Contacts of the helix formed by residues 83 - 98 (chain B) in PDB entry 3HW4
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 ASP 83 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ASP* 3.1 39.3 - - - +
84A ARG 3.4 0.3 + - - -
85A THR* 2.9 45.7 + - + +
86A MET* 3.3 8.3 + - - +
81B GLY 4.0 0.2 + - - -
82B ARG* 1.3 74.3 - - - +
84B ARG* 1.3 59.6 + - - +
85B THR 3.0 23.8 + - - +
86B MET* 3.2 15.4 + - + +
87B ALA* 2.8 23.6 + - - +
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Residues in contact with ARG 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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23A GLU* 4.4 1.6 - - - -
84A ARG* 4.3 18.4 - - + +
85A THR* 3.0 13.0 + - - +
88A TRP* 5.8 5.0 - - - -
23B GLU* 3.4 29.4 + - - +
24B TYR* 3.0 40.0 + - - -
82B ARG 3.4 3.0 + - - +
83B ASP* 1.3 70.1 + - - +
85B THR* 1.3 65.5 - - - +
87B ALA* 4.0 5.6 - - - -
88B TRP* 2.9 37.7 + - + +
106B LEU* 3.6 24.9 - - + +
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Residues in contact with THR 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS* 4.4 18.6 - - + +
23A GLU* 2.5 44.4 + - + +
82A ARG 4.5 1.0 + - - -
83A ASP* 3.5 19.9 - - - +
84A ARG* 2.7 25.7 + - - +
83B ASP* 3.0 12.4 + - - -
84B ARG* 1.3 78.8 - - - +
86B MET* 1.3 53.2 + - - +
88B TRP* 3.9 0.9 - - - -
89B THR* 2.7 39.7 + - - +
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Residues in contact with MET 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASP* 4.4 12.7 + - - +
82B ARG* 4.0 30.3 - - + +
83B ASP* 3.2 18.3 + - + +
85B THR* 1.3 75.5 - - - +
87B ALA* 1.3 64.0 + - - +
89B THR* 3.2 8.1 + - - -
90B VAL* 2.9 35.0 + - + +
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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
----------------------------------------------------------
79B ILE* 3.7 22.6 - - + +
82B ARG* 4.0 10.8 - - + +
83B ASP 2.8 16.9 + - - +
84B ARG* 3.8 2.2 - - - +
85B THR 3.4 0.2 - - - -
86B MET* 1.3 76.3 - - - +
88B TRP* 1.3 58.1 + - - +
90B VAL* 3.2 7.4 + - - +
91B VAL* 3.0 31.0 + - - +
106B LEU* 3.5 34.1 - - + -
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Residues in contact with TRP 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 3.3 4.0 - - + +
84A ARG* 3.1 24.0 - - - +
84B ARG* 2.9 28.8 + - + +
85B THR 4.1 2.2 - - - +
87B ALA* 1.3 76.8 - - - +
89B THR* 1.3 56.7 + - - +
91B VAL* 3.7 21.6 - - + +
92B ASN* 2.9 39.6 + - - +
102B LYS* 3.9 7.4 - - + -
103B PRO* 3.4 26.5 - - + -
104B LYS 3.6 10.8 - - - -
105B PHE* 3.8 10.5 - - - -
106B LEU* 3.4 41.6 - - + +
257B TMP 2.9 72.0 + + + -
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Residues in contact with THR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS* 4.5 8.2 + - + +
22A LYS* 3.7 43.7 - - + +
23A GLU* 3.6 15.8 + - - +
85B THR* 2.7 27.4 + - - +
86B MET* 3.5 9.6 - - - -
87B ALA 3.2 0.2 - - - -
88B TRP* 1.3 76.7 - - - +
90B VAL* 1.3 58.5 + - + +
92B ASN* 3.4 2.3 + - - +
93B SER* 2.9 31.6 + - - -
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Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLU* 3.8 31.0 - - + -
79B ILE* 3.8 15.9 - - + -
82B ARG* 4.1 19.3 - - - +
86B MET* 2.9 24.3 + - + +
87B ALA* 3.7 7.2 - - - +
89B THR* 1.3 73.8 - - + +
91B VAL* 1.3 66.3 + - - +
93B SER* 3.6 6.0 - - - -
94B ILE* 3.0 32.1 + - + +
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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
----------------------------------------------------------
79B ILE* 4.0 10.8 - - + -
87B ALA 3.0 19.0 + - - +
88B TRP* 3.7 26.0 - - + +
90B VAL* 1.3 75.8 - - - +
92B ASN* 1.3 64.2 + - - +
94B ILE* 3.5 2.3 + - - +
95B CYS* 3.1 28.8 + - - -
102B LYS* 4.0 6.5 - - + -
103B PRO* 3.8 29.2 - - + -
106B LEU* 4.0 7.2 - - + -
107B PRO* 3.7 26.5 - - + -
117B PHE* 3.9 20.3 - - + -
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Residues in contact with ASN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS 3.6 12.8 - - - +
23A GLU 3.0 18.9 - - - +
25A GLY* 3.2 25.4 - - - +
88B TRP* 2.9 25.8 + - - +
89B THR 3.8 1.6 - - - +
90B VAL 3.3 0.2 - - - -
91B VAL* 1.3 77.5 - - - +
93B SER* 1.3 53.0 + - - +
95B CYS* 3.4 5.1 + - - +
96B ASN* 2.8 44.9 + - - +
102B LYS* 2.9 40.0 - - - +
257B TMP 3.1 10.6 - - - +
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Residues in contact with SER 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B THR* 2.9 19.8 + - - -
90B VAL* 3.6 8.7 - - - -
92B ASN* 1.3 71.6 - - - +
94B ILE* 1.3 65.4 + - - +
96B ASN* 3.3 9.2 + - - +
97B THR* 2.8 34.6 + - - -
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Residues in contact with ILE 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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77B GLU* 4.1 3.4 - - + -
79B ILE* 4.8 0.4 - - + -
90B VAL* 3.0 38.1 + - + +
91B VAL 3.8 3.6 - - - +
93B SER* 1.3 76.6 - - - +
95B CYS* 1.3 60.5 + - - +
97B THR* 4.6 3.8 - - - -
98B THR* 2.9 42.5 + - + +
110B TYR* 3.5 66.2 - - + +
112B TYR* 3.9 24.0 - - + +
117B PHE* 3.9 11.2 - - + -
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Residues in contact with CYS 95 (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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91B VAL 3.1 22.0 + - - +
92B ASN* 3.7 7.6 - - - +
94B ILE* 1.3 73.1 - - - +
96B ASN* 1.3 57.6 + - - +
98B THR* 2.6 24.1 - - - +
99B GLY* 3.4 14.4 - - - -
100B VAL* 3.3 23.3 - - - +
101B GLU 3.8 0.2 - - - -
102B LYS* 3.7 37.0 - - + +
103B PRO* 4.2 0.4 - - - -
117B PHE* 3.7 20.9 - - - -
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Residues in contact with ASN 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLY* 5.1 9.9 - - - +
92B ASN* 2.8 35.0 + - - +
93B SER* 3.3 7.3 + - - +
94B ILE 3.2 0.2 - - - -
95B CYS* 1.3 77.9 - - - +
97B THR* 1.3 64.6 + - - +
98B THR 3.1 2.1 - - - +
99B GLY* 5.3 0.6 - - - -
102B LYS* 5.8 0.5 + - - -
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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
----------------------------------------------------------
93B SER* 2.8 23.0 + - - -
94B ILE* 3.8 4.0 - - - -
96B ASN* 1.3 77.8 - - - +
98B THR* 1.3 71.2 + - + +
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Residues in contact with THR 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 ILE* 2.9 24.0 + - + +
95B CYS 2.6 23.9 - - - +
96B ASN 3.1 2.6 - - - -
97B THR* 1.3 87.4 - - + +
99B GLY* 1.3 54.7 + - - +
100B VAL* 3.1 29.2 + - - +
110B TYR* 3.8 18.5 + - + +
112B TYR* 5.6 5.6 - - + -
115B ASN* 4.1 11.2 - - - +
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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