Contacts of the helix formed by residues 196 - 209 (chain P) in PDB entry 6K71
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 196 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184M PHE* 4.9 16.4 - - + -
188M ARG* 5.8 8.0 - - - +
192P ILE* 3.4 20.2 - - - +
193P ASP 2.4 33.1 + - - -
194P LEU 3.4 10.8 + - - +
195P VAL* 1.3 80.7 - - - +
197P GLU* 1.3 66.4 + - - +
198P SER* 2.7 20.7 + - - -
199P GLN 3.0 13.9 + - - -
200P ALA* 3.8 5.3 + - - -
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Residues in contact with GLU 197 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176M TYR* 4.6 1.8 + - - +
180M LEU* 5.4 13.5 - - + -
196P LYS* 1.3 80.7 - - - +
198P SER* 1.3 54.6 + - - +
199P GLN 3.5 0.4 - - - -
200P ALA* 4.4 9.6 - - - -
201P LYS* 2.7 44.4 + - + +
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Residues in contact with SER 198 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195P VAL* 4.3 10.2 - - - +
196P LYS 2.7 11.1 + - - -
197P GLU* 1.3 78.9 - - - +
199P GLN* 1.3 66.8 + - - +
201P LYS* 3.2 18.1 + - - +
202P GLU* 3.0 32.4 + - - +
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Residues in contact with GLN 199 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161P GLY* 3.1 22.8 + - - -
165P CYS* 2.7 31.9 - - - -
191P LYS* 3.6 12.2 - - - +
195P VAL* 3.2 39.0 - - + +
196P LYS 3.0 7.7 + - - +
198P SER* 1.3 80.8 + - - +
200P ALA* 1.3 52.0 + - - +
202P GLU* 2.9 21.9 - - - +
203P GLN* 2.7 52.0 + - - +
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Residues in contact with ALA 200 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176M TYR* 3.3 20.8 + - + +
184M PHE* 5.9 5.8 - - + -
189P GLN* 3.4 25.9 - - - +
191P LYS* 4.9 2.9 - - + +
195P VAL 5.0 1.7 + - - +
196P LYS 3.8 5.0 + - - +
197P GLU* 4.3 12.1 - - - +
198P SER 3.3 0.4 - - - -
199P GLN* 1.3 78.3 - - - +
201P LYS* 1.3 56.6 + - - +
203P GLN* 3.7 10.5 + - - +
204P TYR* 2.9 32.1 + - - +
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Residues in contact with LYS 201 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176M TYR* 3.7 1.8 + - - +
180M LEU* 6.6 0.2 - - + -
197P GLU* 2.7 24.1 + - + +
198P SER* 3.2 21.8 + - - +
200P ALA* 1.3 77.6 - - - +
202P GLU* 1.3 65.4 + - - +
204P TYR* 3.2 47.0 - - + +
205P GLU* 3.9 4.2 + - - +
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Residues in contact with GLU 202 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165P CYS* 4.0 5.0 - - - +
198P SER 3.0 21.8 + - - +
199P GLN* 2.9 31.1 - - - +
201P LYS* 1.3 83.6 - - - +
203P GLN* 1.3 55.8 + - - +
205P GLU* 3.3 12.1 + - - +
206P GLN* 2.4 65.6 + - - +
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Residues in contact with GLN 203 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159P ILE* 4.8 6.9 - - - +
160P ALA 3.3 25.1 + - - -
161P GLY* 3.8 9.1 - - - -
165P CYS* 5.2 5.5 + - - +
189P GLN* 3.6 35.5 + - + +
191P LYS* 4.4 1.9 - - - +
199P GLN* 2.7 44.0 + - - +
200P ALA* 3.7 5.6 + - - +
201P LYS 3.2 0.4 - - - -
202P GLU* 1.3 77.6 - - - +
204P TYR* 1.3 61.4 + - - +
206P GLN* 3.2 23.4 + - - +
207P ILE* 2.9 37.9 + - + +
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Residues in contact with TYR 204 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176M TYR* 3.5 33.0 - + + -
180M LEU* 5.8 0.9 - - + -
189P GLN* 5.7 0.4 + - - -
200P ALA 2.9 20.7 + - - +
201P LYS* 3.2 40.9 - - + +
203P GLN* 1.3 77.6 - - - +
205P GLU* 1.3 61.7 + - + +
207P ILE* 3.3 11.8 - - + +
208P LEU* 2.9 46.2 + - + +
221P ILE* 4.3 20.4 - - + +
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Residues in contact with GLU 205 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201P LYS 3.9 3.8 + - - +
202P GLU* 3.3 14.1 + - - +
203P GLN 3.3 0.2 - - - -
204P TYR* 1.3 84.0 - - + +
206P GLN* 1.3 58.8 + - - +
208P LEU* 3.6 20.1 - - + +
209P ALA* 3.0 29.7 + - + +
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Residues in contact with GLN 206 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586J ASN* 6.1 0.4 - - - +
165P CYS* 2.8 43.2 - - - +
166P PRO* 3.7 11.5 - - + +
202P GLU* 2.4 45.3 + - - +
203P GLN* 3.3 28.9 - - - +
205P GLU* 1.3 75.1 - - - +
207P ILE* 1.3 61.0 + - + +
209P ALA* 3.1 19.7 + - - +
210P PHE* 3.1 24.8 - - + -
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Residues in contact with ILE 207 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159P ILE* 4.3 21.8 - - + -
187P ILE* 3.6 33.9 - - + +
189P GLN* 5.3 7.2 - - + +
203P GLN* 2.9 36.8 + - + +
204P TYR* 3.3 13.7 - - + +
206P GLN* 1.3 74.8 - - + +
208P LEU* 1.3 61.0 + - + +
209P ALA 3.2 0.2 - - - -
210P PHE* 3.3 41.1 + - + +
211P VAL* 3.4 9.7 - - - +
216P ALA 5.2 0.3 - - - +
221P ILE* 3.7 28.9 - - + -
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Residues in contact with LEU 208 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173M ASP* 5.6 5.8 - - - +
187P ILE* 6.0 0.7 - - - -
204P TYR* 2.9 40.2 + - + +
205P GLU* 3.6 23.3 - - + +
207P ILE* 1.3 74.7 - - + +
209P ALA* 1.3 51.8 + - + +
210P PHE 3.1 5.5 + - - -
211P VAL* 3.4 20.0 - - + +
212P GLN* 2.4 30.3 + - - +
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Residues in contact with ALA 209 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582J LYS* 3.4 18.4 + - - -
586J ASN* 5.5 8.7 - - + +
587J ILE 5.3 0.6 - - - +
588J SER* 5.9 9.1 - - - -
205P GLU* 3.0 14.0 + - + +
206P GLN* 3.1 15.1 + - - +
208P LEU* 1.3 76.3 - - + +
210P PHE* 1.3 64.0 + - + -
212P GLN* 3.1 19.3 - - - +
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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