Contacts of the helix formed by residues 100 - 118 (chain A) in PDB entry 1OBA
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 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A SER* 2.9 10.4 + - - +
99A GLY* 1.3 77.0 - - - +
101A ALA* 1.3 59.1 + - - +
102A GLN* 3.4 12.1 + - - +
103A ALA* 2.9 42.5 + - + +
104A ASN* 3.0 12.0 + - - -
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Residues in contact with ALA 101 (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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98A SER 4.4 0.6 + - - -
99A GLY 3.7 4.2 + - - -
100A ASP* 1.3 72.5 + - - +
102A GLN* 1.3 57.3 + - - +
104A ASN* 3.3 3.9 + - - +
105A THR* 2.9 33.0 + - - -
133A ASP 4.5 6.1 - - - +
134A ASN* 3.3 32.6 - - - +
135A VAL* 4.2 6.3 - - - +
136A ASP* 6.2 0.9 - - + -
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Residues in contact with GLN 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 ASP* 3.2 10.1 + - - +
101A ALA* 1.3 79.2 - - - +
103A ALA* 1.3 58.1 + - - +
105A THR* 3.4 6.6 + - - -
106A ASN* 2.7 70.1 + - - +
136A ASP* 5.2 1.0 - - - +
139A GLN* 3.0 41.3 + - - -
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Residues in contact with ALA 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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66A GLY* 3.5 29.5 - - - +
68A VAL* 4.8 0.6 - - - +
98A SER* 4.2 1.6 - - - +
100A ASP* 2.9 27.1 + - + +
102A GLN* 1.3 76.4 - - - +
104A ASN* 1.3 64.7 + - - +
106A ASN* 3.4 8.6 + - - +
107A ALA* 3.0 20.6 + - - +
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Residues in contact with ASN 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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65A GLY 3.2 14.0 + - - +
66A GLY* 3.3 2.0 - - - -
93A TYR* 3.1 21.5 + - - +
98A SER* 2.6 57.4 + - - +
100A ASP 3.0 8.9 + - - +
101A ALA* 3.4 2.7 - - - +
103A ALA* 1.3 78.5 - - - +
105A THR* 1.3 61.4 + - - +
107A ALA* 3.6 1.9 + - - +
108A CYS* 3.0 29.1 + - - -
134A ASN* 2.9 34.6 - - - +
135A VAL* 3.6 6.3 - - + -
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Residues in contact with THR 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 ALA 2.9 18.5 + - - -
102A GLN* 3.5 14.0 - - - +
104A ASN* 1.3 77.5 - - - +
106A ASN* 1.3 51.9 + - - +
108A CYS* 3.2 7.5 + - - +
109A LEU* 2.8 43.6 + - + +
135A VAL* 3.6 5.1 - - - -
136A ASP* 3.0 31.8 + - - +
139A GLN* 3.9 35.4 - - + +
140A ILE* 4.2 9.4 - - + -
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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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68A VAL* 4.2 14.9 - - + +
102A GLN* 2.7 48.0 + - - +
103A ALA* 3.4 8.6 + - - +
105A THR* 1.3 74.7 - - - +
107A ALA* 1.3 61.1 + - - +
109A LEU* 3.1 13.9 + - - +
110A ARG* 2.9 29.5 + - - +
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Residues in contact with ALA 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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64A PHE* 3.5 27.8 - - + -
65A GLY 4.1 0.4 - - - +
66A GLY 4.0 4.0 - - - -
67A ASP 3.7 22.9 - - - +
68A VAL* 3.8 13.4 - - + +
71A ALA* 3.5 7.0 - - + +
103A ALA 3.0 17.4 + - - +
104A ASN 3.9 1.8 - - - +
106A ASN* 1.3 76.3 - - - +
108A CYS* 1.3 58.1 + - - +
110A ARG* 3.3 1.5 + - - +
111A PHE* 3.0 28.6 + - - +
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Residues in contact with CYS 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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64A PHE* 4.2 4.3 - - - -
91A LEU* 3.8 21.3 - - + +
93A TYR* 3.6 43.3 - - - -
104A ASN 3.0 23.7 + - - +
105A THR* 3.4 7.2 - - - +
107A ALA* 1.3 75.8 - - - +
109A LEU* 1.3 57.4 + - - +
111A PHE* 3.3 1.7 + - - +
112A MET* 3.0 35.7 + - + +
124A TYR* 4.0 8.7 - - - -
135A VAL* 4.5 3.1 - - - -
140A ILE* 4.4 13.5 - - + -
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Residues in contact with LEU 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 THR* 2.8 38.0 + - + +
106A ASN* 3.1 13.9 + - - +
108A CYS* 1.3 75.3 - - - +
110A ARG* 1.3 59.1 + - - +
112A MET* 3.4 22.7 + - + +
113A GLN* 2.8 32.2 + - - +
139A GLN* 4.3 10.1 - - + +
140A ILE* 4.0 17.7 - - + -
143A GLN* 3.5 42.7 - - - +
144A PHE* 4.0 9.2 - - + -
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Residues in contact with ARG 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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68A VAL* 3.6 25.8 - - + +
71A ALA* 5.2 0.4 - - + -
72A GLU* 2.7 30.5 + - + +
106A ASN 2.9 16.5 + - - +
107A ALA 3.3 3.6 + - - +
109A LEU* 1.3 74.8 - - - +
111A PHE* 1.3 65.9 + - - +
113A GLN* 3.5 22.6 + - - +
114A MET* 3.1 64.0 + - + +
117A ASP* 4.4 5.1 + - - -
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Residues in contact with PHE 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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60A HIS* 3.6 32.3 - + + -
64A PHE* 3.8 18.6 - + + -
71A ALA* 3.4 19.7 - - + +
74A GLU* 4.0 2.2 - - + -
75A ALA* 3.3 26.9 - - + +
78A PHE* 3.9 19.5 - + - -
91A LEU* 3.6 35.2 - - + -
107A ALA 3.0 17.4 + - - +
108A CYS 3.5 5.4 - - - +
109A LEU 3.2 0.2 - - - -
110A ARG* 1.3 77.4 - - - +
112A MET* 1.3 65.3 + - - +
114A MET* 3.2 20.9 + - - +
115A ILE* 3.3 35.4 + - + +
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Residues in contact with MET 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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91A LEU* 4.0 18.8 - - + -
108A CYS 3.0 20.3 + - - +
109A LEU* 3.8 13.2 - - + +
111A PHE* 1.3 78.9 - - - +
113A GLN* 1.3 62.2 + - - +
115A ILE* 3.2 6.7 + - + +
116A ALA* 3.0 19.9 + - - +
122A PRO* 3.5 24.2 - - + +
123A ILE 4.7 1.1 - - - +
124A TYR* 4.0 24.2 - - - -
140A ILE* 3.1 42.2 - - + -
144A PHE* 3.3 33.9 - - + -
147A SER* 4.8 3.4 - - - -
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Residues in contact with GLN 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 LEU 2.8 22.3 + - - +
110A ARG* 3.8 22.2 - - - +
111A PHE 3.2 0.2 - - - -
112A MET* 1.3 73.5 - - - +
114A MET* 1.3 58.5 + - - +
116A ALA* 3.2 10.0 + - - +
117A ASP* 2.8 66.3 + - - +
143A GLN* 4.6 7.1 - - - +
144A PHE* 3.3 23.8 - - + -
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Residues in contact with MET 114 (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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72A GLU* 3.2 57.7 - - + +
75A ALA* 3.9 15.9 - - + -
76A GLN* 5.0 11.2 - - - +
79A LEU* 3.8 10.4 - - + +
110A ARG* 3.1 57.3 + - + +
111A PHE* 3.2 6.7 + - - +
113A GLN* 1.3 74.1 - - - +
115A ILE* 1.3 65.4 + - - +
117A ASP* 3.8 8.4 - - + +
118A ALA* 3.2 23.4 + - - +
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Residues in contact with ILE 115 (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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75A ALA* 5.4 2.0 - - + -
78A PHE* 4.4 5.6 - - + -
79A LEU* 4.5 17.7 - - + -
89A LEU* 3.7 45.8 - - + +
90A VAL 4.9 1.1 - - - -
91A LEU* 5.0 1.3 - - + +
111A PHE* 3.3 43.7 + - + +
112A MET* 3.2 11.2 + - + +
113A GLN 3.2 0.4 - - - -
114A MET* 1.3 79.5 - - + +
116A ALA* 1.3 62.0 - - - +
118A ALA 3.2 6.8 + - - -
119A GLY 3.5 0.5 + - - -
120A TYR* 3.2 31.3 + - + -
122A PRO* 3.8 20.6 - - + -
123A ILE 5.4 0.2 - - - +
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Residues in contact with ALA 116 (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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112A MET 3.0 12.6 + - - +
113A GLN* 3.2 17.2 + - - +
115A ILE* 1.3 79.3 - - - +
117A ASP* 1.3 61.2 + - - +
119A GLY* 3.2 13.7 + - - -
120A TYR 3.3 12.5 + - - +
122A PRO* 3.9 14.4 - - + -
144A PHE* 4.1 12.1 - - + -
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Residues in contact with ASP 117 (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 ARG* 4.4 6.9 + - - -
113A GLN* 2.8 50.7 + - - +
114A MET* 4.0 9.5 - - + +
115A ILE 3.3 0.2 - - - -
116A ALA* 1.3 77.6 - - - +
118A ALA* 1.3 58.7 + - - +
119A GLY* 3.1 1.7 + - - -
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Residues in contact with ALA 118 (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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79A LEU* 3.8 19.5 - - + -
114A MET 3.2 18.3 + - - +
115A ILE 3.6 6.3 - - - +
116A ALA 3.2 0.8 - - - -
117A ASP* 1.3 75.8 - - - +
119A GLY* 1.3 58.8 + - - +
120A TYR* 3.4 24.9 - - + -
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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