Contacts of the helix formed by residues 196 - 206 (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 CYS 196 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B ASP* 5.0 0.2 - - - +
46B ARG* 5.7 2.2 - - - +
53B MET* 3.9 16.7 - - - +
77B ALA* 6.1 1.0 - - - +
78B GLU* 5.7 1.5 - - - +
194B PRO* 3.3 0.8 - - - +
195B LYS* 1.3 93.8 - - - +
197B GLY* 1.3 58.9 + - - +
200B GLN* 3.3 35.4 + - + +
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Residues in contact with GLY 197 (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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44B ASP* 3.1 17.5 - - - -
53B MET* 4.5 8.0 - - - +
77B ALA* 5.5 0.5 - - - +
194B PRO* 3.1 24.3 + - - +
195B LYS 3.5 1.2 + - - -
196B CYS* 1.3 80.7 - - - +
198B TYR* 1.3 65.9 + - - -
199B THR 3.2 3.1 + - - -
200B GLN* 3.4 0.3 + - - +
201B MET* 3.2 18.7 + - - +
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Residues in contact with TYR 198 (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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13B PHE* 4.1 10.5 - + - -
42B SER* 3.4 31.4 - - - +
44B ASP* 2.7 20.2 + - - +
55B HIS* 3.8 13.5 - + - -
60B HIS* 2.6 38.6 + - + -
62B PHE* 3.3 29.3 + + + +
79B MET* 5.5 0.9 - - + -
192B GLY 4.1 0.2 + - - -
193B MET* 3.6 6.9 - - - -
194B PRO* 3.5 26.6 - - + +
197B GLY* 1.3 69.3 - - - -
199B THR* 1.3 58.6 + - - +
201B MET* 3.1 13.2 + - - +
202B ILE* 2.7 37.3 + - + +
352B MET* 3.5 30.5 - - + -
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Residues in contact with THR 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 3.7 27.6 - - + +
39B GLY* 5.6 0.7 - - - -
42B SER 4.9 0.2 + - - -
43B TYR* 3.2 21.4 - - + +
44B ASP* 2.8 43.7 + - - +
198B TYR* 1.3 76.1 - - - +
200B GLN* 1.4 65.4 + - - +
202B ILE* 3.1 6.2 + - - -
203B LYS* 2.7 33.5 + - + +
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Residues in contact with GLN 200 (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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53B MET* 6.1 0.2 - - + -
76B HIS 4.3 1.1 - - - +
196B CYS* 3.3 38.6 - - + +
197B GLY 3.4 2.5 + - - +
198B TYR 3.3 0.2 - - - -
199B THR* 1.4 84.3 - - - +
201B MET* 1.3 66.1 + - - +
203B LYS* 3.6 31.1 + - - +
204B SER* 3.0 23.6 + - - -
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Residues in contact with MET 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 3.6 33.9 - - + -
62B PHE* 5.0 2.2 - - + -
72B TYR* 5.1 0.9 - - + -
73B ILE* 2.8 52.9 - - + -
76B HIS* 3.5 25.4 + - + +
77B ALA* 4.0 15.7 - - + +
79B MET* 5.5 1.6 - - - +
194B PRO* 5.0 4.3 - - + -
197B GLY 3.2 10.7 + - - +
198B TYR* 3.1 19.9 + - - +
200B GLN* 1.3 79.0 - - - +
202B ILE* 1.3 56.6 + - - +
204B SER* 3.2 4.0 + - - -
205B ILE* 3.1 34.9 + - + +
356B ILE* 4.4 0.7 - - + -
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Residues in contact with ILE 202 (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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11B ALA 3.8 14.8 - - - +
13B PHE* 3.6 52.5 - - + +
16B ALA* 3.9 12.3 - - + -
38B ILE* 4.3 6.3 - - + -
39B GLY* 3.9 29.4 - - - +
42B SER* 4.4 5.2 - - - -
198B TYR* 2.7 25.3 + - + +
199B THR 3.9 2.5 - - - +
201B MET* 1.3 68.4 - - - +
203B LYS* 1.3 60.5 + - - +
204B SER 3.1 1.8 - - - -
205B ILE* 3.2 7.8 + - + +
206B LEU* 2.8 47.7 + - + +
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Residues in contact with LYS 203 (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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38B ILE* 3.7 17.9 - - + +
199B THR* 2.7 18.6 + - + +
200B GLN* 3.6 32.2 + - - +
202B ILE* 1.3 78.5 - - - +
204B SER* 1.3 59.2 + - - +
206B LEU* 3.3 7.2 + - - +
207B ASN* 3.2 22.6 + - + +
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Residues in contact with SER 204 (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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20B ARG* 2.9 17.2 + - - -
75B LYS 4.5 1.0 + - - -
76B HIS* 2.7 43.6 + - - +
200B GLN 3.0 17.2 + - - -
201B MET 3.6 4.5 - - - -
202B ILE 3.1 0.4 - - - -
203B LYS* 1.3 75.0 - - - +
205B ILE* 1.3 65.6 + - - +
206B LEU 3.1 1.3 - - - -
207B ASN* 3.2 13.1 + - - +
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Residues in contact with ILE 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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13B PHE* 4.1 26.7 - - + -
16B ALA* 3.4 35.7 - - + +
17B VAL* 3.9 2.9 - - + +
20B ARG* 3.0 33.2 + - + +
72B TYR* 3.5 31.2 - - + +
76B HIS* 3.7 21.5 - - + -
201B MET* 3.1 28.4 + - + +
202B ILE* 3.2 15.0 + - + +
204B SER* 1.3 75.5 + - - +
206B LEU* 1.3 59.1 + - - +
211B ILE* 4.1 0.5 - - - +
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Residues in contact with LEU 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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11B ALA* 4.6 8.5 - - + +
16B ALA* 3.8 18.8 - - + -
31B ILE* 3.7 32.1 - - + -
38B ILE* 3.9 29.6 - - + -
202B ILE* 2.8 40.5 + - + +
203B LYS* 3.7 6.7 - - - +
204B SER 3.1 0.6 - - - -
205B ILE* 1.3 73.4 - - - +
207B ASN* 1.3 56.8 + - - +
208B HIS 3.2 8.7 + - - +
211B ILE* 3.6 24.4 - - + +
213B VAL* 4.2 21.5 - - + +
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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