Contacts of the helix formed by residues 198 - 209 (chain C) in PDB entry 4KNF
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 ALA 198 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159C TRP* 3.7 19.2 - - + -
194C VAL 3.4 16.7 + - - +
195C VAL* 3.0 18.2 + - + +
197C TRP* 1.3 77.3 - - - +
199C ILE* 1.3 62.0 + - + +
200C TYR 3.3 0.2 - - - -
201C PRO* 3.2 16.6 - - - +
202C ALA* 3.2 12.5 + - - +
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Residues in contact with ILE 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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195C VAL* 4.1 9.2 - - + +
196C GLY* 3.2 19.1 - - - +
197C TRP 3.0 0.6 + - - -
198C ALA* 1.3 78.9 - - + +
200C TYR* 1.3 56.8 + - - +
202C ALA* 3.3 8.2 - - + +
203C GLY 2.9 23.2 + - - -
223C ILE* 3.3 25.1 - - + +
226C LEU* 4.5 15.7 - - + +
227C ALA* 3.7 22.7 - - + +
230C VAL* 4.1 33.2 - - + -
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Residues in contact with TYR 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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98C TRP* 3.4 31.4 - + - -
197C TRP* 3.1 20.5 + - - -
199C ILE* 1.3 73.6 - - - +
201C PRO* 1.4 62.5 - - + +
203C GLY* 2.7 24.3 + - - -
204C TYR* 2.9 11.1 + - - +
224C TYR* 3.5 13.6 - + + -
227C ALA* 3.1 33.6 + - + -
228C ASP* 2.8 33.6 + - - -
231C ASN* 3.2 26.7 - - - +
301C RET 3.3 62.1 - - + +
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Residues in contact with PRO 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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152C PHE* 3.6 24.0 - - + -
156C MET* 4.0 11.9 - - + -
159C TRP* 4.1 12.6 - - + -
197C TRP 3.1 13.2 - - - +
198C ALA* 3.2 20.0 - - - +
200C TYR* 1.4 87.0 - - + +
202C ALA* 1.3 56.9 + - - +
204C TYR* 3.6 7.3 - - + +
205C ALA* 2.9 31.7 + - - +
301C RET 3.8 33.5 - - + -
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Residues in contact with ALA 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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198C ALA 3.2 13.5 + - - +
199C ILE* 3.3 14.4 - - + +
200C TYR 3.2 0.2 - - - -
201C PRO* 1.3 77.7 - - - +
203C GLY* 1.3 61.9 - - - +
205C ALA* 3.3 5.6 + - - +
206C ALA* 3.1 23.9 + - - +
223C ILE* 4.4 9.5 - - + +
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Residues in contact with GLY 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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199C ILE 2.9 7.9 + - - -
200C TYR 2.7 14.3 + - - -
202C ALA* 1.3 71.4 - - - +
204C TYR* 1.3 61.2 + - - -
206C ALA* 3.3 3.1 + - - +
207C GLY 3.1 18.4 + - - -
220C LEU* 3.5 15.6 - - - +
223C ILE* 3.5 30.6 - - - +
224C TYR* 4.3 6.3 - - - -
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Residues in contact with TYR 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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138C GLY* 3.8 24.2 - - - -
141C GLY* 3.4 19.2 - - - -
142C GLU* 3.7 26.7 - - + -
148C VAL* 2.9 25.8 + - - +
151C ALA* 4.0 0.2 - - - +
152C PHE* 3.3 40.3 + + + -
200C TYR 2.9 12.8 + - - +
201C PRO* 3.6 9.2 - - + +
203C GLY* 1.3 70.5 - - - +
205C ALA* 1.3 61.7 + - - +
207C GLY 3.3 1.0 + - - -
208C TYR* 3.0 38.4 + + + +
209C LEU* 4.0 10.8 - - + -
220C LEU* 4.0 4.3 - - - -
224C TYR* 3.8 13.2 - - - +
301C RET 3.9 20.4 - - + -
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Residues in contact with ALA 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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152C PHE* 4.7 7.2 - - + -
201C PRO 2.9 17.0 + - - +
202C ALA* 3.6 6.5 - - - +
204C TYR* 1.3 76.7 - - - +
206C ALA* 1.3 60.7 + - - +
207C GLY 3.0 0.2 + - - -
209C LEU* 2.8 56.6 + - + -
210C MET* 3.8 5.6 - - - +
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Residues in contact with ALA 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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202C ALA 3.1 12.5 + - - +
203C GLY 3.6 9.0 - - - +
205C ALA* 1.3 74.8 - - - +
207C GLY* 1.3 59.6 + - - +
210C MET* 3.5 28.0 - - + +
216C TYR* 3.5 18.7 - - - +
219C ASN* 4.5 13.7 - - + +
223C ILE* 3.9 20.2 - - + -
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Residues in contact with GLY 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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203C GLY 3.1 12.0 + - - -
204C TYR 3.3 2.9 + - - -
205C ALA 3.1 0.8 - - - -
206C ALA* 1.3 78.3 - - - +
208C TYR* 1.3 68.3 + - - +
209C LEU 3.9 0.2 - - - -
210C MET* 5.5 0.4 - - - -
214C GLY 4.3 2.1 - - - +
215C VAL* 3.2 14.2 - - - +
216C TYR* 3.1 39.8 + - - +
220C LEU* 4.3 8.9 - - - +
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Residues in contact with TYR 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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89C THR* 4.6 4.9 - - - +
91C THR* 4.2 5.5 + - - -
141C GLY 4.8 0.7 - - - -
142C GLU* 2.7 63.3 + - + +
148C VAL* 3.6 38.1 - - + +
204C TYR* 3.0 36.3 + + + +
207C GLY* 1.3 78.8 - - - +
209C LEU* 1.3 68.6 + - + +
210C MET 3.7 2.4 + - - -
211C GLY 5.6 0.4 + - - -
212C GLY* 6.0 0.3 + - - -
214C GLY 5.4 3.1 - - - -
215C VAL* 3.9 32.2 - - + +
220C LEU* 3.6 24.9 - - + +
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Residues in contact with LEU 209 (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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148C VAL* 3.7 26.9 - - + -
149C LEU* 3.9 28.3 - - + +
152C PHE* 3.6 44.2 - - + -
204C TYR* 4.0 2.7 - - + -
205C ALA* 2.8 28.7 + - + +
208C TYR* 1.3 96.6 - - + +
210C MET* 1.3 66.4 + - - +
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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