Contacts of the strand formed by residues 248 - 257 (chain B) in PDB entry 5ISO
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 VAL 248 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243B SER 4.6 0.9 - - - +
244B ILE* 3.6 5.9 - - - +
245B LYS 3.3 24.6 + - - +
246B ASP* 3.2 22.0 - - - +
247B GLY* 1.3 81.5 - - - +
249B MET* 1.3 60.3 + - - +
250B VAL* 4.3 19.9 - - + +
267B TYR* 4.4 12.1 - - + -
268B LYS 3.4 11.9 - - - +
269B PRO* 4.4 5.8 - - + -
270B ILE* 4.9 0.2 - - - -
55E LEU* 3.7 18.8 - - + -
59E LYS* 3.7 25.6 - - + +
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Residues in contact with MET 249 (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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544A ALA* 3.7 34.1 - - - +
547A ILE* 3.7 25.8 - - + -
241B ALA* 5.3 3.4 - - + -
242B LEU 5.2 1.8 - - - +
244B ILE* 3.5 33.4 - - + +
248B VAL* 1.3 74.8 - - - +
250B VAL* 1.3 59.5 + - - +
251B LEU* 3.6 30.5 - - + +
266B LEU 3.5 1.7 - - - +
267B TYR* 3.8 1.0 - - - -
268B LYS* 2.8 46.5 + - + +
270B ILE* 3.8 20.9 - - + +
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Residues in contact with VAL 250 (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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402A TRP* 3.4 28.2 - - + -
241B ALA* 3.3 7.6 - - - +
242B LEU* 3.2 46.4 + - + +
243B SER 5.7 0.8 + - - +
248B VAL* 4.3 10.5 - - + +
249B MET* 1.3 76.7 - - - +
251B LEU* 1.3 66.3 + - - +
265B LEU* 4.6 1.6 - - + -
266B LEU 3.3 8.5 - - - +
267B TYR* 3.4 54.5 - - + -
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Residues in contact with LEU 251 (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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402A TRP* 3.9 2.2 - - - -
540A PHE* 3.3 46.6 - - + +
543A CYS* 4.5 1.3 - - + -
544A ALA* 3.9 20.4 - - + +
547A ILE* 4.2 8.1 - - + -
239B LEU* 3.9 19.3 - - + -
240B TYR 3.4 4.3 - - - +
241B ALA* 3.7 15.3 - - + -
249B MET* 3.6 30.1 - - + -
250B VAL* 1.3 82.8 - - - +
252B SER* 1.3 62.1 + - - +
265B LEU* 3.2 5.5 - - - +
266B LEU* 2.9 36.7 + - + +
268B LYS* 6.1 2.0 - - + -
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Residues in contact with SER 252 (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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402A TRP* 3.6 22.0 - - - -
540A PHE* 3.7 4.7 - - - -
215B LEU* 3.6 14.1 - - - +
239B LEU* 3.7 2.8 - - - +
240B TYR* 2.8 45.5 + - - +
251B LEU* 1.3 76.6 - - - +
253B ALA* 1.3 64.5 + - - +
263B THR* 4.5 4.1 - - - +
264B THR 3.0 17.3 - - - -
265B LEU* 3.9 10.1 - - - -
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Residues in contact with ALA 253 (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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539A PHE* 4.4 5.4 - - + -
540A PHE* 3.6 11.8 - - + -
237B ASN 4.6 1.6 - - - -
238B HIS 3.2 24.7 - - - +
240B TYR* 4.9 4.0 - - - -
252B SER* 1.3 77.7 - - - +
254B THR* 1.3 64.0 + - - +
255B HIS* 3.6 28.6 + - + +
262B VAL 3.7 1.0 - - - +
263B THR* 3.3 3.9 - - - -
264B THR* 3.0 27.6 + - - -
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Residues in contact with THR 254 (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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214B ILE* 4.1 13.1 - - + +
231B PRO* 4.1 17.9 - - + -
235B MET* 4.4 12.1 + - - -
236B LEU* 3.4 31.6 - - + +
237B ASN 2.9 28.0 + - - +
238B HIS 4.6 1.2 + - - -
240B TYR* 5.8 1.2 - - - -
253B ALA* 1.3 73.2 - - - +
255B HIS* 1.3 64.8 + - - +
261B TYR* 4.2 8.7 - - + -
262B VAL 3.2 9.4 - - - +
263B THR* 2.6 27.2 + - - +
45E SER* 5.7 1.6 - - - +
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Residues in contact with HIS 255 (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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471A SER* 3.1 24.2 + - - -
535A HIS* 5.1 9.4 - + - -
536A THR* 3.7 38.1 + - + +
539A PHE* 4.4 9.6 - + - -
236B LEU* 4.7 0.9 - - - -
237B ASN* 3.0 31.2 + - - -
253B ALA* 3.6 30.4 + - + +
254B THR* 1.3 76.4 - - - +
256B ARG* 1.3 66.2 + - - +
257B TYR 3.8 0.7 + - - -
261B TYR* 3.6 1.9 - - - -
262B VAL* 2.8 39.5 + - + +
264B THR* 5.4 1.8 + - - -
162E ASN* 5.5 4.3 - - - +
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Residues in contact with ARG 256 (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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134A MET* 4.1 24.7 - - - +
166A ASP* 2.8 49.3 + - - +
233B HIS* 4.6 4.0 - - - +
236B LEU* 4.3 12.6 - - + +
237B ASN* 5.1 1.8 + - - -
255B HIS* 1.3 76.0 - - - +
257B TYR* 1.3 60.7 + - - +
258B LYS* 3.0 31.1 + - - +
259B LYS* 5.6 2.1 - - - +
260B LYS 3.4 8.5 - - - +
261B TYR* 3.8 33.0 + - + -
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Residues in contact with TYR 257 (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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255B HIS 3.8 2.0 + - - -
256B ARG* 1.3 72.6 - - - +
258B LYS* 1.3 92.0 + - + +
259B LYS 3.1 0.5 + - - -
260B LYS* 2.8 38.4 + - + +
262B VAL* 5.2 5.4 - - + +
39E TYR* 3.7 30.1 - + - -
42E ILE* 5.4 1.3 - - + -
134E PRO* 3.7 22.4 - - + +
135E ASN* 4.2 10.0 + - - -
157E ASP* 3.4 35.8 + - + -
159E GLU* 3.8 13.8 + - - -
160E SER* 5.4 1.1 - - - -
164E LEU* 3.7 37.0 - - + -
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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
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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