Contacts of the helix formed by residues 101 - 113 (chain A) in PDB entry 1OIX
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 ASN 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ASP* 2.8 40.2 + - - +
97A LEU* 3.0 37.8 + - - +
98A THR 4.0 2.7 - - - +
99A TYR 3.1 0.6 - - - -
100A GLU* 1.3 73.9 - - - +
102A VAL* 1.3 65.0 + - - +
103A GLU 3.1 2.9 - - - -
104A ARG* 2.8 52.3 + - - +
105A TRP* 3.3 15.7 + - + +
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Residues in contact with VAL 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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89A LEU* 3.9 25.6 - - + -
91A TYR* 4.3 4.9 - - + -
98A THR 3.7 12.9 + - - +
99A TYR* 3.0 31.4 + - + +
101A ASN* 1.3 76.9 - - - +
103A GLU* 1.3 62.9 - - - +
105A TRP* 3.1 10.9 + - - +
106A LEU* 2.9 24.3 + - + +
121A LEU* 3.9 23.8 - - + -
142A PHE* 3.8 30.7 - - + -
148A LEU* 5.2 0.7 - - + -
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Residues in contact with GLU 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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100A GLU 3.7 11.1 + - - +
101A ASN 3.1 1.0 - - - -
102A VAL* 1.3 77.5 - - + +
104A ARG* 1.3 63.3 + - - +
106A LEU* 3.3 18.1 + - - +
107A LYS* 3.0 22.0 + - - +
110A ARG* 4.9 5.4 + - - -
142A PHE* 3.6 31.5 - - + -
146A ASN* 4.4 8.1 + - - -
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Residues in contact with ARG 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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97A LEU* 5.8 0.6 - - - +
101A ASN* 2.8 45.8 + - + +
103A GLU* 1.3 80.1 - - - +
105A TRP* 1.3 59.9 + - + +
107A LYS* 3.3 9.6 + - + +
108A GLU* 3.0 27.5 + - - +
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Residues in contact with TRP 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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17A ILE* 3.8 28.0 - - + +
18A GLY* 3.4 36.1 - - - -
19A ASP* 2.9 30.0 + - - +
69A GLY* 3.4 30.5 - - - -
71A GLU* 3.5 13.5 - - - -
76A ILE* 4.2 10.1 - - + -
89A LEU* 3.8 24.9 - - + -
90A VAL 5.5 0.7 - - - -
98A THR 5.3 2.5 - - - -
101A ASN* 3.3 25.0 + - + +
102A VAL* 3.1 10.4 + - - +
104A ARG* 1.3 75.5 - - + +
106A LEU* 1.3 60.2 + - - +
108A GLU* 3.1 33.6 + - + +
109A LEU* 2.8 32.1 + - - +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 3.7 20.4 - - + -
102A VAL* 2.9 15.1 + - + +
103A GLU* 3.6 25.1 - - - +
105A TRP* 1.3 78.3 - - - +
107A LYS* 1.3 56.2 + - - +
109A LEU* 3.2 7.0 + - + +
110A ARG* 2.9 43.5 + - + +
119A ILE* 4.4 13.2 - - + -
142A PHE* 4.1 20.6 - - + -
146A ASN* 4.0 21.3 - - + +
148A LEU* 4.0 26.2 - - + -
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Residues in contact with LYS 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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103A GLU 3.0 13.5 + - - +
104A ARG* 3.3 14.4 - - + +
106A LEU* 1.3 75.3 - - - +
108A GLU* 1.3 59.4 + - - +
110A ARG* 3.1 31.8 + - - +
111A ASP* 2.9 69.1 + - - +
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Residues in contact with GLU 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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71A GLU* 2.5 33.4 - - - +
76A ILE* 3.6 14.4 - - - +
81A TYR* 2.6 29.3 + - + +
104A ARG* 3.0 14.2 + - - +
105A TRP* 3.1 26.7 + - - +
107A LYS* 1.3 77.4 - - - +
109A LEU* 1.3 54.6 + - - +
111A ASP* 3.3 7.2 + - - +
112A HIS* 2.9 47.9 + - + +
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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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17A ILE* 3.7 23.1 - - + -
81A TYR* 3.6 27.8 - - + -
87A ALA* 4.0 15.3 - - + -
89A LEU* 4.3 7.9 - - + -
105A TRP 2.8 15.3 + - - +
106A LEU* 3.5 9.9 - - + +
108A GLU* 1.3 73.9 - - - +
110A ARG* 1.3 61.6 + - - +
113A ALA* 2.8 49.1 + - + +
114A ASP 5.1 0.7 - - - +
117A ILE* 4.4 7.9 - - + -
119A ILE* 3.8 42.2 - - + -
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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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103A GLU* 4.9 5.3 + - - -
106A LEU* 2.9 23.8 + - + +
107A LYS* 3.1 56.8 + - - +
109A LEU* 1.3 78.3 - - + +
111A ASP* 1.3 66.0 + - - +
113A ALA 4.0 8.4 - - - +
115A SER* 6.5 1.3 - - - +
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Residues in contact with ASP 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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78A SER* 5.6 0.3 - - - -
107A LYS* 2.9 50.6 + - - +
108A GLU* 3.8 5.6 - - - +
109A LEU 3.2 0.2 - - - -
110A ARG* 1.3 82.9 + - - +
112A HIS* 1.4 78.2 + - + +
113A ALA 5.1 0.2 - - - -
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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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76A ILE 4.1 15.6 + - - -
77A THR* 4.3 2.5 - - - -
78A SER* 3.0 48.6 + - - +
81A TYR* 3.3 30.1 - - + +
82A ARG* 5.6 0.2 - - - -
108A GLU* 2.9 36.5 + - + +
111A ASP* 1.4 94.5 + - + +
113A ALA* 1.3 60.5 + - - +
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Residues in contact with ALA 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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81A TYR* 3.8 21.1 - - + +
109A LEU* 2.8 43.1 + - + +
110A ARG* 4.0 8.5 - - - +
111A ASP 5.1 0.2 - - - -
112A HIS* 1.3 79.5 - - - +
114A ASP* 1.3 68.8 + - - +
115A SER* 3.5 2.6 + - - -
117A ILE* 4.1 13.7 - - + -
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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