Contacts of the strand formed by residues 268 - 276 (chain B) in PDB entry 1SIW
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 268 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B MET* 4.2 11.6 - - + -
10B VAL 3.5 5.2 - - - +
11B LEU* 3.5 19.0 - - + +
22B CYS* 3.1 30.2 - - - -
42B ASN* 3.0 29.1 + - - -
181B PRO* 3.6 11.7 - - - +
183B LEU* 3.9 14.6 - - - +
259B CYS* 3.2 38.4 + - - -
260B SER* 4.1 23.1 - - - +
263B CYS* 4.0 8.8 - - + +
266B ARG* 3.6 0.6 - - - +
267B ILE* 1.3 89.7 - - + +
269B TYR* 1.3 64.5 + - - +
455B ARG* 3.8 10.7 + - - +
456B PHE* 3.4 19.6 - - - -
802B SF4 3.3 17.0 - - - -
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Residues in contact with TYR 269 (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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9B MET* 3.2 9.5 - - - +
10B VAL* 2.9 42.6 + - + +
12B ASN* 4.7 9.4 - - + -
15B LYS* 4.1 2.2 + - - +
266B ARG 4.1 6.5 + - - -
267B ILE* 3.3 26.0 - - - -
268B ARG* 1.3 75.1 - - - +
270B LEU* 1.3 61.1 + - - +
329B PRO* 4.0 14.4 - - + -
330B VAL* 3.6 4.0 - - + +
333B MET* 3.3 39.0 - - + -
446B TYR* 2.5 34.7 + - + -
447B LEU* 3.6 13.3 + - + +
450B ALA* 3.6 11.1 - - - +
454B ASP 4.6 2.0 - - - -
455B ARG* 3.2 39.7 - - + +
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Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 4.1 4.9 - - + -
8B GLY 3.5 13.9 - - - +
9B MET* 3.6 33.9 - - + -
246B PHE* 3.9 13.2 - - + -
251B ILE* 5.5 1.6 - - + -
256B PRO* 3.6 33.7 - - + -
257B THR* 3.7 7.2 - - + +
260B SER* 3.5 21.1 - - - +
269B TYR* 1.3 74.8 - - - +
271B GLY* 1.3 58.8 + - - +
329B PRO* 3.6 6.0 - - - +
330B VAL* 3.9 1.8 - - - -
455B ARG 2.8 10.9 + - - +
456B PHE* 4.0 8.9 - - + -
457B VAL 2.9 27.5 + - - -
458B VAL* 3.8 19.3 - - + -
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Residues in contact with GLY 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 4.0 5.0 - - - +
8B GLY* 2.7 38.7 + - - +
270B LEU* 1.3 75.3 - - - +
272B VAL* 1.3 62.8 + - - -
328B SER* 3.3 16.8 + - - -
329B PRO* 4.1 5.6 - - - -
330B VAL* 3.3 10.1 - - - +
457B VAL 3.9 8.7 - - - -
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B SER* 4.2 3.6 - - - -
6B GLN 3.4 9.0 - - - +
7B VAL* 4.2 9.4 - - + +
271B GLY* 1.3 72.6 - - - -
273B LEU* 1.3 75.3 + - - +
274B LEU* 4.1 6.1 - - + -
321B VAL* 4.0 18.6 - - + -
324B ALA* 4.1 8.7 + - + -
325B ALA* 3.6 34.4 - - + +
328B SER* 2.9 25.6 + - - -
331B TYR* 4.6 1.0 - - - +
457B VAL 4.2 2.4 + - - +
459B PRO* 3.5 39.7 - - + -
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B SER* 3.6 1.6 - - - -
6B GLN* 2.8 32.4 + - - +
8B GLY* 4.8 4.7 - - - +
271B GLY 4.4 2.0 - - - +
272B VAL* 1.3 84.8 - - - +
274B LEU* 1.3 61.4 - - - +
275B TYR* 3.9 4.4 + - - -
300B PHE* 3.7 46.9 - - + -
330B VAL* 3.8 22.9 - - + +
331B TYR* 3.9 41.1 - - + +
334B ALA* 5.7 2.2 - - + -
335B MET* 5.4 0.4 - - + -
352B MET* 3.7 23.1 - - + +
354B TRP* 6.3 1.1 - - + -
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Residues in contact with LEU 274 (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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3B ILE* 4.3 18.8 - - + -
4B ARG 3.4 6.1 - - - +
5B SER* 3.5 27.8 - - - -
272B VAL* 4.1 7.9 - - + -
273B LEU* 1.3 74.8 - - - +
275B TYR* 1.3 59.8 + - - +
300B PHE* 3.4 6.6 - - - +
301B LEU* 2.8 42.1 + - + +
303B PRO* 4.3 12.8 - - + -
308B VAL* 4.2 20.6 - - + -
309B ILE* 6.1 1.3 - - + -
312B ALA* 4.7 8.7 - - + -
317B ILE* 4.5 11.7 - - + -
321B VAL* 4.8 0.9 - - + +
322B ILE* 5.1 9.2 - - + -
325B ALA* 4.1 20.8 - - + +
331B TYR* 6.1 0.2 - - - -
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Residues in contact with TYR 275 (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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2B LYS 3.4 1.0 - - - +
3B ILE* 3.5 2.4 - - - -
4B ARG* 2.9 73.5 + - + +
5B SER 4.1 12.1 + - - -
6B GLN* 4.2 9.2 - - + -
188B LEU* 3.7 37.0 - - + -
203B LYS* 3.5 20.8 - - - +
204B ARG 5.5 0.7 + - - -
205B GLU* 5.2 1.7 + - - -
208B GLY* 4.9 2.1 - - - -
273B LEU 4.2 9.0 - - - +
274B LEU* 1.3 76.1 - - - +
276B ASP* 1.3 60.8 + - - +
277B ALA* 3.4 31.1 + - + -
280B ILE* 4.0 11.0 - - + -
299B VAL* 3.4 18.4 - - + +
300B PHE* 4.4 8.3 - - + -
301B LEU* 4.0 5.6 - - - -
352B MET* 4.8 2.9 - - + -
221C VAL* 5.8 0.3 - - - +
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Residues in contact with ASP 276 (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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1B MET* 3.5 40.2 + - + +
2B LYS 3.0 20.1 + - - -
275B TYR* 1.3 73.6 - - - +
277B ALA* 1.3 62.1 + - - +
278B ASP* 2.9 18.7 + - - +
279B ALA* 3.0 31.5 + - + +
280B ILE* 3.8 8.5 - - - +
282B ARG* 5.4 1.7 + - - -
299B VAL* 3.1 18.1 + - - +
301B LEU* 4.1 9.8 - - + +
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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