Contacts of the helix formed by residues 199 - 211 (chain B) in PDB entry 1Y67
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 ASN 199 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B GLN 4.2 6.7 + - - +
87B ILE 2.7 19.4 + - - +
88B MET 3.9 18.0 + - - +
89B GLY* 4.2 7.5 - - - +
197B VAL 3.3 2.0 + - - -
198B VAL* 1.3 71.3 - - - +
200B TRP* 1.3 61.8 + - - +
201B ASP* 3.1 23.9 + - - +
202B GLU* 3.2 18.6 + - - +
203B VAL* 3.2 21.8 + - - +
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Residues in contact with TRP 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ASN* 3.5 42.6 + - - +
99B GLN* 3.6 24.7 - - - +
100B PRO* 3.7 26.5 - - + -
104B LEU* 4.0 8.6 - - + +
108B ILE* 4.4 9.9 - - + -
115B PHE* 3.5 28.8 - + - -
118B PHE* 3.9 11.7 - + - -
137B LEU* 4.8 2.7 - - + -
170B LEU* 3.8 21.5 - - + -
195B TRP* 3.9 15.0 + + - -
198B VAL* 3.4 22.6 + - + +
199B ASN* 1.3 70.4 + - - +
201B ASP* 1.3 61.8 + - - +
203B VAL* 3.7 30.9 - - + +
204B SER* 2.9 32.7 + - - -
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Residues in contact with ASP 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B SER* 5.7 0.7 + - - -
199B ASN* 3.1 11.7 + - - +
200B TRP* 1.3 78.7 - - - +
202B GLU* 1.3 61.3 + - - +
204B SER* 3.5 6.8 + - - -
205B LYS* 3.1 27.0 + - - +
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Residues in contact with GLU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLN* 3.3 35.5 - - - +
87B ILE* 3.8 8.1 - - + -
199B ASN* 3.2 22.8 + - - +
201B ASP* 1.3 75.6 - - - +
203B VAL* 1.3 65.3 + - - +
205B LYS* 2.9 39.3 + - - +
206B ARG* 2.8 61.2 + - - +
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Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 4.1 7.9 - - + -
104B LEU* 3.6 17.0 - - + -
137B LEU* 4.7 1.1 - - + -
169B ILE* 3.5 42.8 - - + +
170B LEU* 4.0 25.6 - - + -
198B VAL* 4.1 3.4 - - + -
199B ASN 3.2 14.5 + - - +
200B TRP* 3.5 28.7 + - + +
202B GLU* 1.3 75.0 - - - +
204B SER* 1.3 57.3 + - - +
206B ARG* 3.2 4.8 + - - +
207B TYR* 2.9 26.5 + - - +
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Residues in contact with SER 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PRO* 5.1 0.3 - - - +
101B SER 4.1 11.4 + - - -
104B LEU* 3.4 29.0 + - - +
200B TRP 2.9 19.4 + - - -
201B ASP* 3.7 7.4 - - - -
203B VAL* 1.3 73.8 - - - +
205B LYS* 1.3 65.6 + - - +
207B TYR* 3.2 5.7 + - - +
208B ALA* 3.0 25.6 + - - +
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Residues in contact with LYS 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B ASP* 3.1 12.5 + - - +
202B GLU* 2.9 40.3 + - - +
204B SER* 1.3 74.7 - - - +
206B ARG* 1.3 59.4 + - + +
208B ALA* 3.6 5.7 + - - +
209B ALA* 3.1 27.8 + - - +
205C LYS* 4.1 41.0 - - + +
209C ALA* 6.5 0.9 - - + -
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Residues in contact with ARG 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B MET* 3.7 33.5 - - - +
86B GLN* 2.8 32.9 + - - +
87B ILE* 3.8 8.3 - - - +
167B THR* 5.6 0.3 - - - +
168B PRO 4.9 5.1 + - - +
169B ILE* 3.6 36.3 - - + +
202B GLU* 2.8 40.2 + - - +
203B VAL 3.2 7.2 + - - +
205B LYS* 1.3 75.4 - - + +
207B TYR* 1.3 59.8 + - - +
209B ALA* 3.6 6.5 - - - +
210B ALA* 2.9 30.1 + - - +
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Residues in contact with TYR 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B GLU* 4.2 25.1 + - + -
104B LEU* 3.9 24.2 - - + -
107B ALA* 3.2 24.6 - - + +
139B VAL* 3.8 21.5 - - + -
142B GLY 4.4 5.1 + - - -
144B LEU* 3.9 25.4 - - + -
169B ILE* 3.8 13.7 - - + +
203B VAL 2.9 13.1 + - - +
204B SER* 3.2 9.2 + - - +
206B ARG* 1.3 74.5 - - - +
208B ALA* 1.3 70.3 + - + +
210B ALA* 3.1 3.7 + - - +
211B LYS* 2.9 60.5 + - + +
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Residues in contact with ALA 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B SER 3.0 16.6 + - - +
205B LYS* 3.8 6.7 - - - +
207B TYR* 1.3 84.5 - - + +
209B ALA* 1.3 61.6 + - - +
211B LYS* 3.4 19.9 + - - +
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Residues in contact with ALA 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B LYS 3.1 18.5 + - - +
206B ARG* 3.6 8.1 - - - +
208B ALA* 1.3 76.0 - - - +
210B ALA* 1.3 62.5 + - - +
211B LYS 3.2 4.9 + - - -
212C LEU* 3.5 44.7 - - + +
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Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B VAL* 3.9 33.3 - - + +
142B GLY* 6.0 0.2 - - - -
167B THR* 4.0 26.0 + - + -
169B ILE* 4.4 1.3 - - + -
206B ARG 2.9 18.8 + - - +
207B TYR 3.1 3.3 + - - +
209B ALA* 1.3 73.5 - - - +
211B LYS* 1.3 60.7 + - - +
212C LEU* 6.1 0.2 - - - -
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Residues in contact with LYS 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B VAL* 4.4 11.0 - - + -
142B GLY* 3.1 33.0 + - - -
207B TYR* 2.9 53.3 + - + +
208B ALA* 3.5 16.4 - - - +
209B ALA 3.1 4.6 - - - -
210B ALA* 1.3 82.2 - - - +
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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