Contacts of the helix formed by residues 160 - 169 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405A TYR 4.3 4.5 - - - +
38B LYS* 5.1 1.1 - - - +
39B LEU* 3.3 44.9 - - + +
155D ILE* 3.6 13.2 - - + -
156D ARG 6.0 0.2 - - - +
157D ASP* 3.2 25.2 + - + +
158D PRO 3.0 1.0 - - - -
159D ILE* 1.3 78.6 - - + +
161D PHE* 1.3 59.6 + - - +
162D PRO* 3.4 1.6 - - - -
163D SER* 3.3 9.9 + - - -
164D PHE* 2.9 27.4 + - - +
185D PHE* 4.0 20.6 - - + -
189D ARG* 3.5 44.9 - - + +
191D GLU* 4.6 4.7 - - - +
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Residues in contact with PHE 161 (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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61B MET* 4.5 1.6 - - + -
64B PHE* 3.7 18.6 - + - -
74D VAL* 4.5 9.0 - - + -
75D 3AH 5.7 3.4 - + - -
153D PHE* 3.8 31.9 - + - -
155D ILE* 3.5 13.5 - - + +
158D PRO 3.0 15.0 + - - +
160D LEU* 1.3 75.7 - - - +
162D PRO* 1.3 70.2 - - + +
164D PHE* 3.3 2.7 + + - +
165D ILE* 2.9 53.8 + - + +
2003D HEM 3.5 77.6 - + + -
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Residues in contact with PRO 162 (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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386A TYR 5.8 0.9 - - - +
60B GLU* 4.3 25.6 - - + +
61B MET* 3.7 19.7 - - + -
64B PHE* 3.8 40.2 - - + -
158D PRO 3.6 8.5 - - - +
159D ILE* 3.9 8.3 - - - +
160D LEU 3.7 2.7 - - - -
161D PHE* 1.3 93.6 - - + +
163D SER* 1.3 56.0 + - - +
165D ILE* 3.4 1.2 + - - +
166D HIS* 2.9 43.2 + - + -
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Residues in contact with SER 163 (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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386A TYR* 4.5 7.8 - - - +
403A ASN 4.7 0.9 - - - -
404A TYR* 3.4 19.1 - - - +
405A TYR* 3.0 49.2 + - - +
38B LYS* 4.4 9.5 + - - -
60B GLU* 4.5 1.6 + - - -
160D LEU* 3.3 10.7 + - - -
161D PHE 3.2 0.4 - - - -
162D PRO* 1.3 76.8 - - - +
164D PHE* 1.3 66.0 + - - +
166D HIS* 3.3 3.8 + - - -
167D SER* 3.0 19.6 + - - -
185D PHE* 4.2 4.5 - - - -
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Residues in contact with PHE 164 (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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116D VAL* 6.0 3.4 - - + -
153D PHE* 3.7 23.6 - + - -
154D PHE* 3.4 43.1 - + + -
155D ILE* 4.3 8.5 - - + -
160D LEU 2.9 17.6 + - - +
161D PHE* 3.7 4.7 - + - +
163D SER* 1.3 74.5 - - - +
165D ILE* 1.3 80.7 + - + +
167D SER* 2.6 25.3 + - - -
168D GLN* 3.0 38.2 + - + +
185D PHE* 3.6 34.0 - + + -
186D TRP* 3.4 22.9 - - - -
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Residues in contact with ILE 165 (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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64B PHE* 3.8 16.2 - - + -
68B ARG* 5.1 0.7 - - - +
73D VAL 4.8 0.4 - - - +
74D VAL* 3.4 31.0 - - + -
116D VAL* 4.5 15.5 - - + -
153D PHE* 5.5 0.9 - - + -
161D PHE* 2.9 55.3 + - + +
162D PRO 3.8 3.4 - - - +
164D PHE* 1.3 90.5 - - + +
166D HIS* 1.3 65.0 - - + +
168D GLN* 2.9 18.4 + - + +
169D LYS* 3.0 30.6 + - + +
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Residues in contact with HIS 166 (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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386A TYR* 3.1 24.0 - - - +
387A GLN* 5.0 0.2 - - - -
388A ARG* 4.5 14.1 - - + +
403A ASN* 2.7 46.0 + - - +
64B PHE* 4.3 8.5 - + - -
67B GLU* 2.7 38.8 + - - -
68B ARG* 6.2 0.4 - - - -
162D PRO* 2.9 25.9 + - + -
163D SER* 3.5 8.9 - - - +
164D PHE 3.2 0.2 - - - -
165D ILE* 1.3 77.0 - - + +
167D SER* 1.3 62.7 + - - +
169D LYS* 3.0 22.0 + - + +
170D ARG 4.4 0.3 - - - +
181D MET* 3.1 15.9 - - - +
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Residues in contact with SER 167 (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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404A TYR* 4.3 8.5 - - - +
163D SER 3.0 12.8 + - - -
164D PHE* 2.6 28.5 + - - -
166D HIS* 1.3 76.4 - - - +
168D GLN* 1.3 62.1 + - - +
169D LYS 3.6 3.1 + - - +
178D ASP 4.4 0.2 - - - +
181D MET* 3.6 36.9 + - - +
182D VAL* 3.3 27.0 + - - +
185D PHE* 3.9 17.9 - - - +
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Residues in contact with GLN 168 (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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116D VAL* 6.2 2.9 - - + +
117D ALA* 3.7 24.2 - - + +
128D ASP* 4.5 14.5 + - - -
129D PRO* 6.0 1.2 - - - +
154D PHE* 5.6 1.4 - - - -
164D PHE* 3.0 46.2 + - + +
165D ILE* 2.9 15.5 + - + +
167D SER* 1.3 79.1 + - - +
169D LYS* 1.3 61.8 + - + +
177D LYS* 4.1 10.6 - - - +
182D VAL* 3.7 26.0 - - - +
186D TRP* 3.5 26.7 - - - -
199D LEU* 5.5 4.2 - - - +
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Residues in contact with LYS 169 (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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68B ARG* 3.4 20.1 - - - +
71D GLU* 5.1 4.9 + - - -
72D ARG 5.4 0.4 + - - -
73D VAL 3.3 28.2 + - - -
74D VAL* 4.0 6.4 - - - +
75D 3AH 5.5 0.2 + - - -
76D ALA* 5.9 0.8 - - - +
116D VAL 4.1 3.0 + - - -
117D ALA* 2.8 43.3 + - + +
118D GLY 4.8 3.4 + - - -
119D GLU* 4.8 9.6 + - - +
165D ILE* 3.0 32.1 + - + +
166D HIS* 3.0 15.9 + - + +
167D SER 4.2 4.3 - - - +
168D GLN* 1.3 84.4 - - + +
170D ARG* 1.3 71.2 + - + +
171D ASN 3.9 1.0 + - - -
176D LEU 4.2 2.3 - - - +
177D LYS* 4.0 18.0 - - - +
178D ASP 4.3 4.3 + - - -
181D MET* 4.5 2.6 - - - +
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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