Contacts of the helix formed by residues 103 - 116 (chain A) in PDB entry 2H18
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 LYS 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A LEU* 3.6 23.7 - - + +
29A GLN 4.9 8.7 - - - +
30A TYR* 5.0 19.4 - - + -
97A ASP* 6.2 1.8 - - + -
100A ASP* 3.1 39.0 + - + +
102A GLU* 1.3 82.7 + - + +
104A ILE* 1.3 60.2 + - - +
105A GLU 3.3 1.6 - - - -
106A ALA* 3.3 8.4 + - + +
107A SER* 2.9 29.0 + - - -
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Residues in contact with ILE 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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96A VAL* 3.5 30.5 - - + -
97A ASP 4.0 11.0 - - - +
98A ALA* 4.8 1.1 - - - -
100A ASP 3.6 11.9 + - - +
101A GLN* 3.3 19.9 + - - +
103A LYS* 1.3 76.9 - - - +
105A GLU* 1.3 60.6 + - - +
107A SER* 3.2 4.4 + - - -
108A LYS* 2.8 28.1 + - - +
138A LEU* 3.9 23.8 - - + -
143A LEU* 4.2 5.2 - - + -
146A LYS* 3.8 35.9 - - + +
147A MET* 4.1 8.2 - - - +
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Residues in contact with GLU 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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101A GLN 4.7 1.2 + - - -
102A GLU 4.5 7.4 + - - +
103A LYS 3.3 0.2 - - - -
104A ILE* 1.3 79.0 - - - +
106A ALA* 1.3 63.4 + - - +
108A LYS* 3.4 22.0 + - - +
109A ASN* 3.0 44.6 + - - +
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Residues in contact with ALA 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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28A LEU* 4.0 16.6 - - + -
102A GLU 5.0 1.7 + - - +
103A LYS* 3.3 13.2 + - + +
105A GLU* 1.3 80.1 + - - +
107A SER* 1.3 58.6 + - - +
109A ASN* 3.3 6.6 + - - +
110A GLU* 2.9 38.8 + - + +
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Residues in contact with SER 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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28A LEU* 3.6 18.7 - - - +
94A TYR* 2.7 45.3 + - - -
95A MET 4.5 1.0 + - - -
96A VAL* 3.6 24.1 - - - +
103A LYS* 2.9 18.7 + - - -
104A ILE* 3.5 9.0 - - - -
106A ALA* 1.3 77.3 - - - +
108A LYS* 1.3 63.4 + - - +
111A LEU* 3.1 8.7 + - - +
147A MET* 3.7 5.2 - - - +
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Residues in contact with LYS 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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104A ILE 2.8 19.1 + - - +
105A GLU* 3.6 22.5 - - - +
107A SER* 1.3 74.4 - - - +
109A ASN* 1.3 74.2 + - - +
111A LEU* 3.2 2.8 + - - +
112A HIS* 3.0 41.0 + - + -
146A LYS 3.4 20.6 + - - +
147A MET* 3.5 41.7 - - - +
148A ASN* 4.2 11.6 - - + +
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Residues in contact with ASN 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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105A GLU* 3.0 41.2 + - - +
106A ALA* 3.8 5.7 - - - +
108A LYS* 1.3 90.8 - - - +
110A GLU* 1.3 59.0 + - + +
112A HIS* 3.6 6.0 + - - +
113A ASN* 3.0 28.8 + - - +
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Residues in contact with GLU 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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28A LEU* 4.3 9.3 - - + +
72A ILE* 3.8 30.7 - - + +
73A GLY* 3.4 28.8 + - - -
94A TYR* 3.5 15.5 - - - +
106A ALA* 2.9 22.2 + - + +
109A ASN* 1.3 73.7 - - + +
111A LEU* 1.3 60.0 + - - +
113A ASN* 3.4 7.7 + - - +
114A LEU* 2.9 31.0 + - - +
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Residues in contact with LEU 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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92A ILE* 5.4 0.7 - - + -
94A TYR* 3.4 40.0 + - + -
107A SER 3.1 15.1 + - - +
108A LYS 3.2 7.4 + - - +
110A GLU* 1.3 76.8 - - - +
112A HIS* 1.3 62.9 + - + +
114A LEU* 3.2 7.7 + - + +
115A LEU* 3.0 58.4 + - + +
125A VAL* 4.5 6.5 - - + -
127A VAL* 4.0 12.1 - - + -
147A MET* 3.8 21.3 - - + -
149A LEU* 3.8 24.5 - - + -
152A ILE* 4.4 7.4 - - + -
157A ILE* 4.6 0.7 - - + -
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Residues in contact with HIS 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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108A LYS* 3.0 35.4 + - + +
109A ASN* 4.1 5.8 - - - +
111A LEU* 1.3 81.8 - - + +
113A ASN* 1.3 62.5 + - - +
115A LEU* 3.5 6.6 + - - +
116A ASP* 3.2 30.6 + - - +
147A MET 2.8 27.7 + - - -
148A ASN* 3.2 36.1 + - - +
151A ALA* 4.1 6.4 - - + +
152A ILE* 3.9 25.0 - - + +
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Residues in contact with ASN 113 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A ASN 3.0 19.5 + - - +
110A GLU* 3.9 10.1 - - - +
112A HIS* 1.3 76.2 - - - +
114A LEU* 1.3 61.8 + - - +
116A ASP* 3.2 14.3 + - - +
117A LYS* 2.8 37.2 + - - -
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Residues in contact with LEU 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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24A THR* 5.7 1.6 - - + -
26A VAL* 4.0 27.8 - - + -
70A TRP* 4.0 25.6 - - + -
72A ILE* 4.2 13.5 - - + -
83A GLU* 4.2 16.4 - - + +
86A CYS* 5.4 1.1 - - - -
92A ILE* 4.4 15.0 - - + -
94A TYR* 4.6 7.4 - - + -
110A GLU 2.9 18.4 + - - +
111A LEU* 3.4 6.1 - - + +
113A ASN* 1.3 77.2 - - - +
115A LEU* 1.3 67.3 + - + +
116A ASP 3.1 1.4 + - - -
117A LYS* 3.2 23.5 + - - +
120A LEU* 3.6 32.8 - - + +
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Residues in contact with LEU 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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92A ILE* 4.1 13.5 - - + -
111A LEU* 3.0 38.7 + - + +
112A HIS* 3.5 4.7 + - - +
114A LEU* 1.3 80.5 - - + +
116A ASP* 1.3 59.0 + - - +
117A LYS 3.2 7.3 + - - +
120A LEU* 5.5 1.6 - - + -
121A GLN* 6.0 0.7 - - - +
125A VAL* 3.7 27.4 - - + -
152A ILE* 3.7 37.5 - - + -
155A ARG* 3.2 44.8 + - - +
157A ILE* 4.6 2.0 - - + -
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Residues in contact with ASP 116 (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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112A HIS* 3.2 16.5 + - - +
113A ASN* 3.2 16.5 + - - +
114A LEU 3.1 1.4 - - - -
115A LEU* 1.3 79.8 - - - +
117A LYS* 1.3 68.2 + - - +
118A PRO* 4.1 4.5 - - - +
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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