Contacts of the helix formed by residues 103 - 115 (chain A) in PDB entry 2OBF
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 LEU 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A TYR* 3.0 38.6 - - + +
28A GLN* 4.2 15.3 - - - +
30A PHE* 3.4 31.4 - - + +
101A ASP* 3.2 8.3 + - - +
102A PHE* 1.3 94.8 - - + +
104A GLU* 1.3 66.9 + - - +
105A VAL* 3.7 18.4 - - + -
106A ASN* 3.1 13.5 + - - +
107A ARG* 3.3 15.7 + - - +
3001A SAH 3.4 20.2 - - - +
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Residues in contact with GLU 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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102A PHE 3.7 1.4 + - - -
103A LEU* 1.3 71.7 - - - +
105A VAL* 1.3 68.6 + - + +
107A ARG* 3.1 37.3 + - - +
108A GLN* 2.6 64.7 + - - +
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Residues in contact with VAL 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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30A PHE 4.1 14.6 - - - +
32A PRO* 4.0 25.8 - - + +
103A LEU* 3.7 23.1 - - + -
104A GLU* 1.3 84.5 - - + +
106A ASN* 1.3 62.5 + - - +
108A GLN* 3.6 12.8 + - - +
109A GLU* 3.2 20.1 + - - +
112A ARG* 4.4 4.2 + - - -
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Residues in contact with ASN 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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30A PHE* 3.4 17.9 - - - -
32A PRO* 3.1 23.2 - - - +
81A GLY* 3.6 21.2 - - - +
82A PRO* 3.4 14.8 - - - +
101A ASP* 2.9 28.6 + - - +
103A LEU* 3.1 8.5 + - - +
105A VAL* 1.3 73.6 - - - +
107A ARG* 1.3 66.1 + - - +
108A GLN 3.1 1.8 - - - -
109A GLU* 2.9 16.1 + - - +
110A LEU* 3.0 17.0 + - - +
3001A SAH 3.1 23.8 + - - -
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Residues in contact with ARG 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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101A ASP* 2.9 37.9 + - + +
102A PHE 3.1 19.4 + - - -
103A LEU 3.6 4.9 - - - +
104A GLU* 3.1 43.6 + - - +
106A ASN* 1.3 77.4 - - - +
108A GLN* 1.3 57.9 + - + +
110A LEU* 3.5 6.7 + - - +
111A GLY* 3.1 22.2 + - - -
154A VAL* 3.8 33.4 + - + +
155A LEU 3.7 21.3 - - - -
156A PRO* 3.4 24.0 - - - +
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Residues in contact with GLN 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 GLU* 2.6 47.1 + - - +
105A VAL* 3.7 13.0 - - - +
106A ASN 3.1 0.2 - - - -
107A ARG* 1.3 77.6 - - + +
109A GLU* 1.3 64.4 + - - +
111A GLY* 3.3 2.2 + - - +
112A ARG* 3.1 42.2 + - - +
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Residues in contact with GLU 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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32A PRO* 4.3 8.4 - - + +
33A ARG* 2.8 45.8 + - - +
36A LEU* 4.3 7.9 - - + -
82A PRO* 3.6 30.1 - - + +
105A VAL 3.2 12.3 + - - +
106A ASN* 2.9 9.3 + - - +
108A GLN* 1.3 77.0 - - - +
110A LEU* 1.3 63.3 + - - +
112A ARG* 3.0 35.8 + - - +
113A TRP* 3.4 17.5 + - - +
119A GLY 3.8 3.5 - - - +
120A ALA* 4.3 1.2 - - - +
121A PHE* 3.9 10.2 + - + +
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Residues in contact with LEU 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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80A SER* 4.1 15.5 - - - -
81A GLY 3.4 28.0 - - - +
82A PRO* 3.9 11.9 - - + +
83A THR 3.6 22.2 - - - +
84A VAL* 4.1 11.9 - - + -
99A MET* 3.9 18.8 - - + -
100A THR 4.8 3.1 - - - +
101A ASP* 5.6 0.2 - - + -
106A ASN 3.0 10.6 + - - +
107A ARG* 3.5 9.2 - - + +
109A GLU* 1.3 74.5 - - - +
111A GLY* 1.3 55.5 + - - +
113A TRP* 2.8 7.7 + - + +
114A LEU* 2.7 47.5 + - + +
154A VAL* 3.8 23.1 - - + -
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Residues in contact with GLY 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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107A ARG 3.1 11.7 + - - -
108A GLN* 3.3 4.4 + - - -
110A LEU* 1.3 78.0 - - - +
112A ARG* 1.3 55.4 + - - +
114A LEU* 4.2 11.2 - - - +
115A GLN* 2.6 47.3 + - - +
117A GLU* 4.2 3.4 - - - -
154A VAL* 5.3 2.0 - - - +
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Residues in contact with ARG 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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105A VAL 4.4 3.4 + - - -
108A GLN* 3.1 32.3 + - - +
109A GLU* 3.0 51.1 + - - +
110A LEU 3.1 0.2 - - - -
111A GLY* 1.3 77.0 - - - +
113A TRP* 1.3 56.8 + - - +
116A GLU 3.3 1.7 + - - -
117A GLU* 2.7 50.9 + - + +
118A PRO 3.3 24.2 - - - +
119A GLY* 4.2 9.0 + - - -
120A ALA* 3.3 17.7 - - + +
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Residues in contact with TRP 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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84A VAL* 3.8 24.9 - - + -
88A LEU* 5.7 1.1 - - + -
109A GLU 3.4 7.4 + - - +
110A LEU* 2.8 9.4 + - - +
112A ARG* 1.3 78.6 - - - +
114A LEU* 1.3 78.8 + - + +
115A GLN 3.2 0.2 - - - -
116A GLU* 3.1 5.4 + - - -
120A ALA* 3.6 10.9 - - + +
121A PHE* 3.1 28.3 + - + +
122A ASN* 5.3 0.2 - - - +
123A TRP* 3.6 27.9 - + + +
127A SER* 5.2 0.7 - - - -
144A GLU* 3.8 33.6 + - + -
147A LEU* 3.7 32.1 - - + -
148A ARG* 2.9 78.1 + - + +
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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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84A VAL* 5.5 0.9 - - + -
99A MET* 4.7 8.7 - - - -
110A LEU* 2.7 29.5 + - + +
111A GLY* 3.8 4.5 - - - +
113A TRP* 1.3 96.2 - - + +
115A GLN* 1.3 74.0 + - - +
116A GLU* 3.5 2.4 + - - +
147A LEU* 5.0 0.4 - - + +
148A ARG* 3.4 36.1 - - + +
151A VAL* 3.7 37.9 - - + +
154A VAL* 3.5 31.6 - - + -
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Residues in contact with GLN 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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111A GLY* 2.6 26.0 + - - +
114A LEU* 1.3 88.7 + - - +
116A GLU* 1.3 70.2 + - - +
117A GLU* 2.9 32.1 + - + +
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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