Contacts of the helix formed by residues 101 - 115 (chain B) in PDB entry 3HS3
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 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B ASN* 3.2 23.0 + - - +
100B SER* 1.3 73.9 - - - +
102B VAL* 1.3 67.8 + - - +
103B LYS* 3.1 38.1 + - - +
104B LYS* 2.9 45.0 + - + +
105B TYR* 3.2 13.2 + - - -
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Residues in contact with VAL 102 (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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100B SER 3.2 8.8 + - - +
101B ASP* 1.3 74.0 + - - +
103B LYS* 1.3 60.2 + - + +
105B TYR* 3.0 11.3 + - - +
106B GLN* 2.9 34.2 + - - +
125B PHE* 3.9 19.3 - - + -
126B THR* 3.7 32.8 - - - +
128B PRO* 3.8 22.4 - - + -
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Residues in contact with LYS 103 (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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101B ASP* 3.1 23.5 + - - +
102B VAL* 1.3 79.8 - - + +
104B LYS* 1.3 57.7 + - + +
106B GLN* 3.3 17.6 + - - +
107B ASN* 2.9 39.0 + - - +
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Residues in contact with LYS 104 (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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97B SER* 6.5 1.3 - - - -
98B THR* 4.5 11.4 - - + -
99B ASN* 3.2 36.8 - - - +
101B ASP* 2.9 32.2 + - + +
103B LYS* 1.3 75.1 - - + +
105B TYR* 1.3 60.3 + - + +
107B ASN* 3.4 10.9 + - - +
108B ALA* 3.0 28.8 + - - +
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Residues in contact with TYR 105 (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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65B ILE* 3.6 23.7 - - + +
67B PRO* 5.6 2.3 - - - +
97B SER* 4.2 11.0 + - - -
99B ASN 4.2 8.6 + - - -
100B SER* 4.2 22.4 - - - -
101B ASP 3.2 23.7 + - - -
102B VAL* 3.0 9.1 + - - +
104B LYS* 1.3 78.7 - - + +
106B GLN* 1.3 61.2 + - - +
108B ALA* 3.2 5.9 + - - +
109B ILE* 3.0 30.1 + - - +
122B THR* 3.5 16.6 - - - -
123B SER* 2.6 32.0 + - - -
124B ALA 4.3 5.3 + - - -
125B PHE* 3.5 49.8 - + + -
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Residues in contact with GLN 106 (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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102B VAL* 2.9 22.6 + - + +
103B LYS* 3.6 21.0 - - - +
105B TYR* 1.3 78.7 - - - +
107B ASN* 1.3 58.3 + - - +
109B ILE* 3.3 9.3 + - - +
110B ILE* 3.0 36.9 + - + +
125B PHE* 5.0 1.3 - - + -
128B PRO* 3.4 22.6 - - + +
130B ASN* 2.9 34.6 + - - +
131B PHE* 4.1 27.7 - - + +
132B HIS 5.2 0.4 - - - +
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Residues in contact with ASN 107 (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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103B LYS* 2.9 31.1 + - - +
104B LYS* 3.9 10.5 - - - +
105B TYR 3.2 0.2 - - - -
106B GLN* 1.3 74.7 - - - +
108B ALA* 1.3 65.7 + - - +
110B ILE* 3.2 18.7 + - - +
111B ASN* 2.8 35.5 + - - +
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Residues in contact with ALA 108 (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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65B ILE* 3.8 23.6 - - + -
95B SER* 4.6 16.0 + - - -
104B LYS 3.0 18.1 + - - +
105B TYR* 3.5 6.3 - - - +
107B ASN* 1.3 75.8 - - - +
109B ILE* 1.3 62.5 + - - +
111B ASN* 3.3 12.2 + - - +
112B PHE* 3.1 29.4 + - - -
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Residues in contact with ILE 109 (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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65B ILE* 4.2 13.5 - - + -
105B TYR 3.0 19.4 + - - +
106B GLN* 3.5 9.0 - - - +
107B ASN 3.2 0.2 - - - -
108B ALA* 1.3 75.8 - - - +
110B ILE* 1.3 66.8 + - + +
112B PHE* 3.2 9.9 + - - +
113B GLU* 3.0 24.5 + - - +
120B ILE* 3.9 14.1 - - + -
122B THR* 5.1 0.7 - - + -
125B PHE* 4.0 17.0 - - + -
131B PHE* 3.9 32.1 - - + -
132B HIS 5.5 2.5 - - - +
133B LEU* 3.5 33.0 - - + -
137B LEU* 4.7 11.7 - - + -
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Residues in contact with ILE 110 (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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106B GLN* 3.0 25.4 + - + +
107B ASN* 3.2 22.4 + - - +
109B ILE* 1.3 77.8 - - + +
111B ASN* 1.3 60.1 + - - +
113B GLU* 3.1 15.5 + - + +
114B ASN* 2.9 48.8 + - - +
132B HIS 6.2 0.7 - - - +
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Residues in contact with ASN 111 (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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91A THR* 5.6 6.3 - - - +
95B SER* 6.0 1.3 - - - +
107B ASN* 2.8 32.7 + - - +
108B ALA* 3.6 11.0 - - - +
109B ILE 3.2 0.2 - - - -
110B ILE* 1.3 75.8 - - - +
112B PHE* 1.3 67.1 + - + +
114B ASN* 3.3 15.6 + - - +
115B ASN* 3.1 30.2 + - - +
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Residues in contact with PHE 112 (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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91A THR* 4.6 2.2 - - + -
63B GLY* 3.7 12.1 - - - -
64B ILE 3.5 32.3 - - - -
65B ILE* 3.5 25.8 - - + -
93B LEU* 3.4 38.1 - - + -
95B SER* 3.3 28.9 - - - -
108B ALA 3.1 17.6 + - - -
109B ILE* 3.2 10.1 + - - +
111B ASN* 1.3 78.7 - - + +
113B GLU* 1.3 58.1 + - - +
115B ASN* 3.0 18.0 + - - +
116B ASN 3.1 8.8 + - - -
117B VAL* 3.2 27.5 + - + +
120B ILE* 3.9 20.6 - - + -
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Residues in contact with GLU 113 (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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109B ILE* 3.0 20.0 + - - +
110B ILE* 3.5 15.8 - - + +
112B PHE* 1.3 72.4 - - - +
114B ASN* 1.3 58.5 + - - +
115B ASN 3.0 5.4 - - - -
116B ASN* 2.9 20.6 + - - +
117B VAL* 4.8 2.5 - - - +
120B ILE* 4.5 3.1 - - + -
132B HIS 4.8 2.6 - - - +
133B LEU* 2.9 33.0 - - + +
134B ASN* 3.0 20.6 + - - +
135B THR* 2.8 28.7 + - - +
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Residues in contact with ASN 114 (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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110B ILE* 2.9 42.2 + - - +
111B ASN* 3.7 17.0 + - - +
112B PHE 3.3 0.2 - - - -
113B GLU* 1.3 78.8 - - - +
115B ASN* 1.3 63.3 + - - +
116B ASN* 3.2 2.8 + - - +
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Residues in contact with ASN 115 (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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59A SER 4.5 13.2 + - - +
61A MET* 4.8 17.5 - - - +
91A THR* 4.8 8.5 + - - -
61B MET* 3.8 20.4 - - + +
93B LEU* 4.1 26.0 - - + +
111B ASN* 3.1 15.0 + - - +
112B PHE* 3.0 9.5 + - - +
113B GLU 3.0 1.0 - - - -
114B ASN* 1.3 82.8 + - - +
116B ASN* 1.3 68.6 + - - +
117B VAL* 3.3 2.2 + - - -
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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