Contacts of the helix formed by residues 193 - 202 (chain B) in PDB entry 1KYO
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 VAL 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B ASP* 3.1 28.0 + - - +
95B LYS* 4.5 8.2 - - + +
98B LEU* 4.0 13.7 - - + -
192B VAL* 1.3 68.9 - - - +
194B GLU* 1.3 66.8 + - - +
195B ALA* 3.2 4.3 - - + +
196B ASP* 3.0 36.0 + - + +
197B LEU* 2.9 19.8 + - - +
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Residues in contact with GLU 194 (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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19B VAL* 4.1 17.5 - - + +
20B SER* 4.0 2.8 - - - +
21B ALA* 3.4 36.3 + - + +
22B ARG 5.9 0.2 - - - -
23B ASP* 5.4 1.0 - - - +
192B VAL 3.0 5.9 + - - -
193B VAL* 1.3 69.4 - - - +
195B ALA* 1.3 61.8 + - - +
197B LEU* 3.8 4.7 - - - +
198B LYS* 3.2 48.1 + - + +
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Residues in contact with ALA 195 (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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193B VAL* 3.2 4.6 - - + -
194B GLU* 1.3 78.8 - - - +
196B ASP* 1.3 68.6 + - - +
198B LYS* 3.8 2.9 + - - +
199B ARG* 3.4 21.0 + - - +
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Residues in contact with ASP 196 (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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98B LEU* 4.8 2.7 - - + -
193B VAL* 3.0 33.3 + - + +
195B ALA* 1.3 84.7 - - - +
197B LEU* 1.3 59.4 + - - +
198B LYS 3.4 0.2 - - - -
199B ARG* 3.1 30.5 + - - -
200B PHE* 3.0 51.9 + - + -
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Residues in contact with LEU 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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19B VAL* 3.8 15.5 - - + -
20B SER 3.4 25.1 - - - +
21B ALA* 4.7 1.3 - - + -
31B LEU* 3.9 19.5 - - + -
98B LEU* 4.1 18.8 - - + -
102B VAL* 4.1 6.7 - - + -
187B VAL* 4.1 5.4 - - + -
189B GLY* 3.8 24.0 - - - +
192B VAL* 3.7 19.0 - - + +
193B VAL 2.9 9.6 + - - +
194B GLU* 3.3 6.9 + - - +
196B ASP* 1.3 77.0 - - - +
198B LYS* 1.3 52.6 + - - +
200B PHE* 3.2 2.6 + - - -
201B VAL* 2.6 51.4 + - + +
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Residues in contact with LYS 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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19B VAL* 3.7 44.4 + - + +
194B GLU* 3.2 32.3 + - + +
195B ALA* 4.2 3.1 - - - +
197B LEU* 1.3 74.9 - - - +
199B ARG* 1.3 62.0 + - - +
201B VAL* 3.7 6.4 - - - +
202B ASP* 2.8 44.6 + - - +
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Residues in contact with ARG 199 (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 ALA 3.4 15.8 + - - +
196B ASP* 3.1 31.0 + - - +
197B LEU 3.3 0.2 - - - -
198B LYS* 1.3 78.5 - - - +
200B PHE* 1.3 80.0 + - + +
202B ASP* 2.8 29.3 - - - +
203B GLU* 3.2 27.4 + - - +
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Residues in contact with PHE 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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98B LEU* 4.7 10.3 - - + -
99B PRO* 4.0 45.1 - - + -
102B VAL* 3.4 21.2 - - + +
103B ASN* 4.8 3.5 + - - +
196B ASP* 3.0 41.7 + - + +
197B LEU 3.7 2.7 - - - +
199B ARG* 1.3 111.3 - - + +
201B VAL* 1.3 58.9 + - - +
202B ASP 2.7 15.0 - - - +
203B GLU* 4.5 13.2 - - + +
204B SER* 3.1 16.5 - - - -
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Residues in contact with VAL 201 (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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17B LEU* 4.1 25.8 - - + -
19B VAL* 4.3 9.0 - - + -
102B VAL* 4.1 9.4 - - + -
187B VAL* 4.2 21.5 - - + -
197B LEU* 2.6 53.7 + - + +
198B LYS* 3.8 6.3 - - - +
200B PHE* 1.3 73.2 - - - +
202B ASP* 1.3 60.4 + - - +
204B SER* 2.6 21.7 + - - -
206B LEU* 3.6 26.2 - - + +
207B SER* 4.1 4.5 + - - -
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Residues in contact with ASP 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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17B LEU* 5.4 7.5 - - - +
198B LYS* 2.8 30.4 + - - +
199B ARG* 2.8 16.1 - - - +
200B PHE 2.7 12.3 - - - +
201B VAL* 1.3 74.3 - - - +
203B GLU* 1.3 59.7 + - + +
204B SER 2.7 16.8 + - - -
207B SER* 4.4 15.9 - - - -
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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