Contacts of the strand formed by residues 280 - 289 (chain A) in PDB entry 1F0C
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 ASP 280 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A PHE 3.3 0.9 - - - +
228A ASN* 3.6 6.5 - - - -
229A HIS 2.9 29.5 + - - +
278A SER 3.6 8.9 + - - +
279A MET* 1.3 82.5 - - - +
281A ALA* 1.3 70.3 + - - +
282A MET* 3.4 11.0 + - + +
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Residues in contact with ALA 281 (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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226A ALA* 5.0 9.6 - - + -
227A PHE* 3.4 9.6 - - - +
228A ASN* 3.4 12.7 + - - +
280A ASP* 1.3 75.5 - - - +
282A MET* 1.3 64.8 + - - +
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Residues in contact with MET 282 (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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226A ALA* 3.1 6.1 - - - +
227A PHE 2.9 31.1 + - - +
229A HIS* 3.8 18.6 - - + +
230A ALA* 5.9 0.2 - - - -
280A ASP* 3.5 16.6 - - + +
281A ALA* 1.3 80.5 - - - +
283A PHE* 1.3 69.3 + - - +
284A ILE* 3.5 4.5 + - + +
361B THR* 3.0 42.4 - - + +
362B ASN* 5.6 0.7 - - - +
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Residues in contact with PHE 283 (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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224A GLY* 4.3 15.0 - - - -
225A GLU 3.5 11.7 - - - +
226A ALA* 3.8 22.7 - - + -
282A MET* 1.3 77.9 - - - +
284A ILE* 1.3 63.7 + - - +
361B THR 3.5 13.7 - - - +
362B ASN* 4.2 3.3 - - - +
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Residues in contact with ILE 284 (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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223A MET 4.5 0.5 - - - +
224A GLY* 5.4 0.6 - - - +
225A GLU 3.2 16.5 + - - +
227A PHE* 3.9 27.8 - - + +
229A HIS* 3.8 33.0 - - + +
240A ILE* 4.0 13.0 - - + -
282A MET* 3.8 12.1 - - + +
283A PHE* 1.3 78.5 - - - +
285A ASP* 1.3 76.0 + - - +
286A VAL* 3.8 1.8 + - + -
361B THR 3.9 10.1 - - - +
362B ASN 3.2 19.1 - - - +
363B GLU 3.5 21.8 - - - +
364B PHE* 3.7 14.8 - - + +
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Residues in contact with ASP 285 (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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223A MET 3.6 4.9 - - - +
224A TYR* 2.4 59.5 + - + +
284A ILE* 1.3 74.9 - - - +
286A VAL* 1.3 55.7 + - - +
287A HIS* 4.2 16.4 - - - +
362B ASN 2.7 15.7 + - - +
363B GLU* 3.4 9.0 - - + +
364B PHE 2.6 33.8 + - - +
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Residues in contact with VAL 286 (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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198A PHE* 4.1 15.7 - - + -
221A MET 3.7 0.2 - - - +
222A SER* 3.1 4.3 - - - -
223A MET* 2.7 47.8 + - + +
227A PHE* 3.9 24.9 - - + -
240A ILE* 3.7 28.9 - - + -
242A LEU* 4.3 11.7 - - + -
284A ILE* 4.1 2.0 - - + +
285A ASP* 1.3 75.4 - - - +
287A HIS* 1.3 68.0 + - - +
288A ILE* 3.5 27.6 - - + -
364B PHE* 3.7 8.1 - - + -
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Residues in contact with HIS 287 (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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206A TYR* 4.0 12.7 + + + -
220A MET* 3.7 18.2 - - + -
221A MET 2.9 7.6 - - - +
222A SER* 2.7 27.2 + - - -
224A TYR* 3.6 32.0 - + - -
285A ASP* 4.2 9.0 - - + +
286A VAL* 1.3 77.3 + - - +
288A ILE* 1.3 65.7 + - - +
363B GLU* 3.8 32.6 + - + +
364B PHE 2.9 17.0 + - - +
365B CYS* 4.3 15.5 - - + -
366B ALA 2.9 27.9 + - - -
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Residues in contact with ILE 288 (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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198A PHE* 4.8 2.5 - - + -
220A MET* 3.4 5.3 - - - -
221A MET* 2.6 50.0 + - + +
242A LEU* 4.6 9.2 - - + -
250A MET* 5.1 10.8 - - + -
252A VAL* 4.5 13.2 - - + -
286A VAL* 3.5 19.0 - - + -
287A HIS* 1.3 81.3 - - - +
289A PRO* 1.3 85.6 - - + +
291A PHE* 5.0 4.3 - - + -
340A VAL* 5.6 1.1 - - + -
364B PHE* 3.4 34.5 - - + -
366B ALA* 3.6 7.2 - - + -
370B PHE* 4.3 12.6 - - + -
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Residues in contact with PRO 289 (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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208A PHE* 4.3 4.7 - - + -
218A VAL* 4.4 3.6 - - + -
219A SER 3.4 11.9 - - - +
220A MET* 3.7 13.5 - - + -
221A MET* 3.9 7.2 - - - +
288A ILE* 1.3 103.9 - - + +
290A LYS* 1.3 64.8 + - - +
291A PHE* 3.4 13.3 - - + -
340A VAL* 4.1 1.9 - - - +
366B ALA 3.6 23.8 - - - +
370B PHE* 3.7 18.2 - - + -
388B TYR* 3.9 32.5 - - + +
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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