Contacts of the helix formed by residues 101 - 115 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A ASN* 3.3 25.9 + - - +
100A SER* 1.3 74.3 - - - +
102A VAL* 1.3 67.4 + - - +
103A LYS* 3.1 44.3 + - - +
104A LYS* 3.1 40.3 + - + +
105A TYR* 3.1 14.5 + - - -
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A SER 3.5 5.5 + - - +
101A ASP* 1.3 73.4 + - - +
103A LYS* 1.3 58.3 + - + +
105A TYR* 3.1 10.3 + - - +
106A GLN* 2.9 39.6 + - - +
125A PHE* 4.0 22.0 - - + -
126A THR* 3.8 32.3 - - - +
128A PRO* 4.0 17.5 - - + -
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Residues in contact with LYS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ASP* 3.1 23.6 + - - +
102A VAL* 1.3 78.7 - - + +
104A LYS* 1.3 56.1 + - + +
106A GLN* 3.3 16.3 + - - +
107A ASN* 2.9 28.1 + - - +
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Residues in contact with LYS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A SER* 6.2 3.1 - - - -
98A THR* 3.9 13.2 - - - +
99A ASN* 3.1 33.8 + - - +
101A ASP* 3.1 37.4 + - + +
103A LYS* 1.3 74.4 - - + +
105A TYR* 1.3 61.0 + - - +
107A ASN* 3.6 8.8 - - - +
108A ALA* 2.9 29.5 + - - +
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Residues in contact with TYR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ILE* 3.6 23.4 - - + +
67A PRO* 4.1 13.3 - - - +
97A SER* 4.6 7.9 + - - -
99A ASN 4.7 2.2 - - - -
100A SER* 4.1 27.1 - - - -
101A ASP 3.1 23.7 + - - -
102A VAL* 3.1 8.4 + - - +
104A LYS* 1.3 77.8 - - + +
106A GLN* 1.3 62.4 + - - +
108A ALA* 3.1 6.7 + - - +
109A ILE* 3.0 28.8 + - - +
122A THR* 3.5 16.8 - - - -
123A SER* 2.6 36.4 + - - -
124A ALA 4.1 5.8 + - - -
125A PHE* 3.3 48.2 - + + -
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Residues in contact with GLN 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A VAL* 2.9 29.4 + - + +
103A LYS* 3.6 17.7 - - - +
105A TYR* 1.3 75.1 - - - +
107A ASN* 1.3 58.0 + - - +
109A ILE* 3.2 11.1 + - - +
110A ILE* 2.9 39.5 + - + +
125A PHE* 5.1 1.8 - - + -
128A PRO* 3.5 18.0 - - - +
130A ASN* 2.9 36.0 + - - +
131A PHE* 4.1 27.9 - - + +
132A HIS 5.2 0.8 - - - +
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Residues in contact with ASN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LYS 2.9 17.0 + - - +
104A LYS* 3.6 8.9 - - - +
105A TYR 3.2 0.4 - - - -
106A GLN* 1.3 74.6 - - - +
108A ALA* 1.3 65.5 + - - +
110A ILE* 3.3 13.5 + - - +
111A ASN* 2.9 53.6 + - - +
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ILE* 3.8 23.8 - - + -
95A SER* 4.5 16.3 + - - -
104A LYS 2.9 18.0 + - - +
105A TYR* 3.5 6.1 - - - +
107A ASN* 1.3 78.0 + - - +
109A ILE* 1.3 58.9 + - - +
111A ASN* 3.3 10.0 + - - +
112A PHE* 3.0 32.9 + - - -
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Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ILE* 4.1 14.4 - - + -
105A TYR 3.0 19.1 + - - +
106A GLN* 3.5 8.5 - - - +
108A ALA* 1.3 75.2 - - - +
110A ILE* 1.3 67.7 + - + +
112A PHE* 3.1 10.4 + - - +
113A GLU* 3.0 25.5 + - + +
120A ILE* 3.9 22.7 - - + -
122A THR* 5.0 0.4 - - + -
125A PHE* 4.0 17.5 - - + -
131A PHE* 4.0 26.7 - - + -
132A HIS 5.3 2.5 - - - +
133A LEU* 4.1 22.7 - - + -
137A LEU* 4.0 18.8 - - + -
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Residues in contact with ILE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A GLN* 2.9 29.0 + - + +
107A ASN* 3.3 13.0 + - - +
109A ILE* 1.3 77.2 - - + +
111A ASN* 1.3 61.2 + - - +
113A GLU* 3.2 14.8 + - - +
114A ASN* 2.9 42.2 + - - +
132A HIS 5.9 3.1 - - - +
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Residues in contact with ASN 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A SER* 6.2 0.2 - - - +
107A ASN* 2.9 48.8 + - - +
108A ALA* 3.7 7.8 - - - +
110A ILE* 1.3 76.2 - - - +
112A PHE* 1.3 68.3 + - + +
114A ASN* 3.3 19.0 + - - +
115A ASN* 3.2 30.9 + - - +
91B THR* 5.6 5.6 - - - +
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Residues in contact with PHE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLY* 3.7 11.2 - - - -
64A ILE 3.5 32.8 - - - -
65A ILE* 3.5 24.2 - - + -
93A LEU* 3.4 36.8 - - + -
95A SER* 3.3 29.8 - - - -
108A ALA 3.0 19.1 + - - -
109A ILE* 3.1 10.3 + - - +
111A ASN* 1.3 78.7 - - + +
113A GLU* 1.3 59.2 + - - +
115A ASN* 3.0 17.7 + - - -
116A ASN 3.2 8.0 + - - -
117A VAL* 3.3 27.0 + - + +
120A ILE* 3.9 20.9 - - + -
91B THR* 4.6 2.7 - - + -
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Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ILE* 3.0 21.4 + - - +
110A ILE* 3.6 15.0 - - - +
112A PHE* 1.3 74.1 - - - +
114A ASN* 1.3 65.4 + - - +
116A ASN* 3.0 15.3 + - - +
117A VAL* 4.8 3.4 - - - +
120A ILE* 4.4 6.3 - - + -
132A HIS 4.7 1.7 - - - +
133A LEU* 3.6 19.8 - - - +
134A ASN* 2.9 27.9 + - - +
135A THR* 2.7 34.0 + - + +
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Residues in contact with ASN 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ILE* 2.9 35.0 + - - +
111A ASN* 3.6 21.5 + - - +
112A PHE 3.2 0.4 - - - -
113A GLU* 1.3 78.3 - - - +
115A ASN* 1.3 63.4 + - - +
116A ASN* 3.2 2.2 + - - +
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Residues in contact with ASN 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A MET* 3.4 21.9 - - + +
93A LEU* 4.1 27.1 - - + +
111A ASN* 3.2 18.6 + - - +
112A PHE* 3.0 10.6 + - - +
114A ASN* 1.3 79.9 - - - +
116A ASN* 1.3 68.8 + - - +
117A VAL 3.3 2.0 + - - -
59B SER 4.5 9.0 + - - +
61B MET* 4.4 21.8 - - - +
91B THR* 4.8 10.9 + - - -
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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