Contacts of the strand formed by residues 204 - 210 (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 LEU 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A GLU* 4.2 16.1 + - - +
196B VAL* 4.0 10.5 - - + -
197B ARG 3.4 4.7 - - - +
198B ARG* 3.9 21.3 - - + +
203B GLY* 1.3 73.7 - - - -
205B GLU* 1.3 58.8 + - - +
206B TRP 4.2 0.6 + - - -
254B TYR* 3.8 24.2 - - + -
259B TRP* 3.7 33.9 - - + -
266B LYS* 3.6 35.7 - - - +
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Residues in contact with GLU 205 (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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196B VAL* 4.2 1.8 - - - -
197B ARG* 2.8 76.2 + - + +
199B ALA* 6.0 1.5 - - - +
202B LYS* 4.7 17.3 + - - +
203B GLY 4.5 4.2 - - - +
204B LEU* 1.3 76.4 - - - +
206B TRP* 1.3 75.7 + - + +
207B VAL* 4.7 0.8 - - + +
222B SER* 3.9 9.1 + - - +
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Residues in contact with TRP 206 (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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18A ASN 3.9 7.4 - - - -
19A ALA* 2.9 28.4 + - - +
20A MET 3.6 22.0 - - - -
21A PRO* 3.6 30.9 - - + -
194B TYR* 5.6 2.7 - + + -
195B TRP 3.8 5.4 - - - +
196B VAL* 3.9 10.7 - - + +
204B LEU 4.2 0.6 + - - -
205B GLU* 1.3 82.1 - - + +
207B VAL* 1.3 64.0 + - - +
208B SER* 3.6 21.8 - - - -
209B MET* 4.5 9.9 - - + -
218B LYS* 3.8 28.9 - - + -
219B TYR 3.6 9.9 - - - -
220B ALA* 3.5 46.0 - - + +
259B TRP* 4.0 24.3 - - + +
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Residues in contact with VAL 207 (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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195B TRP* 2.8 15.5 + - + +
196B VAL* 4.7 0.7 - - - -
197B ARG* 3.6 49.4 - - + +
205B GLU* 3.9 2.7 - - + +
206B TRP* 1.3 85.1 - - - +
208B SER* 1.3 78.0 + - - +
219B TYR* 3.5 0.5 - - - -
220B ALA* 2.9 26.7 + - + -
222B SER* 5.4 0.4 - - - +
223B VAL* 3.5 13.5 - - + +
227B PHE* 3.6 27.4 - - + -
240B LEU* 4.3 10.3 - - + -
253B TYR* 4.6 2.5 - - + -
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Residues in contact with SER 208 (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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194B TYR* 3.2 5.4 - - - +
195B TRP* 2.8 30.8 + - - +
206B TRP* 3.6 5.8 - - - +
207B VAL* 1.3 90.0 + - - +
209B MET* 1.3 63.5 + - - +
218B LYS 3.4 9.0 - - - -
219B TYR* 3.2 22.1 - - - -
227B PHE* 4.5 1.0 - - - +
229B ILE* 3.8 25.6 - - - -
240B LEU* 3.5 15.0 - - - +
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Residues in contact with MET 209 (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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21A PRO* 3.6 29.8 - - - +
22A TRP 3.9 6.1 - - - -
23A ASN* 3.8 6.5 - - + +
148A SER* 3.6 23.1 - - - +
192B TRP* 3.5 30.7 - - + -
193B MET 3.2 8.5 - - - +
194B TYR* 3.6 28.9 - - + +
206B TRP* 4.5 4.0 - - + -
208B SER* 1.3 78.1 - - - +
210B ILE* 1.3 62.3 + - - +
217B THR* 3.3 3.9 - - - -
218B LYS* 3.0 55.3 + - + +
229B ILE* 3.6 7.0 - - - +
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Residues in contact with ILE 210 (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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192B TRP* 3.3 8.9 - - - -
193B MET* 2.9 33.8 + - + +
209B MET* 1.3 75.7 - - - +
211B ASN* 1.3 70.8 + - - +
214B GLY* 3.7 23.6 - - - +
216B ILE 3.3 12.1 - - - +
217B THR* 3.8 15.0 - - + -
229B ILE* 3.6 22.7 - - + +
230B SER* 3.7 33.0 - - - -
231B ARG* 3.5 15.0 + - - +
238B LEU* 3.6 18.8 - - + -
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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