Contacts of the strand formed by residues 279 - 288 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247K ALA* 3.1 20.6 - - + +
248K LYS* 3.2 19.0 + - - +
270K GLN* 3.3 28.9 - - + +
271K THR 3.5 5.2 - - - +
272K LYS* 3.9 22.9 - - + -
277K GLY 4.5 2.7 - - - +
278K ASP* 1.3 73.3 - - - +
280K VAL* 1.3 60.6 + - - +
281K ILE 3.5 24.9 - - - +
282K SER* 4.0 13.7 - - - -
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Residues in contact with VAL 280 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219K THR* 3.8 17.0 - - + -
246K PHE* 3.7 4.0 - - - +
247K ALA* 2.9 23.0 + - - -
248K LYS* 3.3 23.1 - - + +
249K PRO 3.7 6.3 - - - +
250K VAL* 3.3 28.0 - - + -
256K LEU* 4.7 0.4 - - + -
271K THR* 2.8 36.5 + - + +
272K LYS* 4.2 3.6 - - - +
273K VAL* 3.5 17.5 - - + -
278K ASP* 3.6 6.7 + - + +
279K ILE* 1.3 76.8 - - - +
281K ILE* 1.3 67.2 + - + +
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Residues in contact with ILE 281 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219K THR* 3.6 26.9 - - + +
220K PHE* 3.6 27.6 - - + +
223K SER* 4.7 1.3 - - - +
244K ALA* 3.8 22.9 - - + -
245K ARG 3.3 11.0 - - - +
246K PHE* 4.2 16.8 - - + -
269K PHE* 4.0 17.3 - - + -
270K GLN* 3.5 3.5 - - - -
271K THR* 2.9 41.5 + - - +
279K ILE* 3.5 7.8 - - - +
280K VAL* 1.3 91.2 - - + +
282K SER* 1.3 62.7 + - - +
284K ALA* 4.1 4.5 - - + -
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Residues in contact with SER 282 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245K ARG* 2.8 46.8 + - - +
247K ALA* 4.8 7.7 - - - +
269K PHE 4.7 0.2 - - - -
270K GLN* 4.4 9.6 - - - +
279K ILE* 4.0 16.2 - - - -
280K VAL 4.4 0.2 - - - -
281K ILE* 1.3 75.0 - - - +
283K ASN* 1.3 86.2 + - - +
284K ALA* 3.0 5.5 + - - +
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Residues in contact with ASN 283 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164K ALA* 3.6 17.7 - - + +
165K VAL 2.9 44.7 + - - +
166K ALA* 3.4 21.1 - - - +
167K ILE* 4.4 14.9 + - - +
243K LYS* 4.3 2.1 - - - +
244K ALA* 4.8 0.7 - - - -
245K ARG* 3.7 20.9 - - + +
269K PHE 4.4 2.2 + - - -
270K GLN* 5.1 0.6 + - - +
282K SER* 1.3 96.8 + - - +
284K ALA* 1.3 57.3 + - - +
285K TYR* 4.8 0.9 - - - -
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Residues in contact with ALA 284 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165K VAL 4.4 3.3 - - - +
167K ILE* 5.1 0.9 - - - +
243K LYS 3.0 16.4 - - - +
244K ALA* 3.6 13.0 - - + -
268K HIS* 3.5 5.4 + - - +
269K PHE* 3.0 59.1 + - + +
281K ILE* 4.1 3.6 - - + -
282K SER 3.0 3.8 - - - +
283K ASN* 1.3 79.4 - - - +
285K TYR* 1.3 67.9 + - - +
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Residues in contact with TYR 285 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93K TYR* 4.0 15.4 - + - -
162K LYS* 5.6 2.1 - - - +
163K VAL 4.0 5.8 + - - -
165K VAL* 3.4 38.6 - - + -
241K ALA* 4.7 3.8 - - + -
242K VAL* 3.2 6.1 - - - +
243K LYS* 2.9 62.5 + - + +
266K ARG* 3.2 48.9 + - + -
267K ILE 3.2 14.8 - - - +
268K HIS* 4.1 5.6 - - - +
269K PHE* 3.5 6.0 - - - -
284K ALA* 1.3 79.8 - - - +
286K VAL* 1.3 68.8 + - - +
287K ASP* 3.3 17.9 + - - -
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Residues in contact with VAL 286 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224K ALA* 6.0 1.3 - - - -
227K VAL* 3.1 38.4 - - + -
239K PHE* 3.7 29.2 - - + -
241K ALA 3.0 13.9 - - - +
242K VAL* 4.1 7.9 - - + -
265K ASN 3.8 0.9 - - - +
266K ARG* 3.6 0.5 - - - -
267K ILE* 2.9 36.9 + - + +
269K PHE* 4.3 4.5 - - + -
285K TYR* 1.3 79.7 - - - +
287K ASP* 1.3 66.3 + - - +
288K LEU* 3.8 19.4 + - + -
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Residues in contact with ASP 287 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238K ARG 3.8 0.2 - - - +
240K LYS* 2.9 35.6 + - + +
241K ALA* 2.7 23.7 + - + +
265K ASN* 3.6 4.4 - - + +
266K ARG* 2.7 54.0 + - - +
285K TYR* 3.3 11.8 + - - -
286K VAL* 1.3 74.0 - - - +
288K LEU* 1.3 64.3 + - - +
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Residues in contact with LEU 288 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227K VAL* 5.2 3.4 - - + -
228K LEU* 5.7 0.7 - - - -
231K PHE* 3.2 34.1 - - + +
232K ALA* 3.9 16.2 - - + -
238K ARG* 3.1 29.2 - - + +
239K PHE* 4.2 8.7 - - + -
240K LYS* 4.4 9.6 + - - +
265K ASN* 2.7 36.7 + - + +
267K ILE* 3.7 28.7 - - + -
286K VAL* 3.9 17.7 - - + +
287K ASP* 1.3 80.6 - - - +
289K ALA* 1.3 60.8 + - - +
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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