Contacts of the strand formed by residues 266 - 273 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H VAL* 3.7 27.9 - - - +
263H GLU* 3.0 34.8 + - + +
264H GLY 3.3 0.6 - - - -
265H ASN* 1.3 79.2 - - - +
267H ILE* 1.3 63.9 + - - +
268H HIS* 3.5 33.1 + - + +
285H TYR* 3.3 34.8 + - + -
286H VAL 3.7 3.8 - - - -
287H ASP* 2.7 39.8 + - - +
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Residues in contact with ILE 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227H VAL* 3.9 20.4 - - + -
231H PHE* 3.6 43.7 - - + -
260H MET* 4.1 6.5 - - + -
261H TRP 3.3 7.2 - - - +
262H LYS* 3.5 33.7 - - + -
264H GLY 4.8 3.1 - - - +
265H ASN 5.0 0.4 - - - -
266H ARG* 1.3 75.6 - - - +
268H HIS* 1.3 67.9 + - - +
269H PHE* 3.7 0.7 + - - -
285H TYR* 3.2 2.6 - - - -
286H VAL* 3.0 34.0 + - + +
288H LEU* 3.7 27.4 - - + -
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Residues in contact with HIS 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165H VAL* 3.8 23.1 - - + +
166H ALA 3.6 17.1 + - - -
167H ILE* 4.4 4.0 - - + -
168H PRO* 3.6 23.1 - - + +
260H MET* 3.3 2.1 - - - -
261H TRP* 2.8 37.5 + - + +
263H GLU* 3.6 34.6 - - + +
266H ARG* 3.5 36.2 - - + +
267H ILE* 1.3 75.8 - - - +
269H PHE* 1.3 61.5 + - - +
284H ALA 3.6 12.4 + - - +
285H TYR* 4.1 2.1 - - - +
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Residues in contact with PHE 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167H ILE* 4.3 4.2 - - - +
220H PHE* 5.2 8.5 - + - -
223H SER* 3.6 28.5 - - - -
224H ALA* 4.9 9.0 - - + -
227H VAL* 4.2 15.5 - - + -
242H VAL* 5.3 3.6 - - + -
243H LYS 4.4 0.2 - - - -
244H ALA* 4.4 9.2 - - + -
258H THR* 4.2 3.4 - - + -
259H GLU 3.0 15.7 - - - +
260H MET* 4.2 10.5 - - + -
261H TRP* 4.1 4.3 - - - -
267H ILE 4.1 4.0 - - - -
268H HIS* 1.3 75.1 - - - +
270H GLN* 1.3 64.3 + - - +
271H THR* 3.8 14.6 - - - -
281H ILE* 4.0 9.4 - - + -
283H ASN 4.4 0.3 + - - -
284H ALA* 3.0 57.0 + - + +
285H TYR* 3.5 29.4 - - - -
286H VAL* 4.2 6.1 - - + -
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Residues in contact with GLN 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167H ILE* 3.5 33.1 - - + +
257H GLN 3.6 0.5 - - - +
258H THR* 3.6 1.2 - - - +
259H GLU* 2.8 57.4 + - - +
261H TRP* 3.8 10.5 - - + -
269H PHE* 1.3 75.1 - - - +
271H THR* 1.3 65.8 + - - +
272H LYS* 3.8 9.5 - - - +
279H ILE* 3.3 32.4 - - + +
281H ILE 3.5 15.9 - - - +
282H SER* 4.4 10.1 - - - +
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Residues in contact with THR 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219H THR* 4.0 11.2 - - + -
223H SER* 2.6 34.7 + - - +
256H LEU* 4.4 6.3 - - + -
257H GLN 3.2 13.0 - - - +
258H THR* 4.0 4.0 - - - +
269H PHE* 3.8 3.3 - - - -
270H GLN* 1.3 77.7 + - - +
272H LYS* 1.3 68.8 + - - +
279H ILE* 3.6 4.3 - - - +
280H VAL* 2.8 37.1 + - + -
281H ILE* 2.9 32.6 + - - +
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Residues in contact with LYS 272 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256H LEU* 3.4 5.5 - - - +
257H GLN* 2.8 49.2 + - + +
259H GLU* 3.0 40.2 + - - +
270H GLN* 3.8 11.6 - - - +
271H THR* 1.3 81.9 - - - +
273H VAL* 1.3 67.1 + - - +
277H GLY* 4.0 16.6 + - - +
278H ASP 3.0 15.3 - - - +
279H ILE* 3.9 18.6 - - + -
280H VAL* 4.3 1.6 - - - +
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Residues in contact with VAL 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249H PRO 4.6 2.5 - - - +
250H VAL* 3.9 15.3 - - + -
254H GLN* 3.8 33.7 - - + +
255H THR 3.3 4.5 - - - +
256H LEU* 4.5 7.0 - - + -
272H LYS* 1.3 77.1 - - - +
274H GLN* 1.3 51.2 + - - +
275H GLU* 2.7 31.7 + - + +
276H THR* 3.0 14.6 + - - +
277H GLY* 2.7 32.2 + - - -
278H ASP* 3.1 7.0 + - + +
280H VAL* 3.5 27.1 - - + -
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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