Contacts of the helix formed by residues 103 - 118 (chain B) in PDB entry 2OT3
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 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B CYS* 5.5 6.9 - - - -
30B VAL* 5.8 0.3 - - - +
100B ASP* 2.9 22.2 + - - +
101B ILE 3.3 1.0 - - - -
102B THR* 1.3 80.4 - - - +
104B GLU* 1.3 63.9 + - - +
105B ASP* 3.1 25.6 + - - +
106B SER* 2.6 47.1 + - - +
107B PHE 3.4 2.6 + - - -
142B VAL* 4.2 2.8 - - - +
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Residues in contact with GLU 104 (chain B).
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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102B THR 4.0 0.7 - - - +
103B ASP* 1.3 73.8 + - - +
105B ASP* 1.3 70.7 + - - +
107B PHE* 3.3 5.3 + - + +
108B GLN* 3.0 26.9 + - - +
141B HIS* 2.6 42.6 + - + +
142B VAL* 3.7 21.4 - - + +
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Residues in contact with ASP 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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103B ASP* 3.1 15.2 + - - +
104B GLU* 1.3 89.9 - - - +
106B SER* 1.3 57.1 + - - +
108B GLN* 3.3 9.7 + - - +
109B LYS* 3.1 41.0 + - - +
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Residues in contact with SER 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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30B VAL* 3.9 19.7 - - - -
98B VAL 4.8 1.2 - - - +
99B TYR* 3.4 10.4 - - - +
100B ASP* 2.9 31.6 + - - -
103B ASP* 2.6 33.4 + - - -
105B ASP* 1.3 78.2 - - - +
107B PHE* 1.3 60.9 + - - +
109B LYS* 3.4 14.8 - - - +
110B VAL* 3.4 15.9 + - - +
113B TRP* 5.1 0.7 - - - -
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Residues in contact with PHE 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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99B TYR* 3.9 36.3 - + + -
103B ASP 3.4 0.6 + - - -
104B GLU* 3.3 9.3 + - + +
105B ASP 3.2 0.2 - - - -
106B SER* 1.3 78.9 + - - +
108B GLN* 1.3 67.2 + - - +
109B LYS 3.2 0.2 - - - -
110B VAL* 3.1 17.6 + - + +
111B LYS* 3.3 34.8 + - + +
129B ILE* 4.4 11.4 - - + -
142B VAL* 3.8 27.1 - - + -
146B GLU* 4.1 26.5 - - + -
147B ALA* 3.9 26.0 - - + -
150B TYR* 3.8 33.0 - + + -
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Residues in contact with GLN 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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104B GLU 3.0 13.8 + - - +
105B ASP* 3.4 13.5 - - - +
107B PHE* 1.3 75.9 - - - +
109B LYS* 1.3 62.6 + - + +
111B LYS* 3.3 46.0 + - - +
112B ASN* 3.4 29.0 + - - +
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Residues in contact with LYS 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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27B GLU* 4.1 28.5 + - + +
77B GLY 5.1 3.8 - - - -
79B GLU* 5.6 12.1 - - - +
105B ASP* 3.1 27.6 + - - +
106B SER* 3.4 15.7 - - - +
107B PHE 3.2 0.4 - - - -
108B GLN* 1.3 77.0 - - - +
110B VAL* 1.3 61.6 + - - +
112B ASN* 3.3 11.5 + - - +
113B TRP* 3.1 56.5 + - + -
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Residues in contact with VAL 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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97B LEU* 4.0 28.5 - - + +
98B VAL 4.1 11.9 - - - +
99B TYR* 3.9 22.9 - - + -
106B SER 3.4 13.2 + - - +
107B PHE* 3.1 12.9 + - + +
109B LYS* 1.3 77.5 - - - +
111B LYS* 1.3 56.4 + - - +
113B TRP* 3.1 13.9 + - + +
114B VAL* 2.8 32.7 + - + +
129B ILE* 4.1 27.6 - - + -
150B TYR* 4.4 7.0 - - + -
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Residues in contact with LYS 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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107B PHE* 3.7 23.4 - - + +
108B GLN* 3.3 46.6 + - - +
110B VAL* 1.3 75.8 - - + +
112B ASN* 1.3 65.8 + - - +
114B VAL* 3.6 3.3 + - - +
115B LYS* 3.3 27.4 + - - +
146B GLU* 4.2 16.6 + - - -
150B TYR* 3.4 49.3 + - + +
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Residues in contact with ASN 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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82B HIS* 5.5 9.4 - - + -
108B GLN* 3.4 29.9 + - - +
109B LYS* 3.3 9.8 + - - +
110B VAL 3.2 0.6 - - - -
111B LYS* 1.3 77.9 - - - +
113B TRP* 1.3 67.0 + - + +
115B LYS* 3.3 23.8 + - - +
116B GLU* 3.2 24.0 + - - +
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Residues in contact with TRP 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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25B LEU* 3.5 22.9 - - + -
26B GLY* 3.5 39.7 - - - -
27B GLU 4.2 2.9 - - - -
76B ALA 5.7 0.2 - - - -
77B GLY* 4.0 24.0 - - - -
82B HIS* 4.7 10.3 + + - -
89B TYR* 3.6 21.6 + - - -
97B LEU* 3.4 20.6 - - + -
98B VAL 4.5 8.1 - - - -
106B SER 5.1 0.9 - - - -
109B LYS* 3.1 51.5 + - + -
110B VAL* 3.1 10.7 + - + +
112B ASN* 1.3 74.6 - - + +
114B VAL* 1.3 59.2 + - - +
116B GLU* 3.1 21.7 + - - +
117B LEU* 2.9 31.9 + - - +
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Residues in contact with VAL 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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97B LEU* 4.0 15.3 - - + -
110B VAL* 2.8 26.6 + - + +
111B LYS 3.7 0.7 - - - +
113B TRP* 1.3 72.3 - - - +
115B LYS* 1.3 64.1 + - + +
117B LEU* 3.2 8.2 + - - +
118B ARG* 3.0 31.0 + - + +
127B LEU* 4.0 23.1 - - + -
129B ILE* 4.6 7.0 - - + -
150B TYR* 3.1 32.1 - - + +
154B VAL* 3.8 25.1 - - + -
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Residues in contact with LYS 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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111B LYS* 3.3 14.5 + - - +
112B ASN* 3.3 23.8 + - - +
114B VAL* 1.3 79.9 - - + +
116B GLU* 1.3 62.8 + - + +
118B ARG* 3.6 6.0 + - - +
119B LYS* 2.9 44.7 + - - +
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Residues in contact with GLU 116 (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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82B HIS* 2.9 41.4 + - + +
83B ALA* 5.7 0.2 - - - -
85B GLY* 4.6 0.4 - - - -
86B PRO* 3.5 29.8 - - + +
89B TYR* 4.1 16.6 + - + -
112B ASN 3.2 10.7 + - - +
113B TRP* 3.1 24.6 + - - +
115B LYS* 1.3 74.4 - - + +
117B LEU* 1.3 66.6 + - - +
119B LYS* 3.0 22.6 + - - +
120B MET* 3.7 13.7 + - - +
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Residues in contact with LEU 117 (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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23B VAL* 4.3 4.3 - - + -
25B LEU* 4.1 8.3 - - + -
89B TYR* 3.7 41.7 - - + -
95B ALA* 3.7 30.3 - - + -
97B LEU* 3.9 21.3 - - + -
113B TRP 2.9 20.1 + - - +
114B VAL* 3.7 5.6 - - - +
116B GLU* 1.3 75.6 - - - +
118B ARG* 1.3 63.0 + - + +
120B MET* 3.4 22.5 + - - +
125B ILE* 3.5 23.9 + - + +
127B LEU* 3.9 20.6 - - + -
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Residues in contact with ARG 118 (chain B).
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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114B VAL* 3.0 28.2 + - + +
115B LYS* 3.9 7.2 - - - +
116B GLU 3.1 0.2 - - - -
117B LEU* 1.3 76.3 + - - +
119B LYS* 1.3 61.9 + - + +
120B MET 3.4 4.5 + - - +
124B GLU* 3.3 38.8 + - - +
125B ILE* 3.0 30.1 + - - +
127B LEU* 3.4 26.3 - - + +
154B VAL* 3.0 28.4 + - + +
155B GLY 4.1 6.7 + - - -
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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
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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