Contacts of the helix formed by residues 115 - 130 (chain A) in PDB entry 1I6P
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A GLY* 1.3 70.5 - - - -
116A ILE* 1.3 63.5 + - - +
117A ASN 3.1 1.2 + - - -
118A ASN* 3.1 40.6 + - + +
119A TRP* 4.1 1.6 + - - +
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Residues in contact with ILE 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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66A VAL* 4.0 37.0 - - + -
113A LEU* 3.5 42.0 - - + +
115A LEU* 1.3 78.4 - - - +
117A ASN* 1.3 64.9 + - - +
119A TRP* 3.0 31.5 + - + +
120A LEU* 3.0 24.2 + - + +
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Residues in contact with ASN 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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106A ALA 5.3 0.6 + - - -
110A ASN* 4.3 14.6 - - - +
111A PRO* 3.1 22.2 + - - +
112A GLU* 3.7 3.7 - - - -
113A LEU* 2.8 34.0 + - - +
114A GLY 2.9 19.1 + - - +
116A ILE* 1.3 78.0 - - - +
118A ASN* 1.3 62.2 + - - +
120A LEU* 3.4 16.1 + - - +
121A LEU* 3.2 28.5 + - + +
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Residues in contact with ASN 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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114A GLY 4.7 2.0 + - - -
115A LEU* 3.1 41.5 + - + +
117A ASN* 1.3 76.0 - - - +
119A TRP* 1.3 66.0 + - - +
121A LEU* 3.4 30.7 + - + +
122A HIS* 4.3 7.3 + - - -
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Residues in contact with TRP 119 (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 ASN* 3.7 33.0 - - + -
66A VAL* 2.8 41.9 + - + +
69A LEU* 3.4 20.3 - - + +
71A ILE* 3.6 29.2 - - + -
74A ASP* 3.9 26.7 - - + -
115A LEU 4.1 1.0 + - - +
116A ILE* 3.0 23.1 + - + +
118A ASN* 1.3 78.7 - - - +
120A LEU* 1.3 68.9 + - + +
121A LEU 3.3 1.0 + - - -
122A HIS* 3.4 25.3 + - - +
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Residues in contact with LEU 120 (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 VAL* 4.3 15.7 - - + -
103A GLY* 3.6 28.3 - - - +
106A ALA* 3.7 29.4 - - + -
107A ALA* 3.8 14.7 - - + +
113A LEU* 4.6 4.0 - - + -
116A ILE* 3.0 30.8 + - + +
117A ASN* 3.8 20.6 - - - +
118A ASN 3.3 0.4 - - - -
119A TRP* 1.3 77.3 - - + +
121A LEU* 1.3 59.4 + - - +
122A HIS 3.0 2.7 - - - -
123A ILE* 2.9 37.2 + - + +
124A ARG* 3.3 11.0 + - + +
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Residues in contact with LEU 121 (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 ASN* 5.8 2.2 - - - +
117A ASN* 3.2 17.8 + - + +
118A ASN* 3.6 22.7 - - - +
119A TRP 3.2 1.6 - - - -
120A LEU* 1.3 77.9 - - - +
122A HIS* 1.3 61.5 + - + +
124A ARG* 3.2 31.9 + - + +
125A ASP* 3.0 31.1 + - - +
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Residues in contact with HIS 122 (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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69A LEU* 4.1 13.5 - - + -
71A ILE* 3.4 51.2 - - + +
118A ASN 4.3 8.6 + - - -
119A TRP* 3.4 21.1 + - - +
120A LEU 3.0 0.8 - - - -
121A LEU* 1.3 78.7 - - + +
123A ILE* 1.3 61.4 + - - +
125A ASP* 3.5 21.5 + - - +
126A ILE* 3.4 20.4 - - - +
154A GLN* 6.2 0.7 - - - +
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Residues in contact with ILE 123 (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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67A ALA* 3.5 31.9 - - + -
69A LEU* 3.9 24.0 - - + -
103A GLY 4.1 8.7 - - - +
104A VAL* 4.4 12.3 - - + -
107A ALA* 3.5 16.8 - - + -
120A LEU* 2.9 30.3 + - + +
122A HIS* 1.3 76.5 - - - +
124A ARG* 1.3 64.3 + - - +
125A ASP 3.1 0.2 - - - -
126A ILE* 3.0 18.7 + - + +
127A TRP* 3.0 12.0 + - + +
146A LEU* 4.5 22.4 - - + -
150A ASN* 4.3 9.6 - - - +
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Residues in contact with ARG 124 (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 ALA* 2.8 50.6 + - - +
108A VAL 3.8 7.9 + - - -
110A ASN* 3.6 38.8 + - - +
120A LEU* 3.3 8.9 + - - +
121A LEU* 3.2 35.6 + - + +
123A ILE* 1.3 77.7 - - - +
125A ASP* 1.3 63.0 + - - +
127A TRP* 3.1 27.6 + - + +
128A PHE* 3.0 59.5 + - + -
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Residues in contact with ASP 125 (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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121A LEU* 3.0 21.6 + - - +
122A HIS* 3.5 21.8 + - - +
123A ILE 3.1 0.2 - - - -
124A ARG* 1.3 78.8 - - - +
126A ILE* 1.3 57.4 + - + +
128A PHE* 3.4 16.5 + - - +
129A LYS* 3.0 28.3 + - - +
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Residues in contact with ILE 126 (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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122A HIS 3.4 16.8 - - - +
123A ILE* 3.0 12.6 + - + +
125A ASP* 1.3 76.5 - - + +
127A TRP* 1.3 65.8 + - - +
129A LYS* 3.2 9.8 + - + +
130A HIS* 3.1 33.2 + - + +
146A LEU* 4.1 15.7 - - + +
149A LEU* 4.4 7.2 - - + -
150A ASN* 3.2 31.2 - - + +
153A GLU* 3.9 32.1 - - + -
154A GLN* 3.4 17.3 - - - +
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Residues in contact with TRP 127 (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 ALA 4.9 2.7 - - - -
108A VAL* 4.4 30.7 - - + +
123A ILE 3.0 10.7 + - - +
124A ARG* 3.1 38.1 + - + +
126A ILE* 1.3 78.5 - - - +
128A PHE* 1.3 90.8 + + - +
130A HIS 3.6 2.1 + - - -
131A SER* 3.3 22.2 + - - +
134A LEU* 3.4 26.4 - - + +
146A LEU* 4.1 27.3 - - + +
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Residues in contact with PHE 128 (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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124A ARG* 3.0 49.5 + - + -
125A ASP* 3.7 16.6 - - - +
127A TRP* 1.3 104.9 - + - +
129A LYS* 1.3 66.2 + - - +
131A SER* 2.9 27.0 + - - -
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Residues in contact with LYS 129 (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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125A ASP 3.0 14.6 + - - +
126A ILE* 3.2 14.1 + - + +
128A PHE* 1.3 78.6 - - - +
130A HIS* 1.3 75.1 + - + +
131A SER 3.6 1.6 + - - -
132A SER 5.3 0.3 + - - -
153A GLU* 2.9 34.0 + - - +
156A TYR* 5.2 6.5 - - - -
205A TYR* 3.2 15.2 + - - -
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Residues in contact with HIS 130 (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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126A ILE* 3.1 37.3 + - + +
127A TRP 3.7 4.3 - - - +
128A PHE 3.2 0.2 - - - -
129A LYS* 1.3 90.4 + - + +
131A SER* 1.3 63.8 + - - +
132A SER 3.4 2.9 - - - -
133A LEU* 3.3 19.3 + - + +
134A LEU* 3.0 25.7 + - + +
149A LEU* 3.7 34.1 - - + +
153A GLU* 2.6 30.2 + - - -
205A TYR* 4.1 5.6 - - - -
209A ILE* 3.8 26.1 - - + +
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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