Contacts of the helix formed by residues 115 - 130 (chain B) in PDB entry 1I6O
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 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A LEU* 3.9 30.5 - - + +
78A LEU* 4.1 14.8 - - + +
79A SER* 4.8 2.9 + - - +
82A GLN* 3.5 20.3 + - + +
163A ILE* 4.0 28.5 - - + -
114B GLY* 1.3 69.0 - - - -
116B ILE* 1.3 62.1 + - - +
117B ASN 3.1 0.3 + - - -
118B ASN* 3.0 40.3 + - - +
119B TRP 4.3 0.7 + - - -
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Residues in contact with ILE 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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79A SER* 3.7 38.1 - - - +
82A GLN* 2.7 24.2 + - - +
83A TYR* 3.9 27.1 - - + -
87A VAL* 4.7 0.7 - - + -
66B VAL* 4.0 26.0 - - + -
113B LEU* 3.5 33.0 - - + +
114B GLY 4.2 0.9 - - - +
115B LEU* 1.3 73.6 - - - +
117B ASN* 1.3 66.0 + - - +
118B ASN 3.1 1.0 + - - -
119B TRP* 3.1 10.3 + - + -
120B LEU* 3.1 29.1 + - + +
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Residues in contact with ASN 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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106B ALA 4.6 4.9 + - - -
110B ASN* 4.2 13.3 + - - +
111B PRO 3.2 17.8 + - - +
112B GLU* 3.7 3.3 - - - -
113B LEU* 2.8 38.1 + - - +
114B GLY 2.9 15.6 + - - +
116B ILE* 1.3 77.9 - - - +
118B ASN* 1.3 61.9 + - - +
120B LEU* 3.4 22.9 + - - +
121B LEU* 3.2 28.4 + - + +
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Residues in contact with ASN 118 (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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75A LEU* 4.9 14.1 - - + +
114B GLY 4.7 1.8 + - - -
115B LEU* 3.0 39.0 + - - +
116B ILE 3.0 0.8 - - - -
117B ASN* 1.3 76.0 - - - +
119B TRP* 1.3 66.8 + - - +
121B LEU* 3.2 32.6 + - + +
122B HIS* 4.2 7.3 + - - -
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Residues in contact with TRP 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.2 14.7 - - + +
76A ASN* 3.5 44.2 - - + -
79A SER* 3.7 29.1 + - - +
80A VAL* 6.5 0.2 - - + -
65B ASN* 3.5 28.5 - - + -
66B VAL* 2.8 41.7 + - + +
69B LEU* 3.4 19.1 - - + +
71B ILE* 3.4 31.2 - - + -
74B ASP* 3.7 12.8 - - + -
115B LEU 4.3 0.4 + - - -
116B ILE* 3.1 13.8 + - + +
118B ASN* 1.3 79.4 - - - +
120B LEU* 1.3 67.0 + - + +
121B LEU 3.3 0.7 + - - -
122B HIS* 3.4 26.6 + + - +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A TYR* 5.7 0.7 - - + -
66B VAL* 4.2 15.7 - - + -
103B GLY* 3.6 25.4 - - - +
106B ALA* 3.6 30.1 - - + -
107B ALA* 3.9 15.8 - - + +
113B LEU* 4.7 2.9 - - + -
116B ILE* 3.1 27.2 + - + +
117B ASN* 3.8 22.9 - - - +
118B ASN 3.2 0.4 - - - -
119B TRP* 1.3 79.8 - - + +
121B LEU* 1.3 59.2 + - - +
122B HIS 3.0 2.7 - - - -
123B ILE* 2.9 38.7 + - + +
124B ARG* 3.2 11.7 + - + +
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Residues in contact with LEU 121 (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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110B ASN* 5.8 1.6 - - - +
117B ASN* 3.2 20.8 + - + +
118B ASN* 3.2 27.0 + - + +
120B LEU* 1.3 77.1 - - - +
122B HIS* 1.3 56.8 + - + +
123B ILE 3.1 0.2 - - - -
124B ARG* 3.2 28.0 + - + +
125B ASP* 3.0 35.9 + - - +
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Residues in contact with HIS 122 (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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69B LEU* 4.0 14.6 - - + -
71B ILE* 3.6 45.7 - - + +
118B ASN 4.2 6.4 + - - -
119B TRP* 3.4 25.7 + + - +
120B LEU 3.0 1.0 - - - -
121B LEU* 1.3 79.2 - - + +
123B ILE* 1.3 60.9 + - - +
125B ASP* 3.7 18.8 + - - +
126B ILE* 3.5 19.7 - - - +
154B GLN* 5.4 1.6 + - - +
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Residues in contact with ILE 123 (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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67B ALA* 3.4 33.2 - - + -
69B LEU* 3.9 25.1 - - + -
104B VAL* 4.3 15.7 - - + -
107B ALA* 3.7 15.5 - - + -
120B LEU* 2.9 28.3 + - + +
122B HIS* 1.3 76.4 - - - +
124B ARG* 1.3 63.6 + - - +
125B ASP 3.1 1.6 - - - -
126B ILE* 3.1 9.7 + - + +
127B TRP* 3.0 18.7 + - - +
146B LEU* 4.1 24.4 - - + +
150B ASN* 3.9 15.0 - - + +
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Residues in contact with ARG 124 (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 ALA* 2.8 50.6 + - - +
108B VAL* 3.3 18.6 + - - +
110B ASN* 3.6 26.8 - - - +
120B LEU* 3.2 12.6 + - - +
121B LEU* 3.2 32.5 + - + +
123B ILE* 1.3 75.0 - - - +
125B ASP* 1.3 65.9 + - - +
127B TRP* 3.2 17.4 + - + +
128B PHE* 3.0 61.2 + - + +
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Residues in contact with ASP 125 (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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121B LEU* 3.0 22.7 + - - +
122B HIS* 3.7 21.4 + - - +
123B ILE 3.1 0.4 - - - -
124B ARG* 1.3 78.0 - - - +
126B ILE* 1.3 58.4 + - + +
128B PHE* 3.5 7.9 + - - +
129B LYS* 2.9 29.2 + - - +
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Residues in contact with ILE 126 (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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122B HIS 3.5 16.6 - - - +
123B ILE* 3.1 8.9 + - - +
125B ASP* 1.3 76.5 - - + +
127B TRP* 1.3 66.5 + - - +
128B PHE 3.1 0.2 - - - -
129B LYS* 3.2 7.5 + - + -
130B HIS* 3.1 42.6 + - + +
146B LEU* 3.9 8.9 - - + +
149B LEU* 3.9 16.4 - - + -
150B ASN* 3.4 30.3 - - + +
153B GLU* 3.5 38.1 - - + -
154B GLN* 3.7 6.5 - - - +
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Residues in contact with TRP 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B VAL* 3.9 35.7 - - + +
123B ILE 3.0 12.1 + - - +
124B ARG* 3.4 24.1 - - + +
126B ILE* 1.3 78.3 - - - +
128B PHE* 1.3 87.8 + + - +
131B SER* 3.4 11.7 + - - -
134B LEU* 3.3 45.8 - - + +
142B ARG* 3.9 44.2 - - + -
143B LEU* 5.0 1.8 - - + -
146B LEU* 3.5 30.9 - - + +
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Residues in contact with PHE 128 (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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124B ARG* 3.0 46.9 + - + +
125B ASP* 3.8 7.9 - - - +
127B TRP* 1.3 97.2 - + - +
129B LYS* 1.3 67.5 + - - +
130B HIS 3.1 1.6 - - - -
131B SER* 2.8 29.0 + - - -
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Residues in contact with LYS 129 (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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125B ASP 2.9 19.6 + - - +
126B ILE* 3.5 9.2 - - + +
128B PHE* 1.3 76.4 - - - +
130B HIS* 1.3 77.2 + - + +
131B SER* 3.7 1.7 + - - -
132B SER 5.3 0.2 + - - -
153B GLU* 3.1 22.9 + - - +
156B TYR* 5.5 3.8 - - - -
205B TYR* 2.9 27.5 + - - -
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Residues in contact with HIS 130 (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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126B ILE* 3.1 37.8 + - + +
127B TRP 3.7 4.3 - - - -
129B LYS* 1.3 97.8 + - + +
131B SER* 1.3 63.3 + - - +
132B SER 3.1 4.7 + - - +
133B LEU* 3.2 13.8 + - + +
134B LEU* 3.0 23.1 + - + +
149B LEU* 3.7 29.7 - - + +
153B GLU* 2.9 28.1 + - - -
205B TYR* 4.4 0.7 - - - -
209B ILE* 3.8 33.6 - - + +
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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