Contacts of the strand formed by residues 295 - 305 (chain B) in PDB entry 3KYB
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 GLY 295 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B THR* 3.6 24.4 + - - +
52B VAL* 3.6 18.7 - - - +
259B TYR 3.7 3.8 - - - -
260B GLN* 3.6 21.4 + - - -
293B HIS* 3.7 9.3 - - - +
294B ASP* 1.3 78.6 - - - +
296B SER* 1.3 59.3 + - - -
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Residues in contact with SER 296 (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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50B THR* 4.1 3.5 - - - +
52B VAL* 4.5 0.4 - - - -
257B PHE 3.8 0.2 - - - +
258B ILE* 3.4 4.0 - - - +
259B TYR* 2.7 43.9 + - - -
261B GLY 3.3 17.5 - - - -
283B GLU* 2.5 43.5 + - - +
285B LYS* 3.2 15.9 - - - +
295B GLY* 1.3 73.9 - - - -
297B VAL* 1.3 62.0 + - - +
298B CYS* 3.8 3.9 + - - -
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ASP* 3.6 20.2 - - + +
50B THR* 3.2 30.1 - - + +
52B VAL* 3.9 14.7 - - + +
54B VAL* 4.0 11.0 - - + -
256B LYS* 3.8 20.6 - - + -
257B PHE 3.7 3.6 - - - +
258B ILE* 4.5 3.1 - - + -
283B GLU* 3.8 0.3 - - - -
284B HIS* 3.2 27.9 + - + +
285B LYS 5.6 0.4 - - - +
295B GLY 4.3 0.2 + - - -
296B SER* 1.3 73.0 + - - +
298B CYS* 1.3 62.3 + - - +
299B TYR* 3.6 31.4 - - + +
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Residues in contact with CYS 298 (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 LYS* 3.3 2.9 - - - +
257B PHE* 2.8 60.2 + - + +
259B TYR* 4.9 0.9 - - - -
263B TYR* 3.7 32.1 - - - -
281B ILE* 4.6 2.7 - - + -
282B THR 3.1 10.5 - - - +
283B GLU* 3.8 23.1 - - - -
296B SER* 4.0 8.5 - - - -
297B VAL* 1.3 77.9 - - - +
299B TYR* 1.3 72.8 + - - +
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Residues in contact with TYR 299 (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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54B VAL* 3.3 25.0 - - + +
55B HIS 5.5 0.4 - - - -
254B PHE* 3.8 34.5 - + + -
255B LYS 3.2 3.1 - - - -
256B LYS* 3.4 41.2 - - + +
257B PHE* 4.2 3.1 - - - -
280B ARG 3.7 0.5 - - - +
281B ILE* 3.2 6.1 - - - +
282B THR* 3.0 36.3 + - - +
284B HIS* 3.4 39.0 - + - -
297B VAL* 3.6 26.4 - - + +
298B CYS* 1.3 77.2 - - - +
300B LYS* 1.3 68.4 + - - +
301B GLU* 3.9 1.4 + - + +
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Residues in contact with LYS 300 (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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253B ASP 3.6 1.2 - - - +
254B PHE* 3.5 3.8 - - - -
255B LYS* 2.8 60.3 + - - +
257B PHE* 3.9 22.4 - - + -
263B TYR* 5.1 4.3 - - - -
278B TYR* 3.8 29.0 + - + -
280B ARG 3.7 4.3 - - - -
281B ILE* 3.8 24.0 - - + -
299B TYR* 1.3 73.1 - - - +
301B GLU* 1.3 60.4 + - - +
302B TYR* 3.7 23.2 - - + +
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Residues in contact with GLU 301 (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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58B GLY* 4.6 0.2 - - - -
59B PRO* 3.6 8.7 - - - +
252B LEU* 4.9 10.0 - - + +
253B ASP 3.5 4.7 - - - -
254B PHE* 3.3 34.3 - - + -
278B TYR* 3.0 4.0 - - - +
279B THR* 2.7 45.9 + - + +
280B ARG* 2.8 63.1 + - - +
282B THR* 3.6 17.6 + - - +
284B HIS* 5.5 0.2 + - - -
299B TYR* 4.4 5.6 - - + +
300B LYS* 1.3 74.5 - - - +
302B TYR* 1.3 58.3 + - - +
393B FMN 4.7 3.3 + - - -
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Residues in contact with TYR 302 (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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251B THR 3.9 0.2 - - - +
252B LEU* 3.2 7.1 - - - -
253B ASP* 2.7 63.9 + - + +
255B LYS* 2.4 47.5 + - + -
277B PRO* 3.7 33.0 - - + +
278B TYR* 3.6 34.2 - + - +
300B LYS* 3.7 18.9 - - + +
301B GLU* 1.3 74.9 - - - +
303B SER* 1.3 62.4 + - - +
304B ARG* 4.1 2.0 + - + +
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Residues in contact with SER 303 (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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158B LYS* 3.4 20.0 - - - +
159B GLN* 3.3 14.9 + - - -
250B ARG* 3.2 25.4 + - - +
251B THR 3.5 7.5 + - - -
252B LEU* 3.8 14.2 - - - +
277B PRO 5.1 3.0 + - - -
279B THR* 4.6 11.4 - - - -
301B GLU 4.3 0.8 + - - -
302B TYR* 1.3 76.1 - - - +
304B ARG* 1.3 64.4 + - - +
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Residues in contact with ARG 304 (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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250B ARG* 3.5 17.4 - - - +
251B THR* 2.7 42.3 + - + +
253B ASP* 2.8 42.5 + - - +
302B TYR* 5.0 2.5 - - + +
303B SER* 1.3 78.4 + - - +
305B ALA* 1.3 68.4 + - - +
307B GLU* 4.1 14.5 + - - -
310B ASP* 2.7 45.4 + - - -
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Residues in contact with ALA 305 (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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249B TYR 4.1 3.8 - - - -
250B ARG* 3.3 17.6 - - - +
251B THR* 3.5 6.8 - - - +
304B ARG* 1.3 85.7 + - - +
306B CYS* 1.3 65.1 + - - +
307B GLU* 3.3 15.8 + - + +
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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