Contacts of the helix formed by residues 197 - 210 (chain B) in PDB entry 1KAF
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 SER 197 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B ASP* 4.8 2.2 + - - -
195B LYS* 3.5 2.9 + - - -
196B ARG* 1.3 76.0 - - - +
198B ALA* 1.3 65.0 + - - +
199B GLU* 3.2 20.4 - - - +
200B ASN* 2.8 34.9 + - - +
201B ILE* 2.9 32.0 + - - +
166C LYS* 4.6 11.9 - - - +
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Residues in contact with ALA 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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113B ASP* 5.4 2.5 + - - -
116B LEU* 3.9 21.2 - - + +
197B SER* 1.3 73.1 - - - +
199B GLU* 1.3 76.0 + - - +
201B ILE* 3.9 2.8 - - - +
202B GLU* 3.2 24.8 + - - +
145C ARG* 5.3 11.6 - - - +
166C LYS* 5.7 1.0 - - - +
168C MET* 6.2 0.2 - - + -
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Residues in contact with GLU 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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197B SER* 3.2 19.9 - - - +
198B ALA* 1.3 90.1 + - - +
200B ASN* 1.3 62.7 + - - +
202B GLU* 3.5 5.6 + - - +
203B ALA* 2.9 29.6 + - - +
168C MET* 3.5 34.2 - - - +
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Residues in contact with ASN 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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160B MET* 4.9 0.7 - - + -
178B ILE 4.7 4.0 - - - +
194B ILE* 3.5 35.2 - - + +
195B LYS* 2.9 32.7 + - - +
196B ARG* 5.2 0.4 - - - -
197B SER* 2.8 25.5 + - - +
199B GLU* 1.3 73.3 - - - +
201B ILE* 1.3 61.2 + - + +
203B ALA* 3.7 6.9 - - - +
204B VAL* 2.8 37.8 + - - +
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Residues in contact with ILE 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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113B ASP* 3.5 46.7 - - + +
116B LEU* 3.9 26.0 - - + -
117B MET* 4.2 22.9 - - + +
120B LEU* 4.2 2.7 - - + -
154B ILE* 4.4 7.2 - - + -
160B MET* 4.0 22.9 - - + -
196B ARG* 5.0 4.5 - - + -
197B SER 2.9 29.2 + - - +
198B ALA* 3.9 3.6 - - - +
200B ASN* 1.3 77.1 - - + +
202B GLU* 1.3 63.3 + - - +
204B VAL* 3.9 0.7 - - - +
205B ILE* 3.2 27.8 + - + +
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Residues in contact with GLU 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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116B LEU* 4.2 8.9 - - + +
120B LEU* 3.0 43.7 - - + +
123B LYS* 5.9 1.6 - - - -
198B ALA 3.2 15.8 + - - +
199B GLU* 3.7 6.1 - - - +
201B ILE* 1.3 80.9 - - - +
203B ALA* 1.3 55.0 + - - +
205B ILE* 4.1 1.0 - - - +
206B THR* 2.7 44.7 + - - +
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Residues in contact with ALA 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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178B ILE* 3.8 23.3 - - + -
194B ILE* 6.5 0.2 - - + -
199B GLU 2.9 18.6 + - - +
200B ASN* 3.7 9.9 - - - +
202B GLU* 1.3 78.3 - - - +
204B VAL* 1.3 57.8 + - - +
206B THR* 3.8 4.5 - - - -
207B VAL* 3.0 35.0 + - - +
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Residues in contact with VAL 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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152B PHE* 4.6 0.2 - - + -
160B MET* 3.7 28.7 - - + -
162B ILE* 3.5 31.0 - - + -
175B PHE* 3.5 8.4 - - + -
178B ILE* 3.8 19.5 - - + -
180B MET* 4.0 17.5 - - + -
194B ILE* 4.1 14.4 - - + -
200B ASN* 2.8 31.4 + - - +
201B ILE 3.9 3.6 - - - +
203B ALA* 1.3 73.4 - - - +
205B ILE* 1.3 59.9 + - + +
207B VAL* 3.4 0.9 + - - -
208B ALA* 3.0 23.6 + - - +
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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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117B MET* 4.7 6.5 - - + +
120B LEU* 3.6 48.2 - - + +
121B LEU* 3.8 21.5 - - + +
124B ASN* 3.8 6.7 - - - +
126B PHE* 4.4 5.1 - - + -
152B PHE* 3.5 35.4 - - + -
160B MET* 3.7 15.0 - - + -
201B ILE* 3.2 20.7 + - + +
202B GLU 4.2 1.6 - - - +
204B VAL* 1.3 72.8 - - - +
206B THR* 1.3 66.9 + - - +
208B ALA* 3.2 5.1 + - - +
209B SER* 3.0 22.0 + - - -
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Residues in contact with THR 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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120B LEU* 5.3 2.6 - - - +
124B ASN* 4.8 6.9 + - - +
202B GLU* 2.7 36.5 + - - +
203B ALA* 3.8 5.8 - - - -
205B ILE* 1.3 76.8 - - - +
207B VAL* 1.3 62.0 + - + +
209B SER* 2.6 27.4 + - - +
210B GLU* 3.4 23.6 - - - +
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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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174B LYS* 3.6 44.1 + - + +
175B PHE* 3.6 23.6 - - + -
178B ILE* 3.8 28.0 - - + -
203B ALA* 3.0 22.3 + - + +
204B VAL 3.6 4.3 - - - +
206B THR* 1.3 77.7 - - + +
208B ALA* 1.3 62.9 + - - +
210B GLU* 3.0 22.9 + - - +
211B LEU* 3.5 11.4 + - + +
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Residues in contact with ALA 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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126B PHE* 3.6 23.0 - - + -
147B ASN* 4.9 3.3 + - - -
149B ILE* 4.3 4.7 - - + +
152B PHE* 3.9 20.9 - - + -
175B PHE* 3.8 20.6 - - + -
204B VAL 3.0 13.8 + - - +
205B ILE* 3.2 9.4 + - - +
207B VAL* 1.3 77.2 - - - +
209B SER* 1.3 60.9 + - - +
210B GLU 3.3 0.5 + - - -
211B LEU* 3.4 20.7 + - - +
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Residues in contact with SER 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASN* 3.5 42.7 + - - -
126B PHE* 3.8 8.3 - - - -
205B ILE 3.0 7.7 + - - -
206B THR* 2.6 25.4 + - - +
208B ALA* 1.3 77.3 - - - +
210B GLU* 1.3 63.5 + - - +
211B LEU 3.4 4.3 + - - +
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Residues in contact with GLU 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B LYS* 4.5 18.1 + - - +
206B THR* 3.4 28.6 - - + +
207B VAL* 3.0 17.2 + - - +
209B SER* 1.3 82.5 - - - +
211B LEU* 1.3 66.9 + - - +
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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