Contacts of the strand formed by residues 279 - 288 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247C ALA* 3.1 21.3 - - + +
248C LYS* 3.2 18.9 + - - +
270C GLN* 3.3 28.7 - - + +
271C THR 3.5 4.7 - - - +
272C LYS* 3.9 22.7 - - + -
277C GLY 3.6 2.9 + - - +
278C ASP* 1.3 71.8 - - - +
280C VAL* 1.3 62.2 + - - +
281C ILE 3.5 26.0 - - - +
282C SER* 4.0 13.0 - - - -
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Residues in contact with VAL 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C THR* 3.9 9.4 - - + -
246C PHE* 3.7 4.0 - - - +
247C ALA* 2.9 23.3 + - - -
248C LYS* 3.3 24.0 - - + +
249C PRO 3.6 6.1 - - - +
250C VAL* 3.3 34.1 - - + -
256C LEU* 4.7 0.2 - - + -
271C THR* 2.7 42.8 + - + +
272C LYS* 4.2 3.4 - - - +
273C VAL* 3.6 17.7 - - + -
278C ASP* 3.6 5.1 + - + +
279C ILE* 1.3 76.1 - - - +
281C ILE* 1.3 61.9 + - - +
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Residues in contact with ILE 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C THR* 3.7 16.6 - - + +
220C PHE* 3.7 39.0 - - + +
223C SER* 4.7 1.3 - - - +
244C ALA* 3.9 22.4 - - + -
245C ARG 3.3 9.0 - - - +
246C PHE* 4.2 13.7 - - + -
269C PHE* 4.0 18.2 - - + -
270C GLN* 3.5 4.4 - - - -
271C THR* 2.9 42.0 + - - +
279C ILE* 3.5 7.8 - - - +
280C VAL* 1.3 91.6 - - + +
282C SER* 1.3 63.3 + - - +
284C ALA* 4.1 4.5 - - + -
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Residues in contact with SER 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C ARG* 2.8 47.2 + - - +
247C ALA* 4.9 7.7 - - - +
270C GLN* 4.4 9.4 - - - +
279C ILE* 4.0 16.2 - - - -
281C ILE* 1.3 75.0 - - - +
283C ASN* 1.3 87.6 + - - +
284C ALA* 2.9 5.7 + - - +
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Residues in contact with ASN 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C ALA* 3.7 17.0 - - + +
165C VAL 2.8 45.6 + - - +
166C ALA* 3.3 22.9 - - - +
167C ILE* 4.3 14.8 + - - +
243C LYS* 4.4 1.9 - - - +
244C ALA* 4.9 0.2 - - - -
245C ARG* 3.7 21.4 - - + +
269C PHE 4.4 2.8 + - - -
270C GLN* 5.6 0.2 + - - -
282C SER* 1.3 95.7 + - - +
284C ALA* 1.3 57.5 + - - +
285C TYR* 4.7 0.7 - - - -
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Residues in contact with ALA 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C VAL 4.5 1.2 - - - +
167C ILE* 5.2 1.2 - - - +
243C LYS 3.0 18.6 - - - +
244C ALA* 3.6 14.1 - - + -
268C HIS* 3.5 7.6 + - - +
269C PHE* 3.0 59.8 + - + +
281C ILE* 4.1 3.6 - - + -
282C SER 3.0 4.2 - - - +
283C ASN* 1.3 80.1 - - - +
285C TYR* 1.3 65.0 + - - +
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Residues in contact with TYR 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C TYR* 3.9 20.3 - + - -
162C LYS* 5.7 1.0 - - - +
163C VAL 4.1 5.5 + - - -
165C VAL* 3.6 37.5 - - + -
241C ALA* 4.7 3.8 - - + -
242C VAL* 3.2 5.3 - - - +
243C LYS* 2.9 59.0 + - + +
266C ARG* 3.2 51.0 + - + -
267C ILE 3.2 14.8 - - - +
268C HIS* 4.1 5.4 - - - +
269C PHE* 3.6 6.3 - - - -
284C ALA* 1.3 78.7 - - - +
286C VAL* 1.3 68.0 + - - +
287C ASP* 3.2 17.9 + - - -
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Residues in contact with VAL 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C ALA* 6.0 0.9 - - - -
227C VAL* 3.2 37.9 - - + -
239C PHE* 3.7 29.8 - - + -
241C ALA 2.9 14.4 - - - +
242C VAL* 4.1 8.7 - - + -
266C ARG* 3.7 0.3 - - - -
267C ILE* 3.0 37.4 + - + +
269C PHE* 4.3 5.4 - - + -
285C TYR* 1.3 78.4 - - - +
287C ASP* 1.3 66.7 + - - +
288C LEU* 3.8 19.9 + - + -
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Residues in contact with ASP 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C LYS* 3.0 34.9 + - + +
241C ALA* 2.7 25.4 + - + +
265C ASN* 3.6 3.9 - - + +
266C ARG* 2.8 53.9 + - - +
285C TYR* 3.2 11.9 + - - -
286C VAL* 1.3 74.4 - - - +
288C LEU* 1.3 63.7 + - - +
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Residues in contact with LEU 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C VAL* 5.2 4.5 - - + -
228C LEU* 5.6 0.7 - - - -
231C PHE* 3.1 35.2 - - + +
232C ALA* 3.8 15.7 - - + -
238C ARG* 3.1 25.4 - - - +
239C PHE* 4.2 11.7 - - + -
240C LYS* 4.5 8.0 + - - +
265C ASN* 2.7 38.6 + - + +
267C ILE* 3.8 26.0 - - + -
286C VAL* 3.9 17.3 - - + +
287C ASP* 1.3 82.3 - - - +
289C ALA* 1.3 64.7 + - - +
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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