Contacts of the helix formed by residues 197 - 210 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C ASP* 4.9 2.7 + - - -
195C LYS* 3.6 1.6 + - - -
196C ARG* 1.3 77.9 - - - +
198C ALA* 1.3 65.8 + - - +
199C GLU* 3.5 7.3 + - - +
200C ASN* 2.9 34.2 + - - +
201C ILE* 2.9 31.1 + - - +
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Residues in contact with ALA 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C ASP* 5.4 2.7 + - - -
116C LEU* 3.8 24.4 - - + +
197C SER* 1.3 73.6 - - - +
199C GLU* 1.3 64.6 + - + +
201C ILE* 3.5 3.0 + - - +
202C GLU* 3.3 22.9 + - - +
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Residues in contact with GLU 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C SER* 3.1 7.7 + - - +
198C ALA* 1.3 80.4 - - + +
200C ASN* 1.3 59.8 + - - +
202C GLU* 3.4 5.6 + - - +
203C ALA* 2.9 29.2 + - - +
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Residues in contact with ASN 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C MET* 4.9 1.1 - - + -
178C ILE 5.2 2.1 - - - +
194C ILE* 3.6 35.8 - - + +
195C LYS* 2.8 34.0 + - - +
196C ARG* 5.1 0.2 - - - -
197C SER* 2.9 25.5 + - - +
199C GLU* 1.3 74.7 - - - +
201C ILE* 1.3 66.3 + - + +
203C ALA* 4.1 7.6 - - - +
204C VAL* 2.9 30.7 + - - +
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Residues in contact with ILE 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C ASP* 3.7 46.4 - - + +
116C LEU* 4.0 20.6 - - + -
117C MET* 4.0 26.5 - - + -
120C LEU* 4.5 0.4 - - + -
154C ILE* 4.3 6.7 - - + -
160C MET* 3.8 27.3 - - + +
196C ARG* 5.0 4.0 - - + -
197C SER 2.9 27.9 + - - +
198C ALA 3.9 3.8 - - - +
200C ASN* 1.3 75.1 - - - +
202C GLU* 1.3 62.2 + - - +
204C VAL* 3.6 1.6 + - - +
205C ILE* 3.2 28.6 + - + +
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Residues in contact with GLU 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C LEU* 5.7 1.9 - - + +
120C LEU* 3.6 34.8 - - + +
123C LYS* 4.9 9.0 + - - -
198C ALA 3.3 13.8 + - - +
199C GLU* 3.8 5.2 - - - +
200C ASN 3.2 0.2 - - - -
201C ILE* 1.3 77.5 - - - +
203C ALA* 1.3 64.1 + - - +
205C ILE* 3.4 2.0 + - - +
206C THR* 2.8 40.9 + - - +
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Residues in contact with ALA 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C ILE* 3.9 19.5 - - + +
194C ILE* 6.2 0.9 - - + -
199C GLU 2.9 18.3 + - - +
200C ASN* 3.6 11.4 - - - +
202C GLU* 1.3 77.8 - - - +
204C VAL* 1.3 63.7 + - - +
206C THR* 3.7 5.4 - - - -
207C VAL* 3.0 29.3 + - + +
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Residues in contact with VAL 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C PHE* 4.7 3.8 - - + -
160C MET* 3.9 14.4 - - + -
162C ILE* 3.3 34.5 - - + -
175C PHE* 3.4 9.7 - - + -
178C ILE* 4.0 14.4 - - + -
180C MET* 4.0 18.8 - - + -
194C ILE* 3.9 27.1 - - + -
200C ASN 2.9 21.5 + - - +
201C ILE 3.9 3.4 - - - +
203C ALA* 1.3 76.6 - - - +
205C ILE* 1.3 59.2 + - - +
207C VAL 3.4 1.0 + - - -
208C ALA* 3.0 23.7 + - - +
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Residues in contact with ILE 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C MET* 3.6 39.3 - - + +
120C LEU* 3.6 28.3 - - + +
121C LEU* 4.0 24.0 - - + -
124C ASN* 3.7 22.0 - - - +
126C PHE* 4.2 5.7 - - + -
152C PHE* 4.6 4.3 - - + -
160C MET* 4.2 10.3 - - + -
201C ILE* 3.2 22.9 + - + +
202C GLU 4.0 2.0 - - - +
204C VAL* 1.3 77.0 - - - +
206C THR* 1.3 58.3 + - - +
208C ALA* 3.3 8.0 + - - +
209C SER* 3.0 26.7 + - - -
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Residues in contact with THR 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ASN* 5.0 5.5 + - - +
202C GLU* 2.8 36.1 + - - +
203C ALA* 3.7 6.1 - - - -
204C VAL 3.2 0.2 - - - -
205C ILE* 1.3 75.1 - - - +
207C VAL* 1.3 66.3 + - + +
209C SER* 2.7 25.6 + - - +
210C GLU* 3.2 30.1 + - - +
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Residues in contact with VAL 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C LYS* 3.8 32.8 + - + +
175C PHE* 3.7 24.2 - - + -
178C ILE* 3.6 31.2 - - + -
203C ALA* 3.0 22.4 + - - +
204C VAL 3.7 4.3 - - - +
206C THR* 1.3 77.4 - - + +
208C ALA* 1.3 64.6 + - - +
210C GLU* 3.1 17.1 + - - +
211C LEU* 3.4 14.0 + - + +
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Residues in contact with ALA 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C PHE* 3.7 23.2 - - + -
147C ASN* 4.6 5.2 + - - -
149C ILE* 4.1 4.7 - - + -
152C PHE* 4.1 17.7 - - + -
175C PHE* 3.6 21.1 - - + -
204C VAL 3.0 17.0 + - - +
205C ILE* 3.5 7.4 - - - +
207C VAL* 1.3 78.2 - - - +
209C SER* 1.3 60.4 - - - +
210C GLU 3.3 0.5 + - - -
211C LEU* 3.4 20.4 + - - +
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Residues in contact with SER 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ASN* 3.6 35.7 + - - -
126C PHE* 4.1 8.3 - - - -
205C ILE 3.0 13.9 + - - -
206C THR* 2.7 23.2 + - - +
208C ALA* 1.3 76.3 - - - +
210C GLU* 1.3 67.2 + - - +
211C LEU* 3.5 2.5 + - - +
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Residues in contact with GLU 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C LYS* 3.2 19.1 + - - +
206C THR* 3.2 32.7 + - - +
207C VAL* 3.1 10.8 + - - +
209C SER* 1.3 86.3 + - - +
211C LEU* 1.3 63.4 + - - +
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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