Contacts of the helix formed by residues 99 - 116 (chain A) in PDB entry 1OLY
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 THR 99 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A HIS* 1.4 79.8 - - - +
100A ASP* 1.3 64.6 + - - +
101A PHE* 3.6 7.1 + - - +
102A THR* 3.2 25.2 + - - +
103A LYS* 3.1 21.9 + - - +
134A GLN* 4.8 11.7 - - - +
137A ALA* 3.9 27.0 - - + +
141A THR* 3.8 9.0 - - + +
217B THR* 4.4 10.1 - - - +
218B SER* 5.7 2.5 - - - +
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Residues in contact with ASP 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA* 4.1 4.2 - - + +
46A ASP* 3.2 39.8 - - - +
69A ASN 5.5 1.4 - - - +
70A GLY* 3.4 23.6 - - - -
71A ASP* 3.4 21.9 + - - +
74A SER* 5.3 0.3 - - - -
99A THR* 1.3 72.5 - - - +
101A PHE* 1.3 55.6 + - - +
103A LYS* 3.0 27.9 + - - +
104A CYS* 2.7 36.8 + - - +
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Residues in contact with PHE 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 4.4 5.8 - - + -
24A LEU* 3.0 44.4 - - + +
45A ALA* 4.5 0.6 - - - +
99A THR* 3.1 9.5 + - - +
100A ASP* 1.3 79.1 - - - +
102A THR* 1.3 61.5 + - - +
104A CYS* 3.1 5.6 + - - +
105A LEU* 3.0 52.6 + - + +
124A THR* 3.1 39.5 - - + -
138A SER* 5.0 5.4 - - - -
141A THR* 2.8 43.5 - - + -
142A LEU* 5.0 2.9 - - + -
153A ILE* 4.7 3.1 - - + -
155A ILE* 3.6 16.4 - - + -
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Residues in contact with THR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A HIS* 4.3 17.4 - - + +
99A THR* 3.2 15.5 + - - -
101A PHE* 1.3 78.0 - - - +
103A LYS* 1.3 64.0 + - - +
105A LEU* 3.1 18.8 + - - +
106A LYS* 3.2 17.2 + - + +
141A THR* 2.8 14.9 - - - +
144A GLN* 2.6 37.8 + - + +
148A ILE* 3.7 21.1 - - + -
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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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71A ASP* 4.7 2.6 + - - -
93A THR* 2.8 60.4 + - + +
95A ASP* 3.3 31.9 + - + +
98A HIS* 2.7 35.7 + - + +
99A THR 3.1 13.4 + - - +
100A ASP* 3.0 21.9 + - - +
102A THR* 1.3 78.2 - - - +
104A CYS* 1.3 62.3 + - - +
106A LYS* 3.2 26.7 + - + +
107A MET* 3.1 25.4 + - + +
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Residues in contact with CYS 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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22A VAL* 3.8 30.7 - - + -
43A ALA* 4.2 4.0 - - - -
44A CYS 4.2 13.0 - - - -
45A ALA* 4.0 12.1 - - + -
67A PHE* 3.9 23.8 - - - -
69A ASN* 4.7 9.6 - - + +
100A ASP 2.7 21.9 + - - +
101A PHE* 3.1 6.5 + - - +
103A LYS* 1.3 74.5 - - - +
105A LEU* 1.3 57.0 + - + +
107A MET* 3.2 8.0 + - - +
108A LEU* 2.9 24.9 + - - +
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Residues in contact with LEU 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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22A VAL* 4.4 19.5 - - + -
101A PHE* 3.0 58.0 + - + +
102A THR* 3.1 11.2 + - - +
104A CYS* 1.3 72.1 - - - +
106A LYS* 1.3 66.1 + - - +
108A LEU* 3.1 9.7 + - + +
109A GLN* 2.9 24.3 + - - +
122A ILE* 4.6 12.1 - - + -
141A THR* 4.7 4.9 - - - -
142A LEU* 6.0 0.2 - - + -
145A ALA* 4.4 11.2 - - + -
148A ILE* 3.9 18.5 - - + +
149A THR* 5.9 1.9 - - + +
153A ILE* 3.9 28.0 - - + -
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Residues in contact with LYS 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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93A THR* 6.4 0.2 - - - +
95A ASP* 5.2 8.5 + - - +
98A HIS* 6.2 2.8 - - + -
102A THR* 3.6 13.2 - - + +
103A LYS* 3.2 33.3 + - + +
105A LEU* 1.3 78.8 - - - +
107A MET* 1.3 73.7 + - + +
109A GLN* 3.2 4.6 + - - +
110A LYS* 3.1 20.6 + - - +
148A ILE* 3.9 27.1 - - + -
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Residues in contact with MET 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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67A PHE* 4.1 3.1 - - + -
69A ASN* 2.9 33.7 - - - +
91A ILE* 3.8 33.7 - - + -
92A SER 4.8 0.9 - - - +
93A THR* 3.8 16.6 - - + -
103A LYS* 3.1 12.2 + - + +
104A CYS 3.2 4.5 + - - +
106A LYS* 1.3 91.9 - - + +
108A LEU* 1.3 64.1 + - - +
110A LYS* 3.2 19.5 + - - +
111A LYS* 3.0 28.6 + - + +
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A CYS* 4.0 20.0 - - + -
21A LEU 5.8 0.9 - - - +
22A VAL* 4.2 13.0 - - + -
41A LEU* 3.2 35.0 - - + +
43A ALA* 5.2 4.0 - - + -
67A PHE* 4.2 16.3 - - + -
104A CYS 2.9 14.0 + - - +
105A LEU* 3.4 13.5 - - + +
107A MET* 1.3 77.4 - - - +
109A GLN* 1.3 57.4 + - - +
111A LYS* 3.1 5.2 + - - +
112A ILE* 2.8 39.5 + - + +
122A ILE* 3.6 46.9 - - + -
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Residues in contact with GLN 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 LEU 2.9 12.8 + - - +
106A LYS* 3.5 8.3 - - - +
108A LEU* 1.3 76.4 - - - +
110A LYS* 1.3 63.4 + - - +
112A ILE* 3.1 20.8 + - - +
113A GLU* 3.0 56.6 + - - +
148A ILE* 3.5 27.1 - - + +
149A THR* 2.6 32.5 + - - -
150A PRO* 4.5 8.7 - - - +
151A PHE* 4.4 8.2 - - - -
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Residues in contact with LYS 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 LYS 3.1 12.2 + - - +
107A MET* 3.2 23.7 + - - +
109A GLN* 1.3 75.0 - - - +
111A LYS* 1.3 75.5 + - + +
113A GLU* 3.3 13.7 + - - +
114A GLU* 2.9 56.4 + - + +
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Residues in contact with LYS 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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41A LEU* 3.9 7.6 - - + -
66A GLU* 3.1 27.5 + - - +
67A PHE* 4.2 15.9 - - + -
89A GLU* 4.3 16.4 - - - +
91A ILE* 4.0 28.5 - - - +
107A MET* 3.0 21.7 + - - +
108A LEU 3.4 6.7 - - - +
110A LYS* 1.3 87.1 - - + +
112A ILE* 1.3 65.2 + - - +
114A GLU* 3.3 14.2 + - - +
115A LYS* 2.9 45.8 + - - +
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Residues in contact with ILE 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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20A CYS* 4.5 5.4 - - - -
41A LEU* 5.2 0.2 - - + -
108A LEU* 2.8 46.1 + - + +
109A GLN* 3.1 27.3 + - - +
111A LYS* 1.3 76.7 - - + +
113A GLU* 1.3 52.3 + - - +
115A LYS* 3.4 1.9 + - - -
116A ASP* 2.7 28.9 + - - -
117A LEU* 2.9 47.5 + - + +
119A VAL* 4.3 21.3 - - + -
122A ILE* 4.7 9.4 - - + -
151A PHE* 4.7 16.8 - - + -
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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 GLN* 3.0 51.2 + - - +
110A LYS* 3.5 11.3 - - - +
112A ILE* 1.3 75.4 - - - +
114A GLU* 1.3 61.3 + - + +
116A ASP* 2.5 32.3 + - - +
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Residues in contact with GLU 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 LYS* 2.9 58.2 + - + +
111A LYS* 3.9 13.9 + - - +
113A GLU* 1.3 78.9 - - + +
115A LYS* 1.3 64.8 + - + +
116A ASP* 3.3 8.0 + - - +
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Residues in contact with LYS 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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41A LEU* 3.6 13.0 - - + +
66A GLU* 2.9 40.4 + - - +
111A LYS* 2.9 37.0 + - + +
114A GLU* 1.3 76.3 - - + +
116A ASP* 1.3 70.6 + - - +
117A LEU* 3.3 42.8 + - + +
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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 ILE 2.7 6.4 + - - -
113A GLU* 2.5 31.3 + - - +
114A GLU 3.7 5.5 - - - +
115A LYS* 1.3 82.1 - - - +
117A LEU* 1.4 65.9 + - - +
118A LYS* 3.8 8.7 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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