Contacts of the helix formed by residues 160 - 169 (chain B) in PDB entry 1DGH
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 LEU 160 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ILE* 3.7 11.7 - - + -
157B ASP* 3.3 23.8 + - + +
158B PRO 3.1 1.0 - - - -
159B ILE* 1.3 80.2 - - + +
161B PHE* 1.3 60.4 + - - +
162B PRO 3.4 1.6 - - - -
163B SER* 3.2 9.5 + - - -
164B PHE* 2.8 27.5 + - - +
185B PHE* 4.0 16.7 - - + -
189B ARG* 3.8 40.2 - - + +
191B GLU* 4.9 4.3 - - - +
405C TYR 3.9 19.3 - - - +
38D LYS* 5.1 1.8 - - - +
39D LEU* 3.3 39.0 - - + +
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Residues in contact with PHE 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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74B VAL* 4.6 6.7 - - + -
75B 3AH 5.8 3.6 - + - -
116B VAL* 6.2 0.2 - - + -
153B PHE* 3.8 31.9 - + - -
155B ILE* 3.5 12.4 - - + +
158B PRO 3.0 15.3 + - - +
160B LEU* 1.3 77.5 - - - +
162B PRO* 1.3 67.5 - - + +
164B PHE* 3.1 3.7 + + - +
165B ILE* 2.9 54.1 + - + +
2001B HEM 3.4 80.5 - + + -
61D MET* 4.3 1.3 - - + -
64D PHE* 3.7 18.8 - + - -
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Residues in contact with PRO 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B PRO 3.6 7.9 - - - +
159B ILE 3.9 7.4 - - - +
160B LEU 3.7 2.9 - - - -
161B PHE* 1.3 93.3 - - + +
163B SER* 1.3 55.9 + - - +
165B ILE* 3.4 1.4 + - - +
166B HIS* 3.0 42.1 + - + +
386C TYR 5.8 1.1 - - - +
60D GLU* 4.3 27.1 - - + +
61D MET* 3.8 19.7 - - + -
64D PHE* 3.8 40.2 - - + -
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Residues in contact with SER 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE 5.2 0.2 + - - -
160B LEU* 3.2 10.5 + - - -
161B PHE 3.2 0.6 - - - -
162B PRO* 1.3 76.7 - - - +
164B PHE* 1.3 65.7 + - - +
166B HIS* 3.2 2.9 + - - +
167B SER* 3.0 19.8 + - - -
185B PHE* 4.2 3.8 - - - -
386C TYR* 4.6 4.6 - - - +
403C ASN 4.6 1.3 - - - -
404C TYR* 3.3 20.6 - - - +
405C TYR* 2.9 48.9 + - - +
38D LYS* 4.5 4.2 + - - -
60D GLU* 4.5 10.4 + - - -
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Residues in contact with PHE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B VAL* 6.1 2.0 - - + -
153B PHE* 3.7 23.3 - + - -
154B PHE* 3.3 44.6 - + + -
155B ILE* 4.4 5.4 - - + -
160B LEU 2.8 19.2 + - - +
161B PHE* 3.1 7.6 + + - +
163B SER* 1.3 72.6 - - - +
165B ILE* 1.3 81.3 + - + +
167B SER* 2.6 24.1 + - - -
168B GLN* 3.1 35.8 + - + +
185B PHE* 3.5 33.1 - + + -
186B TRP* 3.3 24.0 - + - -
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Residues in contact with ILE 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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73B VAL 4.7 0.2 - - - +
74B VAL* 3.5 29.4 - - + -
116B VAL* 4.6 12.3 - - + -
153B PHE* 5.4 0.4 - - + -
161B PHE* 2.9 58.1 + - + +
162B PRO 3.7 3.8 - - - +
164B PHE* 1.3 91.4 - - + +
166B HIS* 1.3 63.8 + - + +
168B GLN* 3.0 18.5 + - + +
169B LYS* 3.0 31.8 + - + +
64D PHE* 3.8 16.4 - - + -
68D ARG* 5.0 0.7 - - - +
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Residues in contact with HIS 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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162B PRO* 3.0 30.3 + - + +
163B SER 3.2 5.8 + - - +
165B ILE* 1.3 77.7 - - + +
167B SER* 1.3 61.5 + - - +
169B LYS* 3.1 21.0 + - + +
170B ARG 4.4 1.7 - - - +
181B MET* 3.1 16.6 - - - +
386C TYR 3.2 23.5 + - - -
387C GLN* 5.0 0.2 - - - -
388C ARG* 4.3 14.8 - - + +
403C ASN* 2.7 47.0 + - + +
64D PHE* 4.3 8.7 - + - -
67D GLU* 2.7 37.9 + - - -
68D ARG* 6.1 0.4 - - - -
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Residues in contact with SER 167 (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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163B SER 3.0 12.8 + - - -
164B PHE* 2.6 29.2 + - - -
166B HIS* 1.3 76.0 - - - +
168B GLN* 1.3 61.7 + - - +
169B LYS 3.7 3.3 + - - +
178B ASP 4.3 0.5 - - - +
181B MET* 3.4 37.8 - - - +
182B VAL* 3.3 27.4 + - - +
185B PHE* 3.8 18.2 - - - +
404C TYR* 4.1 8.5 - - - +
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Residues in contact with GLN 168 (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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116B VAL* 6.5 0.7 - - + -
117B ALA* 3.8 24.2 - - + +
128B ASP* 4.4 15.0 + - - -
129B PRO* 6.0 0.8 - - - +
154B PHE* 5.7 1.2 - - - -
164B PHE* 3.3 41.5 - - + +
165B ILE* 3.0 14.8 + - + +
167B SER* 1.3 82.5 + - - +
169B LYS* 1.3 63.0 + - + +
177B LYS* 5.2 8.0 - - - +
182B VAL* 3.8 18.7 - - - +
186B TRP* 3.2 33.6 - - - -
199B LEU* 5.5 4.2 - - - +
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Residues in contact with LYS 169 (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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71B GLU* 5.0 6.3 + - - -
73B VAL 3.2 27.1 + - - -
74B VAL* 4.1 6.4 - - - +
76B ALA* 5.9 1.0 - - - +
116B VAL 4.2 3.2 + - - -
117B ALA* 2.7 42.4 + - + +
118B GLY 4.6 4.2 + - - -
119B GLU* 4.7 10.1 + - - +
165B ILE* 3.0 33.4 + - + +
166B HIS* 3.1 12.9 + - + +
167B SER 4.1 4.0 - - - +
168B GLN* 1.3 84.2 - - + +
170B ARG* 1.3 69.3 + - + +
171B ASN 4.1 0.2 + - - -
177B LYS* 4.0 15.3 - - - -
178B ASP 4.2 4.7 + - - -
181B MET* 4.4 1.9 - - - +
68D ARG* 3.3 22.1 - - - +
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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