Contacts of the strand formed by residues 251 - 257 (chain B) in PDB entry 3K74
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 ALA 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197B ARG* 3.8 18.8 - - + -
198B ARG 3.4 24.2 - - - +
199B ALA* 3.8 4.3 - - + +
200B PRO* 4.5 2.9 - - - -
249B ASP 3.4 3.0 + - - +
250B THR* 1.3 78.3 - - - +
252B VAL* 1.3 62.6 + - - +
253B TYR* 3.4 20.3 - - + -
271B GLN* 3.9 8.3 - - - +
272B VAL 2.9 30.7 + - - +
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ARG* 3.2 2.4 - - - -
198B ARG* 2.7 46.4 + - + +
251B ALA* 1.3 71.9 - - - +
253B TYR* 1.3 59.0 + - - +
254B TYR* 3.4 36.4 - - + +
268B GLN 4.4 2.2 - - - +
269B GLY* 3.9 5.8 - - - -
270B THR 3.5 23.1 - - - +
271B GLN* 3.3 24.5 - - + +
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Residues in contact with TYR 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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165B GLU* 3.9 1.7 - - - +
179B LEU* 3.5 21.3 - - + -
195B TRP* 4.4 6.5 - + + -
196B VAL 3.4 7.6 - - - -
197B ARG* 2.8 42.8 + - + -
207B VAL* 4.6 4.7 - - + -
227B PHE* 4.1 6.7 - + - -
240B LEU* 4.0 17.7 - - + -
242B MET* 3.4 27.0 - - + +
249B ASP* 2.6 30.7 + - - +
251B ALA* 3.4 17.3 - - + -
252B VAL* 1.3 74.3 - - - +
254B TYR* 1.3 59.9 + - - +
269B GLY* 3.2 2.8 - - - -
270B THR* 2.8 36.2 + - - +
272B VAL* 3.6 27.1 - - + -
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Residues in contact with TYR 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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165B GLU* 3.3 7.6 - - - +
195B TRP* 3.4 9.7 - - - -
196B VAL* 2.8 45.8 + - + +
198B ARG* 2.0 41.3 + - + -
204B LEU* 3.8 26.0 - - + -
252B VAL* 3.4 35.0 - - + +
253B TYR* 1.3 72.3 - - - +
255B CYS* 1.3 59.0 + - - +
266B LYS* 3.7 25.4 - - + -
267B GLY 3.4 20.4 - - - -
268B GLN* 3.4 21.9 + - - -
269B GLY* 3.5 9.0 - - - -
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Residues in contact with CYS 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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163B LEU* 3.8 13.7 - - - +
165B GLU* 2.9 21.3 + - - +
181B CYS* 2.1 54.5 - - + -
193B MET* 4.9 2.0 - - + -
194B TYR 3.2 9.9 - - - +
195B TRP* 4.1 6.5 - - + -
238B LEU* 3.9 13.9 - - + -
254B TYR* 1.3 72.4 - - - +
256B ALA* 1.3 58.4 + - - +
266B LYS* 3.0 22.1 - - - +
267B GLY 3.1 2.3 + - - -
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Residues in contact with ALA 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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163B LEU* 4.3 0.9 - - - -
193B MET* 3.5 10.4 - - - +
194B TYR* 2.9 44.1 + - + +
196B VAL* 4.7 6.5 - - + -
255B CYS* 1.3 75.7 - - - +
257B LYS* 1.3 61.1 - - - +
259B TRP* 4.0 26.7 - - + -
265B LYS 3.0 13.2 - - - +
266B LYS* 3.9 10.1 - - + -
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Residues in contact with LYS 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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163B LEU* 4.2 8.2 - - + +
186B PHE* 3.9 34.5 - - + -
191B TYR* 3.7 34.1 - - + -
192B TRP 4.4 2.0 - - - -
193B MET* 4.1 19.3 - - + -
256B ALA* 1.3 71.7 - - - +
258B ASP* 1.3 95.9 + - - +
259B TRP* 3.0 4.2 + - - -
263B LEU* 3.8 4.9 + - - +
264B ALA* 3.3 0.3 - - - -
265B LYS* 2.8 69.7 + - + +
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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