Contacts of the helix formed by residues 204 - 215 (chain A) in PDB entry 1KKQ
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 LYS 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A THR* 4.7 4.9 - - - -
201A ALA* 3.7 21.7 - - - +
202A ASP 3.1 0.6 - - - -
203A LEU* 1.3 80.3 - - - +
205A SER* 1.3 59.2 + - - +
206A LEU 2.8 8.7 + - - -
207A ALA* 3.6 14.1 + - + +
208A LYS* 4.4 1.9 + - - +
407A VAL* 5.9 5.6 - - + -
410A LEU* 4.4 27.7 - - - +
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Residues in contact with SER 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ALA 3.8 12.2 + - - -
202A ASP* 3.8 9.9 + - - -
204A LYS* 1.3 76.7 - - - +
206A LEU* 1.3 58.1 + - - +
207A ALA 3.3 0.7 - - - -
208A LYS* 3.5 16.6 - - - +
209A ARG* 3.0 36.4 + - - +
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Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ASP 3.6 10.8 + - - +
203A LEU* 3.4 39.3 - - + +
204A LYS 2.8 0.4 - - - -
205A SER* 1.3 77.9 + - - +
207A ALA* 1.3 64.9 + - - +
209A ARG* 3.7 4.6 + - - +
210A ILE* 3.3 36.5 + - + +
294A ILE* 5.9 0.2 - - + -
295A PRO* 3.6 34.5 - - + +
377A LEU* 6.3 0.2 - - + -
400A MET 5.7 0.7 - - - +
403A GLY* 3.9 14.8 - - - -
404A ILE* 4.1 7.9 - - + +
407A VAL* 3.7 23.3 - - + -
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Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A LYS* 3.6 8.8 + - + +
205A SER 3.3 0.4 - - - -
206A LEU* 1.3 76.8 - - - +
208A LYS* 1.3 68.6 + - - +
210A ILE* 3.3 4.5 + - - +
211A TYR* 3.1 18.5 + - - +
377A LEU* 4.0 23.3 - - + +
407A VAL* 3.0 34.2 - - + +
411A HIS* 5.4 7.9 - - + -
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Residues in contact with LYS 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A LYS 4.4 1.7 + - - +
205A SER* 3.4 21.0 + - - +
207A ALA* 1.3 76.0 - - - +
209A ARG* 1.3 55.0 + - + +
210A ILE 2.7 4.4 + - - -
211A TYR* 2.5 35.3 + - + +
212A GLU* 3.0 37.0 + - + +
700E TRP* 5.7 5.4 - - + -
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Residues in contact with ARG 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A SER* 3.0 19.8 + - - +
206A LEU* 3.9 5.6 - - - +
208A LYS* 1.3 78.4 - - + +
210A ILE* 1.3 57.6 + - - +
212A GLU* 4.1 2.6 - - - +
213A ALA* 3.5 20.8 + - - +
293A ALA* 3.4 29.8 + - - +
295A PRO* 4.0 35.6 - - + +
296A GLY 5.5 0.2 - - - +
700E TRP* 3.2 52.5 + - + -
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Residues in contact with ILE 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LEU* 3.3 36.3 + - + +
207A ALA 3.3 4.5 + - - +
208A LYS 2.7 2.4 + - - -
209A ARG* 1.3 73.6 - - - +
211A TYR* 1.3 63.5 + - - +
212A GLU 3.4 0.7 - - - -
213A ALA* 3.9 5.8 - - - -
214A TYR* 3.5 13.0 + - - +
290A PHE* 3.7 7.8 - - + -
294A ILE* 4.2 16.2 - - + -
295A PRO* 3.8 16.6 - - + -
376A SER* 3.6 26.9 - - - +
377A LEU* 3.5 27.8 - - + -
380A ALA* 4.2 9.0 - - + -
404A ILE* 4.1 23.3 - - + -
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Residues in contact with TYR 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ALA 3.1 10.1 + - - +
208A LYS* 2.5 22.8 + - + +
210A ILE* 1.3 72.5 - - - +
212A GLU* 1.3 62.6 + - + +
214A TYR* 3.4 2.5 + + - +
215A LEU* 2.8 57.9 + - + +
223A VAL* 5.9 1.9 - - - +
372A ASP* 3.5 24.9 - - + +
373A SER* 3.4 45.9 + - - +
376A SER* 3.8 8.7 - - - +
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Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A LYS* 3.0 39.2 + - + +
209A ARG 4.4 0.4 - - - +
211A TYR* 1.3 81.0 - - + +
213A ALA* 1.3 66.2 + - - +
214A TYR 3.0 1.6 - - - -
215A LEU* 3.0 13.5 + - + +
216A LYS* 3.0 25.4 + - + +
700E TRP* 2.7 60.1 - - + -
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Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ARG 3.5 18.8 + - - +
210A ILE* 3.8 7.6 - - - +
211A TYR 3.3 0.2 - - - -
212A GLU* 1.3 79.3 - - - +
214A TYR* 1.3 55.4 + - - +
216A LYS* 4.8 0.7 - - - -
217A ASN* 2.6 42.0 + - - +
290A PHE* 3.6 23.1 - - + +
293A ALA* 3.7 27.1 - - + +
294A ILE* 5.2 0.7 - - + -
700E TRP* 5.6 0.2 - - - -
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Residues in contact with TYR 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ILE 3.5 3.0 + - - +
211A TYR* 3.5 8.3 - + - +
212A GLU 3.0 0.2 - - - -
213A ALA* 1.3 77.0 - - - +
215A LEU* 1.3 64.0 + - + +
216A LYS 2.8 11.6 + - - -
217A ASN 3.3 7.4 + - - -
218A PHE* 3.2 49.5 + + + +
220A MET 5.1 0.7 + - - -
221A ASN* 3.9 18.9 + - + +
222A LYS 4.5 0.7 + - - -
290A PHE* 3.6 10.3 - + + -
320A MET* 3.9 20.3 - - - +
323A SER* 4.7 4.3 + - - -
372A ASP* 2.7 52.7 + - + -
375A ILE* 4.0 18.6 - - + +
376A SER* 3.6 36.3 - - - -
379A VAL* 5.1 2.0 - - + -
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Residues in contact with LEU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A TYR* 2.8 64.7 + - + +
212A GLU* 3.0 7.6 + - + +
214A TYR* 1.3 75.9 - - + +
216A LYS* 1.3 61.3 + - - +
218A PHE 5.3 2.0 - - - -
221A ASN* 4.0 25.1 - - - +
223A VAL* 6.2 1.3 - - + -
372A ASP* 4.9 3.6 - - + +
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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