Contacts of the helix formed by residues 104 - 117 (chain A) in PDB entry 1OI4
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 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A LYS* 4.2 7.1 - - + +
100A TYR 5.1 3.1 - - - +
101A LEU* 3.1 15.7 + - - +
102A ARG 3.2 0.8 - - - -
103A GLY* 1.3 78.6 - - - +
105A ASN* 1.3 68.4 + - - +
106A ARG* 2.9 55.3 + - - +
107A PHE* 3.0 28.7 + - + -
108A VAL* 3.4 10.9 + - - +
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Residues in contact with ASN 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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103A GLY 4.1 1.8 + - - -
104A ASP* 1.3 75.9 + - - +
106A ARG* 1.3 68.9 + - - +
108A VAL* 3.7 9.4 - - - +
109A THR* 2.8 40.2 + - - +
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Residues in contact with ARG 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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58A LYS* 3.5 29.9 + - - +
78A SER* 4.8 1.6 + - - -
79A ILE* 3.1 35.6 - - + +
80A ASP* 2.9 43.9 + - - -
104A ASP* 2.9 32.1 + - - +
105A ASN* 1.3 90.1 - - - +
107A PHE* 1.3 57.7 + - - +
109A THR* 3.8 5.6 - - - +
110A PHE* 3.0 22.5 + - - +
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Residues in contact with PHE 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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29A LEU* 4.0 27.4 - - + +
56A ILE 4.2 6.7 - - - -
57A GLU* 3.6 38.4 - - - -
58A LYS* 3.8 13.7 - - + -
79A ILE* 3.4 30.7 - - + -
101A LEU* 3.7 47.6 - - + +
104A ASP* 3.0 35.8 + - + -
106A ARG* 1.3 73.5 - - - +
108A VAL* 1.3 60.8 + - - +
110A PHE* 3.6 2.5 - - - +
111A THR* 2.8 34.2 + - - -
130A LEU* 4.5 4.7 - - + -
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Residues in contact with VAL 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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102A ARG* 3.6 28.9 - - - +
104A ASP 3.6 14.8 - - - +
105A ASN* 3.3 10.0 + - - +
107A PHE* 1.3 76.9 - - - +
109A THR* 1.3 58.3 + - - +
111A THR* 3.3 6.5 + - - -
112A ARG* 2.9 39.0 + - - +
130A LEU* 4.6 4.0 - - + -
133A SER* 3.3 43.7 - - - +
134A ALA* 3.6 6.3 - - - +
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Residues in contact with THR 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 ASN* 2.8 24.8 + - - +
106A ARG* 3.8 5.4 - - - +
108A VAL* 1.3 74.9 - - - +
110A PHE* 1.3 60.4 + - - +
112A ARG* 3.7 21.3 + - - +
113A ASP* 2.9 48.3 + - - +
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Residues in contact with PHE 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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27A ALA* 4.2 6.3 - - + -
29A LEU* 3.9 28.0 - - + -
56A ILE* 4.2 4.5 - - + -
79A ILE* 4.2 16.6 - - + -
82A VAL* 4.1 19.7 - - + -
83A THR 3.8 6.1 - - - -
84A PRO* 3.6 39.4 - - + +
87A PHE* 3.9 24.9 - + - -
90A LEU* 4.2 17.5 - - + -
106A ARG 3.0 18.9 + - - +
107A PHE* 3.6 6.1 - - - +
109A THR* 1.3 76.3 - - - +
111A THR* 1.3 60.9 + - - +
113A ASP* 3.9 1.6 - - - +
114A PHE* 2.9 41.0 + + - +
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Residues in contact with THR 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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29A LEU* 3.4 16.8 - - - +
90A LEU* 4.4 12.5 - - + +
92A LEU* 4.3 10.8 - - + +
107A PHE 2.8 22.0 + - - -
108A VAL* 3.6 5.4 - - - -
110A PHE* 1.3 76.9 - - - +
112A ARG* 1.3 62.3 + - - +
114A PHE* 3.4 1.6 + - - +
115A VAL* 3.0 30.8 + - + +
130A LEU* 3.9 26.7 - - - +
131A LEU* 3.8 28.5 - - + -
134A ALA* 4.1 6.1 - - + -
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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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108A VAL* 2.9 35.7 + - - +
109A THR* 3.7 30.1 + - - +
111A THR* 1.3 76.5 - - - +
113A ASP* 1.3 65.5 + - - +
115A VAL* 3.3 2.8 + - - +
116A ASN* 2.9 49.6 + - - +
133A SER 3.9 5.5 + - - -
134A ALA* 3.2 35.1 + - + +
135A ASP* 5.4 1.4 - - - +
136A VAL* 4.0 8.2 - - + +
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Residues in contact with ASP 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 PRO* 4.0 18.7 - - + +
109A THR* 2.9 35.8 + - - +
110A PHE* 4.0 3.1 - - - +
112A ARG* 1.3 87.7 - - - +
114A PHE* 1.3 61.6 + - - +
116A ASN* 3.4 8.7 + - - +
117A SER* 3.1 22.5 + - - -
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Residues in contact with PHE 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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27A ALA* 5.3 0.2 - - + -
84A PRO* 3.4 40.8 - - + +
87A PHE* 3.8 14.8 - + + -
89A ALA* 3.3 30.7 - - - -
90A LEU* 3.5 20.6 - - + -
110A PHE* 2.9 28.4 + + + +
111A THR 3.7 3.6 - - - +
113A ASP* 1.3 77.7 - - - +
115A VAL* 1.3 61.1 + - - +
117A SER* 2.4 28.2 + - - -
118A GLY 3.7 1.2 + - - -
119A LYS* 3.5 28.6 + - + -
120A PRO 3.3 23.1 - - - -
121A VAL* 3.6 16.2 - - + -
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Residues in contact with VAL 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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90A LEU* 5.8 0.2 - - + -
111A THR* 3.0 22.8 + - + +
112A ARG 3.7 4.0 - - - +
114A PHE* 1.3 77.0 - - - +
116A ASN* 1.3 60.3 + - - +
118A GLY* 3.0 8.1 + - - -
121A VAL* 4.0 17.5 - - + -
131A LEU* 3.8 28.3 - - + -
136A VAL* 3.8 29.2 - - + +
140A ARG* 4.0 22.1 + - - +
170A GLN* 2.8 29.5 + - - +
171A LEU* 4.5 6.5 - - + -
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Residues in contact with ASN 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ARG* 2.9 40.1 + - - +
113A ASP* 3.7 9.3 + - - +
115A VAL* 1.3 78.0 - - - +
117A SER* 1.3 60.2 + - - +
118A GLY* 3.2 0.7 + - - -
136A VAL* 4.1 14.3 - - - +
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Residues in contact with SER 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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84A PRO* 5.9 2.9 - - - -
113A ASP 3.1 11.1 + - - -
114A PHE* 2.4 27.4 + - - -
116A ASN* 1.3 76.4 - - - +
118A GLY* 1.3 59.9 + - - +
119A LYS* 3.2 36.4 + - - +
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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