - +
254F LYS* 4.1 10.1 - - + +
256F MET* 1.4 70.6 - - - +
258F ASN* 1.4 59.3 + - - +
260F ILE* 3.5 9.9 + - + +
261F LYS* 3.1 27.9 + - - +
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Residues in contact with ASN 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254F LYS* 2.9 30.1 + - - +
255F ARG* 3.9 4.6 - - - +
257F MET* 1.4 75.7 - - - +
259F ALA* 1.3 54.5 + - - +
261F LYS* 3.2 14.8 + - + +
262F GLU* 2.7 45.1 + - + +
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Residues in contact with ALA 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F VAL* 3.8 17.3 - - + +
255F ARG 3.1 19.0 + - - +
256F MET* 3.3 8.3 + - - +
258F ASN* 1.3 75.5 - - - +
260F ILE* 1.4 55.6 + - - +
262F GLU* 3.5 7.5 + - - +
263F SER* 2.9 30.1 + - - -
275F PHE* 3.8 7.6 - - + -
278F GLN* 3.5 33.7 - - + +
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Residues in contact with ILE 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185F HIS* 5.6 1.8 - - + +
188F ASP* 4.6 2.0 - - - +
191F LEU* 3.9 37.9 - - + -
203F LEU* 4.5 11.7 - - + -
212F VAL* 4.0 15.7 - - + -
251F ILE* 4.2 24.0 - - + +
256F MET* 3.1 24.5 + - + +
257F MET* 3.7 8.3 - - + +
259F ALA* 1.4 71.4 - - - +
261F LYS* 1.4 65.2 + - - +
263F SER* 2.7 24.8 + - - -
264F TYR* 3.3 25.2 + - + -
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Residues in contact with LYS 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257F MET 3.1 14.6 + - - +
258F ASN* 3.2 19.7 + - - +
260F ILE* 1.4 74.7 - - - +
262F GLU* 1.3 68.6 + - + +
264F TYR* 3.0 22.1 + - - +
265F ASP* 3.2 40.3 + - - +
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Residues in contact with GLU 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258F ASN* 2.7 26.2 + - + +
259F ALA* 3.7 7.4 - - - +
261F LYS* 1.3 76.7 - - + +
263F SER* 1.4 56.7 + - - +
264F TYR 3.3 0.2 - - - -
265F ASP* 3.4 14.0 + - + +
266F TYR* 3.1 22.9 + - - +
275F PHE* 3.4 23.1 - - + -
276F ILE* 5.5 3.1 - - - +
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Residues in contact with SER 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205F ASN* 2.8 21.5 + - - -
208F THR* 2.7 27.4 + - - +
210F THR* 3.4 19.1 - - - -
212F VAL* 3.6 18.2 - - - +
259F ALA 2.9 16.0 + - - -
260F ILE* 2.7 19.4 + - - -
262F GLU* 1.4 75.1 - - - +
264F TYR* 1.3 57.3 + - - +
266F TYR* 3.5 9.9 + - - +
275F PHE* 3.7 14.8 - - - -
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Residues in contact with TYR 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188F ASP* 2.7 42.1 + - - -
190F ASN* 2.9 22.5 + - - +
191F LEU* 4.8 0.4 - - + +
205F ASN* 3.5 28.5 - - - -
207F GLN* 4.0 17.0 - - + -
208F THR* 3.6 18.2 - - + +
260F ILE* 3.4 30.5 - - + -
261F LYS* 3.0 11.1 + - - +
263F SER* 1.3 80.7 + - - +
265F ASP* 1.4 62.9 + - - +
266F TYR 3.5 1.6 + - - +
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Residues in contact with ASP 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261F LYS* 3.2 47.0 + - - +
262F GLU* 3.4 13.3 + - - +
264F TYR* 1.4 76.8 - - - +
266F TYR* 1.3 65.5 + - - +
267F ASN* 3.3 8.1 + - - +
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Residues in contact with TYR 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208F THR* 4.0 21.8 - - - +
210F THR* 3.6 18.6 - - + -
262F GLU 3.1 12.8 + - - +
263F SER 3.5 12.8 - - - +
264F TYR 3.3 2.4 - - - +
265F ASP* 1.3 75.6 - - - +
267F ASN* 1.3 59.6 + - - +
268F PRO* 3.7 33.1 - - + +
271F THR* 3.8 11.7 - - + -
273F ARG 3.0 14.7 + - - -
274F PRO* 3.7 1.1 - - - +
275F PHE* 3.5 47.2 + + + -
575T ARG* 2.8 34.1 + - - -
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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