Contacts of the helix formed by residues 200 - 212 (chain D) in PDB entry 3U8Z
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 ARG 200 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B ASP* 3.7 31.9 + - - +
52B ARG* 3.1 35.3 - - - +
147D GLN 3.7 9.9 - - - +
148D ALA* 3.4 30.2 - - - +
149D LYS 3.8 10.1 + - - -
150D TYR* 3.4 33.2 - - - +
199D ALA* 1.3 77.0 - - + +
201D ASP* 1.3 64.5 + - - +
203D ALA 4.1 0.2 - - - -
204D GLU* 3.2 25.8 + - - +
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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
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52B ARG* 5.4 6.2 - - - +
57B ARG* 3.6 25.1 - - - +
112D GLU* 3.0 36.9 - - + +
115D GLN* 2.9 36.3 + - - +
199D ALA 3.3 5.0 - - - +
200D ARG* 1.3 82.4 - - - +
202D GLU* 1.3 63.0 + - - +
204D GLU* 3.4 8.7 - - - +
205D MET 3.5 1.0 + - - -
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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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115D GLN* 5.5 0.2 - - - +
199D ALA* 3.6 28.3 + - - +
200D ARG 3.5 0.2 - - - -
201D ASP* 1.3 79.2 - - - +
203D ALA* 1.4 55.8 + - - +
205D MET* 3.1 10.6 + - - +
206D GLU* 3.0 35.9 + - + +
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Residues in contact with ALA 203 (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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144D TYR* 3.4 35.9 - - + +
147D GLN* 3.8 11.4 - - + +
148D ALA* 3.5 16.6 - - - +
199D ALA 3.0 19.2 + - - +
200D ARG 4.1 0.2 - - - +
202D GLU* 1.4 71.5 - - - +
204D GLU* 1.3 58.8 + - - +
206D GLU* 3.7 8.2 - - - +
207D TYR* 2.9 30.0 + - - +
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Residues in contact with GLU 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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52B ARG* 4.6 8.0 - - - -
112D GLU* 3.0 23.7 - - - +
115D GLN* 3.4 8.4 - - + +
116D HIS* 2.8 40.7 + - - -
119D PHE* 3.5 39.8 - - + -
148D ALA* 3.9 9.2 - - + +
200D ARG 3.2 18.3 - - - +
201D ASP* 3.4 9.2 - - - +
202D GLU 3.2 0.4 - - - -
203D ALA* 1.3 78.2 - - - +
205D MET* 1.3 56.2 + - - +
207D TYR* 3.5 2.9 - - - +
208D LEU* 3.2 33.7 + - - +
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Residues in contact with MET 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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105D ALA* 3.7 27.4 - - - +
106D GLU* 3.7 38.8 - - + +
109D LEU* 3.8 20.9 - - + +
115D GLN* 3.4 39.6 - - + +
201D ASP 3.5 1.9 + - - +
202D GLU* 3.1 11.3 + - - +
204D GLU* 1.3 76.5 - - - +
206D GLU* 1.3 60.8 + - - +
207D TYR 3.3 0.2 - - - -
208D LEU* 3.2 3.7 + - - -
209D LYS* 3.0 47.0 + - + +
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Residues in contact with GLU 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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106D GLU* 4.7 1.6 - - - +
144D TYR* 3.6 44.4 + - + -
202D GLU* 3.0 23.9 + - + +
203D ALA* 3.7 3.1 - - - +
205D MET* 1.3 76.4 - - - +
207D TYR* 1.4 61.8 + - - +
209D LYS* 2.9 37.1 + - - +
210D ILE* 3.4 27.4 + - - +
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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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119D PHE* 3.4 27.6 - + + -
122D VAL* 4.4 11.4 - - + -
123D LYS* 3.4 44.1 - - + +
126D ILE* 3.5 23.8 - - + +
127D LEU* 5.3 1.4 - - - +
141D LEU* 3.2 63.8 - - + +
144D TYR* 4.2 5.8 - - + +
145D ALA* 4.0 15.9 - - + -
203D ALA 2.9 19.4 + - - +
204D GLU 3.5 6.3 - - - +
206D GLU* 1.4 75.1 - - - +
208D LEU* 1.4 63.1 + - + +
210D ILE 3.3 2.4 + - - -
211D ALA* 3.0 25.2 + - + -
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Residues in contact with LEU 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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105D ALA* 4.1 13.2 - - + -
109D LEU* 3.9 24.2 - - + -
115D GLN* 3.6 30.3 - - + +
118D PHE* 3.9 11.7 - - + +
119D PHE* 3.8 24.2 - - - +
122D VAL* 3.9 22.7 - - + -
204D GLU 3.2 17.7 + - - +
205D MET* 3.2 9.3 + - - +
207D TYR* 1.4 80.2 - - + +
209D LYS* 1.3 54.2 + - - +
211D ALA* 3.7 3.5 - - - +
212D GLN* 2.8 39.1 + - - +
217D TYR* 4.5 8.9 - - + +
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Residues in contact with LYS 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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105D ALA* 5.3 0.4 - - + -
106D GLU* 3.3 37.6 + - + +
205D MET* 3.0 41.5 + - + +
206D GLU* 2.9 36.4 + - - +
207D TYR 3.3 0.4 - - - -
208D LEU* 1.3 72.7 - - - +
210D ILE* 1.3 64.6 + - + +
212D GLN* 3.4 32.4 + - - +
213D ASP* 3.6 14.0 - - - +
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Residues in contact with ILE 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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137D ALA* 4.1 23.8 - - + -
140D LEU* 3.8 25.8 - - + -
141D LEU* 3.8 24.0 - - + +
144D TYR* 3.6 35.4 - - + -
206D GLU 3.4 10.5 + - - +
207D TYR 3.3 6.5 + - - +
209D LYS* 1.3 75.9 - - + +
211D ALA* 1.4 64.9 + - - +
213D ASP* 3.2 21.3 + - - +
214D LEU* 4.0 7.0 + - + +
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Residues in contact with ALA 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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122D VAL* 3.6 31.2 - - + -
126D ILE* 4.8 2.7 - - + -
141D LEU* 4.1 8.5 - - + +
207D TYR* 3.0 19.5 + - + +
208D LEU* 3.3 6.9 + - - +
210D ILE* 1.4 76.9 - - - +
212D GLN* 1.4 57.0 + - - +
214D LEU* 3.0 42.1 + - + +
217D TYR* 3.4 11.8 - - + +
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Residues in contact with GLN 212 (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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102D PRO 4.9 1.6 - - - +
103D GLU 3.7 16.2 - - - +
104D ASN* 4.6 8.7 + - - +
105D ALA* 2.9 34.7 + - - +
106D GLU* 6.1 0.2 - - - +
208D LEU 2.8 21.7 + - - +
209D LYS* 3.4 33.5 + - - +
211D ALA* 1.4 71.5 - - - +
213D ASP* 1.3 66.6 + - - +
214D LEU 3.3 5.3 + - - +
217D TYR* 3.5 37.3 + - + +
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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