Contacts of the helix formed by residues 81 - 91 (chain D) in PDB entry 2HJ9
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 SER 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77D SER 3.9 1.7 + - - -
78D ASN* 2.9 21.2 + - - -
79D SER 4.6 1.2 - - - +
80D LYS* 1.3 79.8 - - - +
82D GLU* 1.3 63.4 + - - +
83D VAL* 3.0 24.9 + - - +
84D ILE* 3.2 14.1 + - - +
85D ARG* 3.3 13.2 + - - +
99D PHE* 3.4 22.1 - - - -
174D ILE* 5.9 0.2 - - - +
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Residues in contact with GLU 82 (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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82C GLU* 3.7 27.2 + - - +
80D LYS 3.7 2.8 + - - -
81D SER* 1.3 73.2 + - - +
83D VAL* 1.3 57.2 + - + +
85D ARG* 3.6 28.6 + - - +
86D ASP* 2.9 57.0 + - - +
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Residues in contact with VAL 83 (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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81D SER* 3.0 15.0 - - - +
82D GLU* 1.3 79.3 - - + +
84D ILE* 1.3 58.0 + - - +
86D ASP* 3.6 6.1 + - - +
87D PHE* 3.2 25.1 + - - +
95D VAL* 4.1 24.1 - - + +
96D LEU* 4.5 9.0 - - + -
99D PHE* 3.6 44.0 - - + -
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Residues in contact with ILE 84 (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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78D ASN* 3.3 31.0 - - + +
79D SER* 4.2 5.6 - - - +
81D SER 3.2 7.6 + - - +
83D VAL* 1.3 74.3 - - - +
85D ARG* 1.3 67.3 + - - +
87D PHE* 3.2 15.3 + - - +
88D TYR* 3.2 22.1 + - + -
96D LEU* 3.9 17.9 - - + -
99D PHE* 4.0 11.7 - - + -
100D PHE* 3.6 24.9 - - + -
117D LEU* 4.3 15.5 - - + -
174D ILE* 3.7 34.1 - - + -
186D SER* 5.3 3.8 - - - +
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Residues in contact with ARG 85 (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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82C GLU* 3.3 25.5 + - - +
83C VAL* 6.1 1.0 - - - +
80D LYS 3.6 23.4 + - - -
81D SER 3.3 7.2 + - - +
82D GLU* 3.6 31.2 + - - +
84D ILE* 1.3 78.7 - - - +
86D ASP* 1.3 65.6 + - - +
88D TYR* 3.3 17.8 + - - +
89D THR* 3.9 7.7 - - + +
174D ILE* 4.3 14.1 - - + +
175D LEU 3.8 8.9 + - - +
176D ASP* 4.6 10.8 - - - +
177D PRO* 3.5 40.7 - - - +
183D LEU* 3.7 21.6 - - + +
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Residues in contact with ASP 86 (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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82D GLU* 2.9 48.4 + - - +
83D VAL* 3.8 6.6 - - - +
85D ARG* 1.3 78.3 - - - +
87D PHE* 1.3 66.1 + - - +
88D TYR 3.1 0.2 - - - -
89D THR* 2.9 22.4 + - - +
90D ASP* 3.0 28.9 + - - +
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Residues in contact with PHE 87 (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 VAL 3.2 14.7 + - - +
84D ILE 3.2 10.0 + - - +
86D ASP* 1.3 75.8 - - - +
88D TYR* 1.3 63.3 + + - +
90D ASP* 4.0 7.4 + - - -
91D ARG* 2.9 65.0 + - + -
92D ASP 3.6 21.3 - - - -
93D THR* 3.7 16.4 - - - -
96D LEU* 3.7 27.4 - - + -
117D LEU* 3.9 16.2 - - + -
124D ILE* 4.0 15.3 - - + -
125D TRP* 3.8 39.0 - + + -
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Residues in contact with TYR 88 (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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84D ILE* 3.2 30.5 - - + -
85D ARG 3.5 10.3 - - - +
86D ASP 3.1 1.2 - - - -
87D PHE* 1.3 78.4 - - - +
89D THR* 1.3 59.1 + - + +
91D ARG* 3.1 29.1 + - - +
117D LEU* 3.9 13.0 - - + +
118D THR 2.7 33.6 + - - -
119D ASP* 4.0 6.5 - - + -
124D ILE* 3.7 20.4 - - + -
174D ILE* 3.8 29.4 - - + +
183D LEU* 3.4 39.5 - - + -
184D GLY* 4.2 2.0 - - - -
185D PHE 3.5 18.0 + - - -
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Residues in contact with THR 89 (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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85D ARG 3.9 11.0 - - - +
86D ASP* 2.9 18.4 + - - +
88D TYR* 1.3 80.4 - - + +
90D ASP* 1.3 62.9 + - - +
91D ARG* 3.8 3.8 - - - +
183D LEU* 6.3 0.4 - - + -
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Residues in contact with ASP 90 (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 ASP* 3.0 27.0 + - - +
87D PHE* 4.0 4.3 - - - -
89D THR* 1.3 81.7 + - - +
91D ARG* 1.3 75.3 + - - +
92D ASP* 3.3 22.5 + - + +
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Residues in contact with ARG 91 (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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87D PHE* 2.9 47.6 + - + +
88D TYR* 3.1 32.5 + - - +
89D THR 4.7 2.7 - - - +
90D ASP* 1.3 83.7 + - - +
92D ASP* 1.3 58.8 + - - +
93D THR* 2.9 14.3 + - - +
119D ASP* 4.2 15.4 + - - +
124D ILE* 3.7 38.8 + - - +
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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