Contacts of the helix formed by residues 86 - 100 (chain B) in PDB entry 2HW6
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 HIS 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B ALA 3.3 1.6 + - - -
85B GLY* 1.3 75.9 - - - +
87B SER* 1.3 64.2 + - - +
88B ARG 3.4 2.0 - - - -
89B SER* 3.6 5.3 + - - -
90B ARG* 3.0 63.3 + - - +
225B GLU* 4.1 20.4 + - + -
342B SO4 3.6 25.6 + - - +
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Residues in contact with SER 87 (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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80B ILE* 3.9 3.1 - - - +
81B GLU 2.8 27.0 + - - -
82B LYS* 3.4 7.5 - - - -
84B ALA 3.2 18.2 + - - -
85B GLY 3.0 1.2 + - - -
86B HIS* 1.3 74.9 - - - +
88B ARG* 1.3 67.7 + - - +
91B VAL* 3.0 28.2 + - - +
120B PHE* 3.5 16.2 - - - -
226B VAL* 3.4 22.8 - - - +
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Residues in contact with ARG 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LYS* 5.6 2.8 - - - +
45A GLU* 2.9 37.4 + - - -
82B LYS* 3.4 47.2 + - - +
83B GLN* 5.0 0.4 - - - +
86B HIS 3.4 0.4 - - - -
87B SER* 1.3 82.2 - - - +
89B SER* 1.3 59.5 + - - +
92B PHE* 3.4 21.1 + - - +
117B ASP 4.5 6.5 + - - -
120B PHE* 3.8 24.9 - - + -
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Residues in contact with SER 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B HIS* 3.6 8.2 + - - +
88B ARG* 1.3 78.0 - - - +
90B ARG* 1.3 65.0 + - - +
92B PHE* 3.8 6.4 - - - +
93B ARG* 3.3 38.6 + - - +
342B SO4 2.9 25.0 + - - -
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Residues in contact with ARG 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B HIS* 3.0 45.3 + - - +
87B SER 4.3 0.4 - - - +
89B SER* 1.3 76.4 + - - +
91B VAL* 1.3 59.9 + - - +
93B ARG* 3.4 16.4 + - - +
94B GLU* 3.0 29.5 + - - +
225B GLU* 3.7 23.6 + - - +
226B VAL* 2.6 48.9 + - + -
227B VAL* 4.5 5.8 - - - +
228B GLU* 3.7 27.4 + - + +
342B SO4 2.7 39.1 + - - +
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 3.8 30.3 - - + -
87B SER* 3.0 21.1 + - - +
90B ARG* 1.3 73.1 - - - +
92B PHE* 1.3 66.3 + - - +
94B GLU* 3.1 11.3 + - + +
95B VAL* 2.8 43.9 + - + +
113B PHE* 4.1 1.8 - - + -
120B PHE* 3.8 36.6 - - + -
122B LEU* 4.1 13.2 - - + -
226B VAL* 4.3 12.3 - - + -
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Residues in contact with PHE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ARG 3.4 19.7 + - - +
89B SER* 3.8 7.0 - - - +
90B ARG 3.4 0.6 - - - -
91B VAL* 1.3 78.5 - - - +
93B ARG* 1.3 75.8 + - + +
95B VAL* 3.5 6.0 + - - +
96B GLU* 3.2 55.6 + - + +
113B PHE* 6.0 3.8 - - - -
120B PHE* 5.4 2.1 - - + -
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Residues in contact with ARG 93 (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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89B SER* 3.3 33.0 + - - +
90B ARG* 3.7 11.1 + - - +
91B VAL 3.2 0.4 - - - -
92B PHE* 1.3 91.3 - - + +
94B GLU* 1.3 65.0 + - - +
96B GLU* 3.6 6.4 + - - +
97B THR* 3.2 26.2 + - - -
228B GLU* 2.6 33.3 + - - +
230B PHE 5.0 1.8 - - - -
231B THR* 5.1 3.8 - - + +
232B ASP* 4.8 15.7 + - - +
342B SO4 3.2 36.8 + - - -
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Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LYS* 5.4 0.4 + - - -
90B ARG 3.0 18.4 + - - +
91B VAL* 3.1 12.9 + - - +
93B ARG* 1.3 74.7 - - - +
95B VAL* 1.3 61.1 + - + +
97B THR* 3.4 1.9 + - - -
98B LEU* 2.8 44.6 + - + +
122B LEU* 5.0 11.3 - - + +
124B PHE* 5.7 0.2 - - - -
191B ASP* 2.6 43.9 - - - +
226B VAL* 5.4 4.3 - - - +
227B VAL 4.9 5.0 - - - +
229B VAL* 3.6 22.2 + - - +
230B PHE* 3.7 19.0 - - + -
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B VAL* 2.8 27.4 + - + +
92B PHE* 3.8 5.8 - - - +
94B GLU* 1.3 75.4 - - + +
96B GLU* 1.3 68.8 + - - +
98B LEU* 3.3 6.4 + - - +
99B TYR* 3.0 53.2 + - + +
110B LEU* 4.1 4.7 - - + -
113B PHE* 3.7 44.2 - - + -
122B LEU* 4.1 15.9 - - + -
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Residues in contact with GLU 96 (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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92B PHE* 3.2 52.2 + - + +
93B ARG* 3.7 6.7 - - - +
95B VAL* 1.3 78.8 - - - +
97B THR* 1.3 63.4 + - - +
99B TYR* 3.4 37.1 - - - +
100B GLN* 3.6 11.8 + - - +
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Residues in contact with THR 97 (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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93B ARG 3.2 16.0 + - - -
94B GLU 3.6 3.1 - - - -
96B GLU* 1.3 77.5 - - - +
98B LEU* 1.3 59.9 + - - +
100B GLN* 2.9 33.3 + - - +
101B CYS* 3.4 9.7 - - - -
166B ILE* 3.7 30.7 - - + -
230B PHE* 3.5 37.4 + - + +
232B ASP* 4.0 21.3 + - - +
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Residues in contact with LEU 98 (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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94B GLU* 2.8 45.1 + - + +
95B VAL* 3.3 5.8 + - - +
97B THR* 1.3 73.1 - - - +
99B TYR* 1.3 62.2 + - - +
101B CYS* 3.2 20.3 + - - +
102B GLN* 3.7 10.2 + - - +
107B ILE* 4.5 14.6 - - + -
108B LEU 4.5 10.8 - - - +
110B LEU* 4.3 18.9 + - + +
122B LEU* 4.3 9.6 - - + -
124B PHE* 4.0 27.1 - - + -
230B PHE* 3.7 36.8 - - + -
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Residues in contact with TYR 99 (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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95B VAL* 3.0 31.7 + - + +
96B GLU* 3.4 31.2 - - - +
98B LEU* 1.3 77.2 - - - +
100B GLN* 1.3 57.9 + - + +
101B CYS 3.1 4.7 + - - -
102B GLN* 3.4 44.6 + - - +
110B LEU* 3.7 21.8 - - + -
111B ILE 5.7 1.8 - - - -
112B GLU* 5.6 0.9 - - - -
113B PHE* 3.3 29.9 + - + +
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Residues in contact with GLN 100 (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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96B GLU 3.7 13.0 - - - +
97B THR* 2.9 15.2 + - - +
99B TYR* 1.3 74.6 - - + +
101B CYS* 1.3 59.4 + - - +
102B GLN 3.7 0.7 - - - -
160B PHE* 3.2 21.1 - - - -
164B LYS* 3.7 36.3 + - + +
166B ILE* 4.0 21.4 - - + +
232B ASP* 5.8 4.2 - - - +
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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