Contacts of the helix formed by residues 197 - 211 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113F ASP* 4.6 5.8 + - - -
195F LYS* 3.6 2.3 + - - -
196F ARG* 1.3 77.5 - - - +
198F ALA* 1.3 64.7 + - - +
199F GLU* 3.6 13.0 + - - +
200F ASN* 2.9 35.5 + - - +
201F ILE* 2.9 33.0 + - - +
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Residues in contact with ALA 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F ASP* 4.7 4.8 + - - +
116F LEU* 3.8 26.3 - - + +
197F SER* 1.3 73.4 - - - +
199F GLU* 1.3 73.1 + - - +
201F ILE* 4.8 0.9 - - - -
202F GLU* 3.1 25.3 + - - +
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Residues in contact with GLU 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197F SER* 3.6 11.7 + - - +
198F ALA* 1.3 91.5 + - - +
200F ASN* 1.3 62.0 + - - +
202F GLU* 3.4 5.0 + - - +
203F ALA* 3.0 28.8 + - - +
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Residues in contact with ASN 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F MET* 5.0 0.7 - - - -
178F ILE 4.9 3.6 - - - +
194F ILE* 3.5 34.8 - - + +
195F LYS* 2.8 34.6 + - - +
196F ARG* 5.2 0.2 - - - -
197F SER* 2.9 22.1 + - - +
199F GLU* 1.3 78.1 - - - +
201F ILE* 1.3 65.4 + - + +
203F ALA* 3.8 5.6 - - - +
204F VAL* 3.0 31.5 + - - +
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Residues in contact with ILE 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F ASP* 3.8 46.2 - - + +
116F LEU* 4.1 16.8 - - + -
117F MET* 4.1 15.3 - - + -
120F LEU* 4.3 0.7 - - + -
154F ILE* 4.2 11.0 - - + -
160F MET* 3.9 26.5 - - + -
196F ARG* 5.1 1.1 - - + -
197F SER 2.9 27.7 + - - +
198F ALA 3.9 2.9 - - - +
200F ASN* 1.3 76.6 - - + +
202F GLU* 1.3 64.6 + - - +
204F VAL* 3.8 0.9 - - - +
205F ILE* 3.1 43.4 + - + +
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Residues in contact with GLU 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F LEU* 4.5 7.4 - - - +
120F LEU* 3.2 39.4 - - + +
123F LYS* 5.8 2.1 + - - -
198F ALA 3.1 18.2 + - - +
199F GLU* 3.7 6.3 - - - +
201F ILE* 1.3 78.6 - - - +
203F ALA* 1.3 62.0 + - - +
205F ILE* 4.0 1.7 - - - +
206F THR* 2.8 40.1 + - - +
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Residues in contact with ALA 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178F ILE* 3.7 24.2 - - + +
194F ILE* 6.3 0.7 - - + -
199F GLU 3.0 17.5 + - - +
200F ASN* 3.8 9.2 - - - +
201F ILE 3.3 0.2 - - - -
202F GLU* 1.3 77.8 - - - +
204F VAL* 1.3 57.3 + - - +
206F THR* 3.3 6.6 + - - -
207F VAL* 3.0 33.4 + - - +
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Residues in contact with VAL 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F PHE* 4.9 1.3 - - + -
160F MET* 3.4 29.6 - - + -
162F ILE* 3.7 25.4 - - + -
175F PHE* 3.7 1.3 - - + -
178F ILE* 3.6 19.1 - - + -
180F MET* 3.9 20.6 - - + -
194F ILE* 4.0 21.1 - - + -
200F ASN 3.0 22.1 + - - +
201F ILE 3.8 2.9 - - - +
203F ALA* 1.3 75.8 - - - +
205F ILE* 1.3 63.4 + - - +
207F VAL* 3.2 4.4 + - - +
208F ALA* 3.0 21.3 + - - +
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Residues in contact with ILE 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F MET* 3.6 29.4 - - + +
120F LEU* 3.4 39.5 - - + +
121F LEU* 4.1 22.7 - - + -
124F ASN* 3.6 27.8 - - + +
126F PHE* 4.7 2.7 - - + -
152F PHE* 4.6 3.1 - - + -
160F MET* 4.2 13.2 - - + -
201F ILE* 3.1 18.1 + - + +
202F GLU 4.2 2.0 - - - +
204F VAL* 1.3 77.6 - - - +
206F THR* 1.3 57.8 + - - +
208F ALA* 3.4 7.2 + - + +
209F SER* 2.9 27.2 + - - -
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Residues in contact with THR 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F ASN* 5.5 3.0 + - - +
202F GLU* 2.8 34.7 + - - +
203F ALA* 3.6 7.0 - - - -
204F VAL 3.2 0.2 - - - -
205F ILE* 1.3 78.9 - - - +
207F VAL* 1.3 63.0 + - + +
209F SER* 2.6 22.5 + - - +
210F GLU* 3.0 39.9 - - + +
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Residues in contact with VAL 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F LYS* 3.8 31.4 - - + +
175F PHE* 3.5 27.6 - - + -
178F ILE* 3.6 31.9 - - + -
203F ALA 3.0 20.2 + - - +
204F VAL 3.6 7.4 - - - +
206F THR* 1.3 78.0 - - + +
208F ALA* 1.3 61.7 + - - +
210F GLU* 3.0 8.3 + - - +
211F LEU* 2.9 24.5 + - - +
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Residues in contact with ALA 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F PHE* 3.7 13.0 - - + -
146F THR* 6.0 0.3 - - - +
147F ASN* 4.9 4.7 + - - -
149F ILE* 4.1 6.7 - - + +
152F PHE* 3.9 30.7 - - + -
175F PHE* 3.7 17.2 - - + -
204F VAL 3.0 15.9 + - - +
205F ILE 3.7 4.3 - - - +
207F VAL* 1.3 77.4 - - - +
209F SER* 1.3 60.9 + - - +
211F LEU* 2.9 23.4 + - - +
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Residues in contact with SER 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F ASN* 3.4 32.1 + - - -
126F PHE* 3.8 15.0 - - - -
205F ILE 2.9 14.9 + - - -
206F THR* 2.6 25.5 + - - +
208F ALA* 1.3 77.7 - - - +
210F GLU* 1.3 65.5 + - - +
211F LEU 3.4 0.4 + - - -
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Residues in contact with GLU 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F LYS* 5.4 0.4 - - - -
206F THR* 3.0 37.5 + - - +
207F VAL* 3.5 5.8 - - - +
209F SER* 1.3 83.9 - - - +
211F LEU* 1.3 77.0 + - - +
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Residues in contact with LEU 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F ASN* 4.1 21.4 + - - +
149F ILE* 5.2 2.6 - - - +
170F HIS* 4.7 7.0 - - + +
171F HIS* 3.4 51.2 - - + +
174F LYS* 3.4 44.6 - - + +
175F PHE* 4.5 7.0 - - - -
207F VAL* 2.9 17.0 + - - +
208F ALA* 2.9 24.2 + - - +
209F SER 3.4 2.8 - - - -
210F GLU* 1.3 85.4 - - - +
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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