Contacts of the helix formed by residues 157 - 167 (chain B) in PDB entry 6DMY
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 157 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B TRP* 3.4 48.6 - - + +
120B VAL* 3.6 21.0 - - - +
150B THR* 4.2 13.2 - - + -
152B ASP* 2.5 41.4 + - - -
154B ASP* 3.7 22.3 + - - +
155B ARG 3.4 0.6 - - - -
156B SER* 1.3 84.9 - - - +
158B TYR* 1.3 59.6 + - - +
159B GLY 3.4 0.9 - - - -
160B MET* 3.6 5.3 + - - +
161B LEU* 3.0 24.9 + - - +
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Residues in contact with TYR 158 (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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149B THR* 3.3 28.3 - - + +
150B THR* 3.5 26.7 - - + -
153B ARG* 3.3 24.6 + - - +
154B ASP 3.1 18.8 - - - -
155B ARG* 3.6 27.8 - - + +
156B SER 3.1 2.0 + - - -
157B LYS* 1.3 80.0 - - - +
159B GLY* 1.3 61.1 + - - +
161B LEU* 3.4 19.2 - - + +
162B ALA* 2.9 28.4 + - - +
175B TYR* 3.6 16.6 - + - +
178B LYS 4.0 11.2 - - - -
179B ALA* 4.0 20.7 + - - -
180B HIS 4.8 2.2 - - - -
181B ILE* 3.8 18.6 - - + +
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Residues in contact with GLY 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PRO* 3.7 15.7 - - - -
42B LEU 3.7 17.4 + - - -
156B SER 4.0 6.0 + - - -
157B LYS 3.4 0.8 - - - -
158B TYR* 1.3 76.2 - - - +
160B MET* 1.3 59.0 + - - +
162B ALA* 3.1 4.2 + - - +
163B ARG* 3.0 24.3 + - - +
175B TYR* 3.7 19.0 + - - -
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Residues in contact with MET 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 5.3 15.7 - - + +
40B THR 5.6 0.7 - - - -
41B PRO* 3.8 20.6 - - + +
116B GLN* 3.8 29.8 - - - +
117B TRP* 4.3 19.1 - - + -
156B SER 5.2 0.6 + - - -
157B LYS* 3.6 9.6 + - - +
159B GLY* 1.3 75.1 - - - +
161B LEU* 1.3 58.1 + - - +
163B ARG* 3.9 18.0 - - + +
164B LEU* 2.9 48.8 + - + +
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Residues in contact with LEU 161 (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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109B LEU* 4.6 1.7 - - + +
113B VAL* 3.7 32.3 - - + -
117B TRP* 4.5 5.8 - - + -
122B LEU* 3.7 13.7 - - + -
148B ILE* 3.9 19.7 - - + -
149B THR* 4.0 25.4 - - - +
150B THR* 4.0 7.4 - - + -
157B LYS 3.0 16.4 + - - +
158B TYR* 3.4 33.4 - - + +
159B GLY 3.2 0.2 - - - -
160B MET* 1.3 77.1 - - - +
162B ALA* 1.3 56.2 + - - +
164B LEU* 3.4 7.2 + - - +
165B ALA* 2.9 24.3 + - - +
181B ILE* 4.4 5.2 - - + -
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Residues in contact with ALA 162 (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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42B LEU* 3.8 19.7 - - + -
158B TYR 2.9 16.3 + - - +
159B GLY 3.7 4.3 - - - +
161B LEU* 1.3 74.5 - - - +
163B ARG* 1.3 62.8 + - - +
165B ALA* 3.0 10.1 + - - +
166B VAL* 2.9 30.8 + - - +
173B VAL* 3.7 8.8 - - + +
175B TYR* 4.5 7.9 - - + -
181B ILE* 3.7 22.9 - - + -
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Residues in contact with ARG 163 (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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39B LEU* 4.0 39.0 - - + +
40B THR* 2.4 61.1 + - - +
41B PRO* 4.2 3.7 - - + -
42B LEU* 3.6 12.8 - - + +
46B GLN* 6.0 0.4 - - - +
48B ILE* 4.2 25.3 - - - +
159B GLY 3.0 15.0 + - - +
160B MET* 3.9 14.4 - - + +
162B ALA* 1.3 74.3 - - - +
164B LEU* 1.3 58.3 + - + +
166B VAL* 3.3 10.0 + - - +
167B GLU* 2.9 37.2 + - - +
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Residues in contact with LEU 164 (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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39B LEU* 5.6 6.7 - - + -
109B LEU* 3.4 12.0 - - + +
112B SER* 3.3 25.8 - - - +
113B VAL* 4.3 15.9 - - + -
116B GLN* 4.0 35.7 - - + +
117B TRP* 4.6 4.3 - - + -
160B MET* 2.9 38.7 + - + +
161B LEU* 3.5 6.1 - - - +
162B ALA 3.2 0.2 - - - -
163B ARG* 1.3 77.5 - - + +
165B ALA* 1.3 57.6 + - - +
167B GLU* 3.4 9.4 - - + +
168B ALA* 2.9 32.4 + - - +
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Residues in contact with ALA 165 (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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109B LEU* 3.8 17.9 - - + -
148B ILE* 4.6 2.7 - - + -
161B LEU 2.9 13.9 + - - +
162B ALA* 3.0 10.4 + - - +
164B LEU* 1.3 76.8 - - - +
166B VAL* 1.3 64.1 + - - +
168B ALA* 3.7 2.1 + - - -
170B PHE* 3.3 29.7 + - + +
173B VAL* 3.7 20.4 - - + -
183B CYS* 3.7 20.0 - - - -
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Residues in contact with VAL 166 (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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42B LEU* 4.6 3.4 - - + -
48B ILE* 4.1 46.9 - - + +
162B ALA 2.9 16.9 + - - +
163B ARG* 3.8 15.9 - - - +
164B LEU 3.3 0.2 - - - -
165B ALA* 1.3 79.6 - - - +
167B GLU* 1.3 69.3 + - + +
168B ALA 3.2 4.4 + - - -
169B GLY* 3.6 8.7 + - - -
170B PHE 4.3 10.7 - - - +
173B VAL* 3.7 23.3 - - + +
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Residues in contact with GLU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.7 39.3 - - + +
112B SER* 5.5 2.4 + - - -
163B ARG* 2.9 28.5 + - - +
164B LEU* 3.4 11.7 - - + +
166B VAL* 1.3 83.7 - - + +
168B ALA* 1.3 56.2 + - - +
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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