Contacts of the helix formed by residues 199 - 211 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86D GLN 4.2 4.4 + - - +
87D ILE 2.7 24.7 + - - +
88D MET 3.9 16.2 + - - +
89D GLY* 4.2 1.6 - - - +
92D GLN* 3.6 24.7 + - - +
197D VAL 3.4 1.0 + - - -
198D VAL* 1.3 70.3 - - - +
200D TRP* 1.3 62.2 + - - +
201D ASP* 3.1 26.9 + - - +
202D GLU* 3.1 14.8 + - - +
203D VAL* 3.1 22.5 + - - +
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Residues in contact with TRP 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D GLN* 4.4 2.6 + - - -
98D ASN* 3.6 42.0 + - - +
99D GLN* 3.7 15.7 - - - +
100D PRO* 3.6 39.5 - - + -
104D LEU* 3.8 14.9 - - + +
108D ILE* 4.4 5.4 - - + -
115D PHE* 3.5 21.7 - + - -
118D PHE* 3.8 23.6 - + - -
137D LEU* 5.0 2.2 - - + -
170D LEU* 3.8 15.0 - - + -
195D TRP* 3.9 14.6 + + - -
198D VAL* 3.5 21.4 + - + +
199D ASN* 1.3 70.0 + - - +
201D ASP* 1.3 61.0 + - - +
203D VAL* 3.8 24.4 - - + +
204D SER* 2.8 35.4 + - - -
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Residues in contact with ASP 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D GLN* 5.8 1.1 - - - -
199D ASN* 3.1 12.9 + - - +
200D TRP* 1.3 77.0 - - - +
202D GLU* 1.3 57.2 + - - +
204D SER* 3.4 6.5 + - - -
205D LYS* 3.0 27.0 + - - +
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Residues in contact with GLU 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D GLN* 3.3 38.6 - - - +
87D ILE* 3.8 15.0 - - + -
199D ASN* 3.1 19.2 + - - +
201D ASP* 1.3 76.7 - - - +
203D VAL* 1.3 61.7 + - - +
205D LYS* 3.3 28.0 + - - +
206D ARG* 2.9 58.4 + - - +
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Residues in contact with VAL 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ILE* 4.0 14.1 - - + -
104D LEU* 3.8 15.5 - - + -
137D LEU* 4.7 0.9 - - + -
169D ILE* 3.5 42.1 - - + +
170D LEU* 4.1 10.1 - - + -
198D VAL* 4.0 20.6 - - + -
199D ASN 3.1 14.8 + - - +
200D TRP* 3.8 20.4 - - + +
202D GLU* 1.3 77.0 - - - +
204D SER* 1.3 56.7 + - - +
206D ARG* 3.3 2.9 + - - +
207D TYR* 2.9 27.2 + - - +
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Residues in contact with SER 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D PRO* 4.9 2.3 - - - +
101D SER 4.3 9.4 + - - -
103D GLU* 4.7 6.7 - - - +
104D LEU* 3.4 29.1 - - - +
200D TRP 2.8 20.0 + - - -
201D ASP* 3.7 7.2 - - - -
203D VAL* 1.3 74.3 - - - +
205D LYS* 1.3 58.9 + - - +
207D TYR* 3.3 4.9 + - - +
208D ALA* 3.0 30.5 + - - +
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Residues in contact with LYS 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D ASP 3.0 13.4 + - - +
202D GLU* 3.3 29.0 + - - +
204D SER* 1.3 74.3 - - - +
206D ARG* 1.3 59.1 + - + +
208D ALA* 3.4 7.3 + - - +
209D ALA* 3.0 28.9 + - + +
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Residues in contact with ARG 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D MET* 3.3 40.8 - - - +
86D GLN* 2.7 31.5 + - - +
87D ILE* 3.8 15.8 - - - +
168D PRO 4.8 3.8 + - - +
169D ILE* 3.7 36.3 - - + +
202D GLU* 2.9 35.9 + - - +
203D VAL 3.5 4.9 - - - +
205D LYS* 1.3 73.6 - - + +
207D TYR* 1.3 59.0 + - - +
209D ALA* 3.3 6.8 + - - +
210D ALA* 2.8 30.7 + - - +
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Residues in contact with TYR 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D GLU* 3.9 28.7 - - + -
104D LEU* 4.0 21.3 - - + -
107D ALA* 3.3 21.1 - - + +
139D VAL* 3.8 20.9 - - + -
143D LYS 6.3 0.4 - - - -
144D LEU* 3.8 25.7 - - + +
169D ILE* 3.7 17.1 - - + +
203D VAL 2.9 19.1 + - - +
204D SER* 3.3 5.6 + - - +
206D ARG* 1.3 71.7 - - - +
208D ALA* 1.3 65.5 + - - +
210D ALA* 3.2 3.2 + - - +
211D LYS* 3.1 70.4 + - + +
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Residues in contact with ALA 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D GLU* 3.5 22.9 - - - +
204D SER 3.0 15.8 + - - +
205D LYS* 3.6 7.6 - - - +
207D TYR* 1.3 75.7 - - - +
209D ALA* 1.3 62.2 + - - +
211D LYS* 3.6 12.9 + - - +
212D LEU* 3.5 24.2 - - + +
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Residues in contact with ALA 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D LYS* 3.0 17.0 + - + +
206D ARG* 3.7 7.6 - - - +
208D ALA* 1.3 73.6 - - - +
210D ALA* 1.3 67.0 + - - +
212D LEU* 3.0 23.3 + - - +
213D VAL* 3.5 13.7 - - + +
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Residues in contact with ALA 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D VAL* 3.8 30.9 - - + +
167D THR* 4.2 21.5 + - + -
169D ILE* 4.2 7.0 - - + -
206D ARG 2.8 18.3 + - - +
207D TYR 3.2 5.8 + - - +
209D ALA* 1.3 75.7 - - - +
211D LYS* 1.3 60.7 + - - +
212D LEU 3.1 1.4 + - - -
213D VAL* 3.4 24.5 + - - +
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Residues in contact with LYS 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D GLU* 2.8 35.5 + - - +
139D VAL* 5.1 9.4 - - + -
207D TYR* 3.1 57.0 + - + +
208D ALA* 3.9 8.3 - - - +
209D ALA 3.3 0.8 - - - -
210D ALA* 1.3 75.0 - - - +
212D LEU* 1.3 63.4 + - + +
213D VAL 3.5 2.9 - - - +
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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