Contacts of the strand formed by residues 285 - 293 (chain B) in PDB entry 5K7W
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 LYS 285 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A GLU* 2.8 32.9 + - - +
456A ILE* 3.5 33.7 - - + -
501A ASP* 3.2 33.4 + - - +
502A VAL* 4.1 5.4 - - + -
237B SER* 3.2 30.8 + - - -
241B LEU* 5.1 1.4 - - - +
260B CYS* 4.4 2.7 - - + -
261B TRP 3.1 19.1 - - - +
262B ILE* 4.1 8.1 - - + -
263B LYS* 4.3 3.2 + - - +
283B ARG 3.7 1.3 - - - -
284B THR* 1.3 80.1 + - - +
286B GLU* 1.3 68.4 + - - +
287B HIS* 2.9 30.2 + - - +
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Residues in contact with GLU 286 (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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197B GLU* 6.0 0.2 - - - +
198B TYR* 3.8 17.7 + - - -
234B TRP* 4.3 8.7 - - + -
236B GLY* 3.5 17.2 - - - +
237B SER* 5.0 2.5 - - - +
259B ILE 3.9 0.2 - - - +
260B CYS* 3.4 3.8 - - - +
261B TRP* 2.8 56.1 + - + +
263B LYS* 2.9 27.5 + - - +
285B LYS* 1.3 78.2 - - - +
287B HIS* 1.3 65.0 + - - +
326B LYS* 2.9 37.5 + - - +
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Residues in contact with HIS 287 (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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454A GLU* 4.0 15.3 - - + -
456A ILE* 4.6 0.7 - - + -
482A HIS* 4.2 3.4 - + - -
234B TRP* 3.8 4.4 - - - -
235B CYS* 2.8 30.6 + - + +
236B GLY 2.9 19.5 + - - +
237B SER* 4.7 2.7 - - - -
241B LEU* 3.7 35.1 - - + +
258B ASP* 2.8 32.7 + - - +
259B ILE 3.7 4.0 - - - -
260B CYS* 3.4 17.2 - - - +
285B LYS* 2.9 37.0 + - + +
286B GLU* 1.3 81.5 - - - +
288B CYS* 1.3 59.3 + - - +
289B LEU* 3.9 6.1 - - + -
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Residues in contact with CYS 288 (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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232B PHE* 3.8 21.8 - - - -
233B LEU 3.3 27.6 - - - -
234B TRP* 3.7 32.7 - - + -
258B ASP* 3.9 1.5 + - - -
259B ILE* 2.8 50.6 + - + +
287B HIS* 1.3 71.2 - - - +
289B LEU* 1.3 65.0 + - - +
290B MET 3.6 1.0 + - - -
330B ILE* 4.0 16.2 - - + -
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Residues in contact with LEU 289 (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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231B ILE* 3.6 1.6 - - - +
232B PHE* 3.4 4.0 - - - -
233B LEU* 2.8 43.2 + - + +
235B CYS* 3.7 27.1 - - + -
240B GLY 4.7 0.2 - - - +
241B LEU* 4.2 5.8 - - + +
244B GLY 4.1 3.1 - - - +
245B ARG* 3.8 57.2 - - + +
248B LEU* 4.4 15.8 - - + +
255B ARG* 4.5 3.6 - - + -
257B GLU 3.9 3.8 - - - +
258B ASP* 3.7 33.0 - - + +
287B HIS* 3.9 4.9 - - + +
288B CYS* 1.3 71.6 - - - +
290B MET* 1.3 59.7 + - - +
291B GLY 4.1 0.3 + - - -
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Residues in contact with MET 290 (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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475A TRP* 4.2 5.2 - - + -
476A LEU* 4.1 12.6 - - + -
230B PHE* 3.7 14.8 - - + -
231B ILE 3.2 5.8 - - - +
232B PHE* 3.6 30.1 - - + -
248B LEU* 4.6 2.2 - - - -
255B ARG* 3.5 5.5 - - - +
256B CYS* 2.8 34.6 + - - -
257B GLU* 2.9 43.9 + - + +
259B ILE* 4.9 3.1 - - + -
288B CYS 3.6 2.6 + - - +
289B LEU* 1.3 74.3 - - - +
291B GLY* 1.3 63.3 + - - +
337B PHE* 3.4 47.3 - - + -
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Residues in contact with GLY 291 (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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230B PHE* 3.2 11.3 - - - +
231B ILE* 2.9 42.2 + - - +
248B LEU* 4.3 4.7 - - - +
253B TYR* 3.9 9.9 - - - -
254B ARG 3.2 12.6 - - - -
256B CYS* 3.9 4.0 - - - -
290B MET* 1.3 74.4 - - - +
292B ILE* 1.3 60.7 + - - -
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Residues in contact with ILE 292 (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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475A TRP* 3.6 33.4 - - + -
229B SER 3.7 2.9 - - - -
230B PHE* 3.6 29.2 - - + -
253B TYR* 3.3 4.8 - - - -
254B ARG* 2.9 80.2 + - + +
256B CYS* 4.0 15.7 - - + -
291B GLY* 1.3 74.7 - - - -
293B LYS* 1.3 71.3 + - - +
294B GLY 4.2 1.3 - - - +
296B VAL* 4.0 14.6 - - + +
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Residues in contact with LYS 293 (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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222B ASP* 4.1 12.4 + - - +
225B ALA* 3.8 24.5 - - + +
226B ALA 3.5 20.2 - - - +
227B PRO* 3.6 11.9 - - + +
228B ARG* 3.3 4.5 - - - +
229B SER* 2.8 34.8 + - - +
251B TRP 2.8 28.5 + - - -
252B GLY* 3.3 21.6 + - - +
253B TYR* 3.6 19.9 - - + -
254B ARG* 4.3 0.7 - - - +
292B ILE* 1.3 77.7 - - - +
294B GLY* 1.3 68.7 + - - +
296B VAL* 4.7 0.2 - - - +
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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