Contacts of the strand formed by residues 266 - 273 (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 ARG 266 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165K VAL* 3.7 27.5 - - - +
263K GLU* 3.0 34.8 + - + +
264K GLY 3.3 0.2 - - - -
265K ASN* 1.3 79.9 - - - +
267K ILE* 1.3 64.6 + - - +
268K HIS* 3.6 32.5 + - + +
285K TYR* 3.2 37.9 + - + -
286K VAL 3.6 3.4 - - - -
287K ASP* 2.7 40.0 + - - +
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Residues in contact with ILE 267 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227K VAL* 3.8 21.8 - - + -
231K PHE* 3.6 45.1 - - + -
260K MET* 4.1 6.5 - - + -
261K TRP 3.4 7.2 - - - +
262K LYS* 3.5 34.3 - - + -
264K GLY 4.8 2.9 - - - +
265K ASN 4.8 0.4 - - - +
266K ARG* 1.3 75.6 - - - +
268K HIS* 1.3 66.6 + - - +
269K PHE* 3.8 0.3 + - - -
285K TYR* 3.2 3.3 - - - -
286K VAL* 2.9 37.5 + - + +
288K LEU* 3.7 27.4 - - + -
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Residues in contact with HIS 268 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165K VAL* 3.7 26.7 + - + +
166K ALA 3.5 17.8 + - - -
167K ILE* 4.4 3.8 - - - -
168K PRO* 3.6 24.0 - - + +
260K MET* 3.3 2.1 - - - -
261K TRP* 2.8 37.9 + - + +
263K GLU* 3.5 36.6 - - + +
266K ARG* 3.6 30.9 - - + +
267K ILE* 1.3 73.6 - - - +
269K PHE* 1.3 63.0 + - - +
284K ALA 3.5 11.9 + - - +
285K TYR* 4.1 2.3 - - - +
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Residues in contact with PHE 269 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167K ILE* 4.4 3.6 - - - +
220K PHE* 5.2 8.5 - + - -
223K SER* 3.5 28.9 - - - -
224K ALA* 4.9 9.4 - - + -
227K VAL* 4.2 14.8 - - + -
242K VAL* 5.3 3.6 - - + -
243K LYS 4.4 0.4 - - - -
244K ALA* 4.4 9.2 - - + -
258K THR* 4.2 3.8 - - + -
259K GLU 3.0 14.1 - - - +
260K MET* 4.2 12.1 - - + -
261K TRP* 4.1 3.8 - - - -
267K ILE 4.1 3.6 - - - -
268K HIS* 1.3 75.6 - - - +
270K GLN* 1.3 64.5 + - - +
271K THR* 3.8 15.0 - - - -
281K ILE* 4.0 9.6 - - + -
283K ASN 4.4 0.5 + - - -
284K ALA* 3.0 58.0 + - + +
285K TYR* 3.5 29.6 - - - -
286K VAL* 4.3 5.4 - - + -
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Residues in contact with GLN 270 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167K ILE* 3.6 33.1 - - + +
257K GLN 3.6 0.9 - - - +
258K THR* 3.6 2.3 - - - +
259K GLU* 2.7 58.5 + - - +
261K TRP* 3.9 10.7 - - + -
269K PHE* 1.3 75.1 - - - +
271K THR* 1.3 62.0 + - - +
272K LYS* 3.9 10.5 - - - +
279K ILE* 3.3 32.6 - - + +
281K ILE 3.5 16.2 - - - +
282K SER* 4.4 9.2 - - - -
283K ASN 5.6 0.2 + - - -
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Residues in contact with THR 271 (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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219K THR* 4.0 11.7 - - + -
223K SER* 2.7 34.0 + - - +
256K LEU* 4.4 5.6 - - + -
257K GLN 3.2 11.7 - - - +
258K THR* 4.0 4.0 + - - +
269K PHE* 3.8 4.3 - - - -
270K GLN* 1.3 77.5 + - - +
272K LYS* 1.3 65.1 + - - +
279K ILE* 3.5 5.0 - - - +
280K VAL* 2.8 42.8 + - + -
281K ILE* 2.9 32.4 + - - +
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Residues in contact with LYS 272 (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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256K LEU* 3.4 6.1 - - - +
257K GLN* 2.8 51.1 + - + +
259K GLU* 3.1 37.8 + - - +
270K GLN* 3.9 11.1 - - - +
271K THR* 1.3 82.1 - - - +
273K VAL* 1.3 67.5 + - - +
274K GLN 3.8 0.9 - - - -
277K GLY* 3.9 16.8 + - - +
278K ASP 3.0 14.6 - - - +
279K ILE* 3.9 19.1 - - + -
280K VAL* 4.3 1.1 - - - +
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Residues in contact with VAL 273 (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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249K PRO 4.6 2.5 - - - +
250K VAL* 3.9 15.9 - - + -
254K GLN* 3.8 34.3 - - + +
255K THR 3.3 2.9 - - - +
256K LEU* 4.5 6.1 - - + -
272K LYS* 1.3 77.5 - - - +
274K GLN* 1.3 51.3 + - - +
275K GLU* 2.7 40.9 + - + +
276K THR* 2.9 14.8 + - - +
277K GLY* 2.7 21.7 + - - -
278K ASP* 3.0 8.2 + - + +
280K VAL* 3.5 26.9 - - + -
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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