Contacts of the strand formed by residues 279 - 288 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247G ALA* 3.1 20.5 - - + +
248G LYS* 3.2 19.4 + - - +
270G GLN* 3.3 28.5 - - + +
271G THR 3.5 5.4 - - - +
272G LYS* 3.9 23.3 - - + -
277G GLY 4.5 2.2 - - - +
278G ASP* 1.3 72.7 - - - +
280G VAL* 1.3 61.5 + - - +
281G ILE 3.6 25.4 - - - +
282G SER* 4.0 13.5 - - - -
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Residues in contact with VAL 280 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G THR* 3.9 9.4 - - + -
246G PHE* 3.7 4.3 - - - +
247G ALA* 2.8 22.9 + - - -
248G LYS* 3.3 22.3 - - + +
249G PRO 3.7 5.4 - - - +
250G VAL* 3.3 34.5 - - + -
256G LEU* 4.7 0.4 - - + -
271G THR* 2.7 42.7 + - + +
272G LYS* 4.2 3.4 - - - +
273G VAL* 3.5 17.5 - - + -
278G ASP* 4.1 6.1 - - + +
279G ILE* 1.3 76.6 - - - +
281G ILE* 1.3 62.0 + - + +
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Residues in contact with ILE 281 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G THR* 3.7 17.0 - - + +
220G PHE* 3.7 38.1 - - + +
223G SER* 4.6 1.8 - - - +
244G ALA* 3.8 22.4 - - + -
245G ARG 3.3 9.4 - - - +
246G PHE* 4.2 13.5 - - + -
269G PHE* 4.0 18.4 - - + -
270G GLN* 3.4 9.0 - - - +
271G THR* 2.9 39.1 + - - +
279G ILE* 3.6 2.7 - - - +
280G VAL* 1.3 94.0 - - + +
282G SER* 1.3 63.7 + - - +
284G ALA* 4.1 4.3 - - + -
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Residues in contact with SER 282 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245G ARG* 2.8 44.9 + - - +
247G ALA* 4.9 7.8 - - - +
270G GLN* 4.4 9.9 - - - +
279G ILE* 4.0 16.2 - - - -
280G VAL 4.4 0.2 - - - -
281G ILE* 1.3 74.3 - - - +
283G ASN* 1.3 88.3 + - - +
284G ALA* 3.0 4.8 + - - -
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Residues in contact with ASN 283 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164G ALA* 3.5 17.2 - - + +
165G VAL 2.9 45.2 + - - +
166G ALA* 3.4 22.0 - - - +
167G ILE* 4.3 14.2 + - - +
243G LYS* 4.3 2.6 - - - +
244G ALA* 4.9 0.5 - - - -
245G ARG* 3.7 21.5 - - + +
269G PHE 4.4 2.4 + - - -
270G GLN* 5.0 0.6 + - - +
282G SER* 1.3 97.3 + - - +
284G ALA* 1.3 57.0 + - - +
285G TYR* 4.8 0.2 - - - -
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Residues in contact with ALA 284 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G VAL 4.4 3.5 - - - +
167G ILE* 5.1 1.2 - - - +
243G LYS 2.9 18.2 - - - +
244G ALA* 3.6 12.6 - - + -
268G HIS* 3.5 5.5 + - - +
269G PHE* 3.0 59.2 + - + +
281G ILE* 4.1 4.0 - - + -
282G SER 3.1 3.8 - - - +
283G ASN* 1.3 80.6 - - - +
285G TYR* 1.3 64.8 + - - +
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Residues in contact with TYR 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G TYR* 3.9 20.1 - + - -
162G LYS* 5.6 1.6 - - - +
163G VAL 4.0 5.9 + - - -
165G VAL* 3.4 37.5 - - + -
241G ALA* 4.7 4.4 - - + +
242G VAL* 3.2 5.9 - - - +
243G LYS* 2.9 57.2 + - + +
266G ARG* 3.2 48.9 + - + -
267G ILE 3.2 14.8 - - - +
268G HIS* 4.1 5.8 - - - +
269G PHE* 3.5 6.1 - - - -
284G ALA* 1.3 78.0 - - - +
286G VAL* 1.3 69.5 + - - +
287G ASP* 3.2 17.5 + - - -
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Residues in contact with VAL 286 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224G ALA* 6.0 1.3 - - + -
227G VAL* 3.1 38.1 - - + -
239G PHE* 3.7 28.9 - - + -
241G ALA 3.0 12.6 - - - +
242G VAL* 4.1 7.9 - - + -
265G ASN 3.8 0.9 - - - +
266G ARG* 3.6 0.3 - - - -
267G ILE* 2.9 37.5 + - + +
269G PHE* 4.3 4.9 - - + -
285G TYR* 1.3 80.2 - - - +
287G ASP* 1.3 66.4 + - - +
288G LEU* 3.8 19.9 + - + -
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Residues in contact with ASP 287 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240G LYS* 3.0 34.3 + - + +
241G ALA* 2.7 24.9 + - + +
265G ASN* 3.5 3.7 - - + +
266G ARG* 2.7 53.7 + - - +
285G TYR* 3.2 11.5 + - - -
286G VAL* 1.3 71.7 - - - +
288G LEU* 1.3 65.6 + - - +
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Residues in contact with LEU 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227G VAL* 5.2 4.5 - - + +
228G LEU* 5.7 0.2 - - - -
231G PHE* 3.2 34.1 - - + +
232G ALA* 4.0 15.3 - - + -
238G ARG* 3.1 28.5 - - + +
239G PHE* 4.2 7.9 - - + -
240G LYS* 4.4 8.4 + - - +
265G ASN* 2.7 38.2 + - - +
267G ILE* 3.8 27.6 - - + -
286G VAL* 3.8 18.2 - - + +
287G ASP* 1.3 83.6 - - - +
289G ALA* 1.3 60.2 + - - +
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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