Contacts of the helix formed by residues 82 - 94 (chain B) in PDB entry 1DWQ
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 ALA 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B ILE* 3.4 26.5 - - + +
10B HIS 3.6 7.6 - - - +
11B THR* 4.3 1.6 + - - +
78B GLY* 3.6 7.9 - - - -
79B GLU 2.8 23.2 + - - +
81B CSA 1.3 73.4 + - - +
83B GLY* 1.3 58.9 + - - +
84B LEU 3.0 0.7 - - - -
85B ASN* 2.8 37.9 + - - +
86B ILE* 3.1 13.3 + - - +
105B SER* 4.0 0.2 - - - -
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Residues in contact with GLY 83 (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 SER 3.8 0.2 + - - -
81B CSA 3.0 1.8 + - - -
82B ALA* 1.3 75.4 - - - +
84B LEU* 1.3 60.5 + - - +
86B ILE* 3.5 6.8 + - - +
87B ALA* 3.2 17.3 + - - +
102B PHE* 3.7 14.1 - - - -
105B SER* 3.0 23.4 + - - -
106B LEU 3.3 13.0 - - - -
108B PRO* 3.6 16.3 - - - +
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Residues in contact with LEU 84 (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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54B PHE* 3.6 32.1 - - + -
81B CSA 3.0 14.0 + - + +
82B ALA 3.0 0.8 - - - -
83B GLY* 1.3 75.2 - - - +
85B ASN* 1.3 59.3 + - - +
87B ALA* 3.4 2.3 + - - +
88B ILE* 3.0 35.4 + - + +
106B LEU* 3.9 23.0 - - + +
108B PRO* 3.8 17.7 - - + -
114B PRO 3.6 23.6 - - - +
117B THR* 5.0 1.8 - - - +
118B VAL* 4.1 5.2 - - + -
179B LEU* 5.7 0.9 - - + -
184B LEU* 3.8 28.5 - - + -
190B PHE* 4.2 14.5 - - + -
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Residues in contact with ASN 85 (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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9B ILE* 3.8 19.1 - - + +
10B HIS 4.3 2.8 + - - -
11B THR* 5.7 0.2 - - - +
38B MET* 4.2 2.6 - - - +
54B PHE* 3.5 18.9 - - - -
57B TYR* 3.6 20.1 + - - -
58B SER* 3.0 31.9 + - - +
61B LEU* 3.8 18.4 - - + +
81B CSA 5.7 0.2 - - - +
82B ALA* 2.8 34.9 + - - +
84B LEU* 1.3 72.7 - - - +
86B ILE* 1.4 66.6 + - - +
88B ILE* 3.4 2.3 + - - +
89B ALA* 2.9 25.8 + - - +
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Residues in contact with ILE 86 (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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9B ILE* 5.9 0.4 - - + -
76B ILE* 3.8 35.9 - - + +
78B GLY* 3.8 15.9 - - - +
82B ALA 3.1 10.0 + - - +
83B GLY* 3.7 7.6 - - - +
84B LEU 3.3 0.2 - - - -
85B ASN* 1.4 73.9 - - + +
87B ALA* 1.3 51.1 + - - +
89B ALA* 3.2 5.0 + - - +
90B ALA* 2.7 39.7 + - + +
97B ILE* 5.1 2.9 - - + +
100B GLY* 4.1 14.8 - - - -
101B VAL 3.5 28.0 - - - +
102B PHE* 3.9 30.5 - - + -
195B TYR* 4.6 4.9 - - + -
198B ILE* 4.8 7.2 - - + -
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Residues in contact with ALA 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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83B GLY 3.2 14.6 + - - +
84B LEU 3.7 2.9 - - - +
85B ASN 3.3 0.2 - - - -
86B ILE* 1.3 78.8 - - - +
88B ILE* 1.3 60.5 + - - +
91B ASP* 3.2 27.4 + - - +
108B PRO* 4.2 2.0 - - + -
190B PHE* 3.7 37.3 - - + -
195B TYR* 3.5 32.0 - - + +
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Residues in contact with ILE 88 (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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54B PHE* 3.7 29.8 - - + +
55B ASP* 3.3 34.3 - - + +
58B SER* 3.6 29.6 - - - +
62B LEU* 4.4 4.9 - - + -
84B LEU* 3.0 22.4 + - + +
85B ASN 3.4 4.0 + - - +
87B ALA* 1.3 76.2 - - - +
89B ALA* 1.3 62.4 + - - +
91B ASP* 3.6 3.2 + - - +
92B ARG* 3.5 31.6 + - - +
184B LEU* 5.3 2.2 - - + -
187B ARG* 3.8 18.9 + - - +
190B PHE* 3.9 13.9 - - + -
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Residues in contact with ALA 89 (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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61B LEU* 3.6 22.0 - - + -
62B LEU* 3.6 14.1 - - + -
65B LEU* 3.6 19.1 - - + -
76B ILE* 4.2 7.6 - - + -
85B ASN 2.9 17.7 + - - +
86B ILE 3.7 3.1 - - - +
88B ILE* 1.3 76.0 - - - +
90B ALA* 1.3 59.4 + - - +
92B ARG 3.1 2.1 + - - -
93B TYR* 2.9 33.3 + - - +
97B ILE* 3.9 1.8 - - - -
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Residues in contact with ALA 90 (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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86B ILE* 2.7 23.0 + - + +
87B ALA 3.9 1.6 - - - +
89B ALA* 1.3 70.5 - - - +
91B ASP* 1.3 62.2 + - - +
94B VAL* 3.1 28.9 + - - +
97B ILE* 3.5 16.1 - - + +
194B GLY* 3.5 1.7 - - - -
195B TYR* 3.8 21.1 - - + -
198B ILE* 3.5 28.9 - - + -
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Residues in contact with ASP 91 (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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87B ALA 3.2 13.7 + - - +
88B ILE* 3.9 7.0 - - - +
89B ALA 3.3 0.2 - - - -
90B ALA* 1.3 77.8 - - - +
92B ARG* 1.3 61.6 + - + +
94B VAL* 4.8 2.1 + - - +
187B ARG* 4.6 7.5 + - - +
189B LYS 4.5 0.5 - - - +
190B PHE* 3.5 17.8 - - - -
191B THR* 2.6 52.1 + - + +
193B LYS* 5.8 3.6 - - - -
194B GLY* 4.0 5.7 - - - -
195B TYR* 2.7 18.6 + - - -
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Residues in contact with ARG 92 (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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55B ASP* 2.8 39.0 + - - +
62B LEU* 3.7 29.1 - - + +
88B ILE* 3.5 14.6 + - - +
89B ALA 3.1 3.2 + - - +
91B ASP* 1.3 82.9 - - + +
93B TYR* 1.3 86.0 + - + +
94B VAL* 3.8 1.8 - - - -
187B ARG* 4.7 3.2 - - - +
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Residues in contact with TYR 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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62B LEU* 3.2 43.1 + - + +
65B LEU* 3.6 30.3 - - + -
66B GLU* 2.7 40.6 + - - +
89B ALA 2.9 17.2 + - - +
90B ALA 3.9 1.6 - - - -
92B ARG* 1.3 100.1 - - + +
94B VAL* 1.3 63.4 + - - +
95B ASP 3.1 3.1 - - - -
96B LYS* 2.8 42.9 + - + +
97B ILE* 3.6 8.5 - - + +
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Residues in contact with VAL 94 (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 LYS* 4.0 1.6 + - - -
90B ALA 3.1 19.4 + - - +
91B ASP 5.5 2.5 - - - +
92B ARG 3.8 1.0 - - - -
93B TYR* 1.3 73.6 - - - +
95B ASP* 1.3 78.2 + - - +
96B LYS 3.2 0.9 + - - -
97B ILE* 3.3 20.7 + - - +
193B LYS 3.7 16.4 - - - +
194B GLY* 3.7 13.7 - - - +
197B SER* 4.0 9.0 - - - -
198B ILE* 3.3 26.5 - - + +
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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