Contacts of the strand formed by residues 266 - 273 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B VAL* 3.8 26.3 - - - +
261B TRP 3.6 0.9 - - - +
263B GLU* 3.0 35.3 + - - +
264B GLY 3.3 0.4 - - - -
265B ASN* 1.3 81.0 - - - +
267B ILE* 1.3 63.1 + - - +
268B HIS* 3.6 32.2 + - + +
285B TYR* 3.2 36.5 + - + -
286B VAL 3.7 3.8 - - - -
287B ASP* 2.8 39.9 + - - +
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Residues in contact with ILE 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B VAL* 3.8 20.4 - - + -
231B PHE* 3.5 44.9 - - + -
260B MET* 4.0 8.1 - - + -
261B TRP 3.4 5.4 - - - +
262B LYS* 3.5 33.9 - - + -
264B GLY 4.8 3.1 - - - +
266B ARG* 1.3 74.5 - - - +
268B HIS* 1.3 70.3 + - - +
269B PHE* 3.7 0.7 + - - -
285B TYR* 3.2 3.4 - - - -
286B VAL* 3.0 33.3 + - + +
288B LEU* 3.8 26.9 - - + -
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Residues in contact with HIS 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B VAL* 3.8 24.0 - - + +
166B ALA 3.7 16.3 + - - -
167B ILE* 4.5 3.7 - - + -
168B PRO* 3.7 24.8 - - + +
260B MET* 3.2 1.9 - - - -
261B TRP* 2.8 37.7 + - + +
263B GLU* 3.5 35.9 - - + +
266B ARG* 3.6 33.7 - - + +
267B ILE* 1.3 75.7 - - - +
269B PHE* 1.3 63.1 + - - +
284B ALA 3.5 11.4 + - - +
285B TYR* 4.1 1.9 - - - +
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Residues in contact with PHE 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ILE* 4.4 2.7 - - - +
220B PHE* 5.2 9.0 - + - -
223B SER* 3.5 28.0 - - - -
224B ALA* 4.9 9.0 - - + -
227B VAL* 4.2 13.9 - - + -
242B VAL* 5.3 3.4 - - + -
243B LYS 4.4 0.4 - - - -
244B ALA* 4.4 9.6 - - + -
258B THR* 4.2 3.6 - - + -
259B GLU 3.0 13.9 - - - +
260B MET* 4.2 11.9 - - + -
261B TRP* 4.1 3.4 - - - -
267B ILE 4.1 3.6 - - - -
268B HIS* 1.3 75.1 - - - +
270B GLN* 1.3 63.7 + - - +
271B THR* 3.7 15.3 - - - -
281B ILE* 4.0 9.9 - - + -
283B ASN 4.4 1.4 + - - -
284B ALA* 2.9 58.4 + - + +
285B TYR* 3.5 29.6 - - - -
286B VAL* 4.3 5.8 - - + -
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Residues in contact with GLN 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ILE* 3.5 34.6 - - + +
257B GLN 3.6 0.5 - - - +
258B THR* 3.5 1.7 - - - +
259B GLU* 2.7 61.4 + - - +
261B TRP* 3.8 10.7 - - + -
269B PHE* 1.3 75.4 - - - +
271B THR* 1.3 64.9 + - - +
272B LYS* 3.8 10.5 - - - +
279B ILE* 3.3 32.8 - - + +
281B ILE 3.5 15.7 - - - +
282B SER* 4.4 9.1 - - - -
283B ASN 5.6 0.2 + - - -
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Residues in contact with THR 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B THR* 4.0 10.8 - - + -
223B SER* 2.6 34.8 + - - +
256B LEU* 4.4 6.1 - - + -
257B GLN 3.3 13.0 - - - +
258B THR* 4.0 4.4 + - - +
269B PHE* 3.7 3.5 - - - -
270B GLN* 1.3 77.9 + - - +
272B LYS* 1.3 71.1 + - - +
279B ILE* 3.5 4.5 - - - +
280B VAL* 2.8 37.1 + - + -
281B ILE* 2.9 31.9 + - - +
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Residues in contact with LYS 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B LEU* 3.4 5.5 - - - +
257B GLN* 2.8 48.8 + - + +
259B GLU* 3.1 41.2 + - - +
270B GLN* 3.8 10.9 - - - +
271B THR* 1.3 81.7 - - - +
273B VAL* 1.3 67.6 + - - +
274B GLN 3.8 0.2 - - - -
277B GLY* 3.9 16.8 + - - +
278B ASP 3.0 14.6 - - - +
279B ILE* 3.9 19.5 - - + -
280B VAL* 4.3 1.6 - - - +
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B PRO 4.6 2.5 - - - +
250B VAL* 3.9 15.0 - - + -
254B GLN* 3.8 35.0 - - + +
255B THR 3.3 4.7 - - - +
256B LEU* 4.5 4.7 - - + -
272B LYS* 1.3 77.5 - - - +
274B GLN* 1.3 50.7 + - - +
275B GLU* 2.7 31.6 + - + +
276B THR* 3.0 15.2 + - - +
277B GLY* 2.7 32.4 + - - -
278B ASP* 3.0 8.6 + - + +
280B VAL* 3.5 28.0 - - + -
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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
------------------------------------------------------------
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