Contacts of the helix formed by residues 197 - 210 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110E MET* 6.4 0.7 - - - -
113E ASP* 3.6 10.5 - - - -
195E LYS* 3.4 3.3 + - - -
196E ARG* 1.3 78.2 - - - +
198E ALA* 1.3 63.9 + - - +
199E GLU* 3.6 7.8 + - - +
200E ASN* 3.0 33.4 + - - +
201E ILE* 2.8 26.1 + - - +
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Residues in contact with ALA 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E MET* 5.0 8.2 - - + +
113E ASP* 3.8 16.1 + - - +
116E LEU* 3.8 26.9 - - + +
197E SER* 1.3 73.0 - - - +
199E GLU* 1.3 62.8 + - - +
201E ILE* 3.5 2.3 + - - +
202E GLU* 3.1 24.8 + - - +
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Residues in contact with GLU 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E SER* 3.1 7.5 + - - +
198E ALA* 1.3 80.4 - - - +
200E ASN* 1.3 60.9 + - - +
202E GLU* 3.5 6.5 + - - +
203E ALA* 3.1 26.2 + - - +
150F ARG* 5.8 2.2 - - - +
163F PHE* 4.6 6.7 - - + -
185F ALA* 4.6 2.1 - - - +
187F ASN* 3.0 18.6 + - - +
189F ASN* 2.9 30.2 - - - +
191F TYR* 2.6 33.2 + - - -
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Residues in contact with ASN 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E MET* 4.7 0.7 - - - -
194E ILE* 3.7 25.2 - - + +
195E LYS* 2.7 61.2 + - - +
196E ARG* 5.2 0.2 - - - -
197E SER* 3.0 20.2 + - - +
199E GLU* 1.3 76.5 - - - +
201E ILE* 1.3 60.2 + - + +
203E ALA* 3.6 4.2 - - - +
204E VAL* 2.8 36.4 + - - +
186F LYS* 5.7 1.4 - - - -
187F ASN* 3.6 18.7 - - - +
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Residues in contact with ILE 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E ASP* 3.3 45.8 - - + +
116E LEU* 4.2 5.2 - - + -
117E MET* 4.0 27.8 - - + +
120E LEU* 4.2 11.2 - - + -
154E ILE* 4.2 12.1 - - + -
160E MET* 3.9 27.1 - - + -
196E ARG* 4.2 8.3 - - + -
197E SER 2.8 23.7 + - - +
198E ALA* 3.8 5.2 - - - +
200E ASN* 1.3 76.7 - - - +
202E GLU* 1.3 63.3 + - - +
204E VAL* 3.9 0.7 - - - +
205E ILE* 3.1 26.6 + - + +
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Residues in contact with GLU 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E LEU* 5.5 1.8 - - + +
120E LEU* 3.6 26.6 - - + +
198E ALA 3.1 15.2 + - - +
199E GLU* 3.8 5.6 - - - +
201E ILE* 1.3 78.9 - - - +
203E ALA* 1.3 58.6 + - - +
205E ILE* 3.9 0.7 - - - +
206E THR* 2.8 45.0 + - - +
145F ARG* 3.6 10.2 + - - -
150F ARG* 3.3 38.4 + - - +
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Residues in contact with ALA 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E ILE* 4.0 10.8 - - + -
194E ILE* 6.1 0.4 - - + -
199E GLU 3.1 17.9 + - - +
200E ASN* 3.6 7.4 - - - +
201E ILE 3.3 0.2 - - - -
202E GLU* 1.3 77.0 - - - +
204E VAL* 1.3 64.0 + - + +
206E THR* 3.3 5.0 + - - -
207E VAL* 3.0 28.5 + - + +
165F TYR* 6.3 2.7 - - + -
187F ASN* 4.0 33.9 - - + +
189F ASN* 5.6 1.8 - - - +
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Residues in contact with VAL 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E PHE* 4.6 3.6 - - + -
160E MET* 3.7 33.0 - - + -
162E ILE* 3.7 29.4 - - + -
175E PHE* 3.6 3.6 - - + -
178E ILE* 4.0 14.1 - - + -
180E MET* 4.0 16.2 - - + -
194E ILE* 3.9 20.0 - - + -
200E ASN 2.8 24.0 + - - +
201E ILE 3.9 0.2 - - - +
203E ALA* 1.3 72.4 - - - +
205E ILE* 1.3 58.5 + - - +
207E VAL* 3.2 5.0 + - - +
208E ALA* 3.0 26.5 + - - +
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Residues in contact with ILE 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E MET* 4.6 2.9 - - + -
120E LEU* 3.9 31.4 - - + +
121E LEU* 3.5 22.0 - - + -
124E ASN* 3.8 25.6 - - + +
126E PHE* 4.5 3.1 - - + -
152E PHE* 3.5 36.6 - - + -
160E MET* 3.9 12.8 - - + -
201E ILE* 3.1 22.4 + - + +
202E GLU 4.1 1.8 - - - +
204E VAL* 1.3 71.7 - - - +
206E THR* 1.3 62.5 + - - +
208E ALA* 3.3 3.4 + - - +
209E SER* 2.8 27.0 + - - -
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Residues in contact with THR 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E ASN* 5.6 2.0 - - - +
202E GLU* 2.8 34.5 + - - +
203E ALA* 3.7 5.4 - - - -
205E ILE* 1.3 78.1 - - - +
207E VAL* 1.3 63.9 + - + +
209E SER* 2.6 23.6 + - - +
210E GLU* 3.0 34.6 + - - +
165F TYR* 4.3 18.4 - - + +
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Residues in contact with VAL 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174E LYS* 3.3 56.2 + - + +
175E PHE* 3.7 20.2 - - + -
178E ILE* 3.6 32.3 - - + -
203E ALA* 3.0 20.2 + - + +
204E VAL 3.5 7.2 - - - +
206E THR* 1.3 77.7 - - + +
208E ALA* 1.3 62.4 + - - +
210E GLU* 3.0 13.0 + - - -
211E LEU* 3.3 5.2 + - + +
166F LYS* 6.4 0.4 - - - +
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Residues in contact with ALA 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E PHE* 3.6 23.9 - - + -
147E ASN* 5.2 0.7 - - - +
149E ILE* 4.7 3.4 - - + -
152E PHE* 3.8 21.3 - - + -
175E PHE* 3.7 23.3 - - + -
204E VAL 3.0 17.6 + - - +
205E ILE 3.6 4.5 - - - +
207E VAL* 1.3 76.7 - - - +
209E SER* 1.3 61.6 + - - +
210E GLU 3.3 1.0 + - - -
211E LEU* 3.4 20.9 + - - +
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Residues in contact with SER 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E ASN* 3.4 37.6 + - - -
126E PHE* 3.8 9.6 - - - -
205E ILE 2.8 13.6 + - - -
206E THR* 2.6 26.5 + - - +
208E ALA* 1.3 76.2 - - - +
210E GLU* 1.3 64.1 + - - +
211E LEU* 3.5 2.5 + - - +
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Residues in contact with GLU 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174E LYS* 3.7 18.7 + - - +
206E THR* 3.0 36.5 + - - +
207E VAL* 3.0 8.2 + - - +
209E SER* 1.3 85.4 - - - +
211E LEU* 1.3 62.9 + - - +
165F TYR* 4.6 8.9 + - - -
166F LYS* 4.9 6.2 + - - -
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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