Contacts of the strand formed by residues 279 - 288 (chain F) in PDB entry 1S9C
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 279 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247F ALA* 3.1 21.1 - - + +
248F LYS* 3.2 17.3 + - - +
270F GLN* 3.3 29.4 - - + +
271F THR 3.6 4.5 - - - +
272F LYS* 3.9 21.3 - - + -
277F GLY 4.5 2.9 - - - +
278F ASP* 1.3 73.3 - - - +
280F VAL* 1.3 60.8 + - - +
281F ILE 3.6 25.1 - - - +
282F SER* 4.1 14.4 - - - -
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Residues in contact with VAL 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219F THR* 3.9 17.0 - - + -
246F PHE* 3.7 4.2 - - - +
247F ALA* 2.8 23.0 + - - -
248F LYS* 3.3 24.0 - - + +
249F PRO 3.6 5.4 - - - +
250F VAL* 3.3 26.5 - - + -
256F LEU* 4.7 0.4 - - + -
271F THR* 2.8 43.4 + - + +
272F LYS* 4.2 3.1 - - - +
273F VAL* 3.5 18.4 - - + -
278F ASP* 4.1 5.8 - - + +
279F ILE* 1.3 77.3 - - - +
281F ILE* 1.3 61.8 + - - +
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Residues in contact with ILE 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219F THR* 3.7 26.5 - - + +
220F PHE* 3.7 28.7 - - + +
223F SER* 4.7 1.3 - - - +
244F ALA* 3.9 21.8 - - + -
245F ARG 3.3 10.1 - - - +
246F PHE* 4.3 14.1 - - + -
269F PHE* 4.0 17.9 - - + -
270F GLN* 3.4 8.3 - - - +
271F THR* 2.8 41.8 + - - +
279F ILE* 3.6 2.8 - - - +
280F VAL* 1.3 91.6 - - + +
282F SER* 1.3 64.3 + - - +
284F ALA* 4.0 4.3 - - + -
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Residues in contact with SER 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245F ARG* 2.8 44.8 + - - +
247F ALA* 4.9 7.7 - - - +
270F GLN* 4.4 9.0 - - - +
279F ILE* 4.1 15.5 - - - -
281F ILE* 1.3 75.0 - - - +
283F ASN* 1.3 89.0 + - - +
284F ALA* 2.9 6.0 + - - +
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Residues in contact with ASN 283 (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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164F ALA* 3.6 16.7 - - + +
165F VAL 2.8 46.5 + - - +
166F ALA* 3.3 22.7 - - - +
167F ILE* 4.3 13.9 + - - +
243F LYS* 4.4 1.4 - - - +
244F ALA* 4.9 0.5 - - - -
245F ARG* 3.8 20.6 - - + +
269F PHE 4.4 2.4 + - - -
270F GLN* 5.1 0.4 + - - +
282F SER* 1.3 98.5 + - - +
284F ALA* 1.3 57.2 + - - +
285F TYR* 4.8 0.7 - - - -
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Residues in contact with ALA 284 (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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165F VAL 4.4 3.1 - - - +
167F ILE* 5.1 1.0 - - - +
243F LYS 3.0 15.9 - - - +
244F ALA* 3.6 12.8 - - + -
268F HIS* 3.6 5.4 + - - +
269F PHE* 3.0 59.9 + - + +
281F ILE* 4.0 4.0 - - + -
282F SER 3.0 4.0 - - - +
283F ASN* 1.3 80.4 - - - +
285F TYR* 1.3 66.6 + - - +
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Residues in contact with TYR 285 (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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93F TYR* 4.0 15.0 - + - -
162F LYS* 5.7 1.4 - - - +
163F VAL 4.0 5.9 + - - -
165F VAL* 3.4 37.9 - - + -
241F ALA* 4.7 4.7 - - + -
242F VAL* 3.2 5.3 - - - +
243F LYS* 2.9 63.7 + - + +
266F ARG* 3.3 48.9 + - + -
267F ILE 3.2 15.3 - - - +
268F HIS* 4.1 6.1 - - - +
269F PHE* 3.5 6.5 - - - -
284F ALA* 1.3 78.2 - - - +
286F VAL* 1.3 68.3 + - - +
287F ASP* 3.3 17.8 + - - -
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Residues in contact with VAL 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224F ALA* 5.9 1.3 - - - -
227F VAL* 3.1 39.0 - - + -
239F PHE* 3.8 28.0 - - + -
241F ALA 3.0 13.5 - - - +
242F VAL* 4.0 9.0 - - + -
265F ASN 3.8 0.2 - - - +
266F ARG* 3.7 0.3 - - - -
267F ILE* 2.9 37.3 + - + +
269F PHE* 4.3 4.7 - - + -
285F TYR* 1.3 79.4 - - - +
287F ASP* 1.3 68.1 + - - +
288F LEU* 3.8 21.2 + - + -
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Residues in contact with ASP 287 (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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240F LYS* 3.0 35.0 + - + +
241F ALA* 2.7 25.6 + - + +
265F ASN* 3.6 4.0 - - + +
266F ARG* 2.8 53.3 + - - +
285F TYR* 3.3 11.2 + - - -
286F VAL* 1.3 73.4 - - - +
288F LEU* 1.3 66.4 + - - +
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Residues in contact with LEU 288 (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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227F VAL* 5.2 4.5 - - + +
228F LEU* 5.7 0.4 - - - -
231F PHE* 3.1 33.4 - - + +
232F ALA* 3.9 16.8 - - + -
238F ARG* 3.0 28.0 - - + +
239F PHE* 4.2 8.7 - - + -
240F LYS* 4.4 7.5 + - - +
265F ASN* 2.8 38.9 + - + +
267F ILE* 3.8 29.2 - - + -
286F VAL* 3.9 16.8 - - + +
287F ASP* 1.3 80.7 - - - +
289F ALA* 1.3 60.3 + - - +
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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