Contacts of the helix formed by residues 112 - 125 (chain A) in PDB entry 3IIL
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 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A GLY 3.4 4.4 + - - +
111A TYR* 1.3 73.7 - - - +
113A GLU* 1.3 60.1 + - - +
114A LYS* 3.5 8.6 + - - +
115A LYS* 3.1 25.7 + - - +
116A LEU* 2.8 29.3 + - - +
181A SO4 3.2 28.2 + - - +
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Residues in contact with GLU 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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112A ASN* 1.3 71.1 - - - +
114A LYS* 1.3 57.3 + - - +
116A LEU* 3.4 10.7 + - + +
117A THR* 2.9 42.5 + - - +
181A SO4 2.8 32.0 + - - +
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Residues in contact with LYS 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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50A GLU* 3.5 50.0 + - - +
51A TYR* 6.0 4.0 - - + -
112A ASN* 3.4 9.8 + - - +
113A GLU* 1.3 78.1 - - - +
115A LYS* 1.3 58.6 + - - +
117A THR* 3.4 5.7 + - - -
118A ASP* 3.0 29.1 + - + +
181A SO4 4.9 1.0 + - - -
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Residues in contact with LYS 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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51A TYR 5.5 9.2 + - - +
52A ASP 6.0 0.4 + - - -
111A TYR* 3.9 46.1 - - + -
112A ASN* 3.1 21.8 + - - +
114A LYS* 1.3 73.8 - - - +
116A LEU* 1.3 66.3 + - - +
118A ASP* 3.4 5.3 + - + +
119A ASN* 2.9 39.8 + - - +
173A LI 4.0 18.9 - - - +
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Residues in contact with LEU 116 (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 TYR* 3.8 45.1 - - + +
106A LEU* 3.6 33.4 - - + +
107A GLU* 3.6 24.5 - - + +
111A TYR* 3.7 23.7 - - + +
112A ASN 2.8 19.8 + - - +
113A GLU* 3.6 8.3 - - + +
115A LYS* 1.3 76.8 - - - +
117A THR* 1.3 56.5 + - - +
119A ASN* 3.4 3.1 + - - +
120A ILE* 2.9 34.4 + - + +
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Residues in contact with THR 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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113A GLU* 2.9 28.2 + - - +
114A LYS* 3.8 6.1 - - - -
116A LEU* 1.3 73.8 - - - +
118A ASP* 1.3 65.7 + - - +
120A ILE* 3.3 9.6 + - + +
121A GLN* 2.9 48.8 + - + +
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Residues in contact with ASP 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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51A TYR* 3.3 44.3 + - + -
114A LYS* 3.0 20.3 + - + +
115A LYS* 3.8 6.7 - - - +
116A LEU 3.4 0.2 - - - -
117A THR* 1.3 76.1 - - - +
119A ASN* 1.3 64.0 + - - +
121A GLN* 3.5 10.6 + - - +
122A CYS* 3.0 27.0 + - - +
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Residues in contact with ASN 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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11A THR* 3.3 13.7 - - + +
12A PRO* 3.4 32.4 - - - +
102A LEU* 4.5 0.2 - - - +
106A LEU* 3.7 25.8 - - + -
111A TYR* 3.8 20.4 - - - -
115A LYS* 2.9 35.1 + - - +
116A LEU 3.9 0.4 - - - +
118A ASP* 1.3 82.8 + - - +
120A ILE* 1.3 66.3 + - - +
122A CYS* 3.2 6.2 + - - +
123A GLU* 3.1 19.6 + - - +
173A LI 4.5 4.9 - - - +
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Residues in contact with ILE 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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99A THR* 3.3 32.3 - - + +
102A LEU* 4.1 16.4 - - + -
103A TYR* 3.5 51.8 - - + +
106A LEU* 4.8 4.7 - - + -
116A LEU* 2.9 17.3 + - + +
117A THR* 3.5 17.3 - - + +
119A ASN* 1.3 77.5 - - - +
121A GLN* 1.3 63.3 + - + +
123A GLU* 3.4 5.0 + - - +
124A ILE* 3.0 31.1 + - + +
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Residues in contact with GLN 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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117A THR* 2.9 41.0 + - + +
118A ASP* 3.8 8.4 - - - +
120A ILE* 1.3 76.8 - - + +
122A CYS* 1.3 60.1 + - - +
124A ILE* 3.7 9.4 - - + -
125A PHE* 2.8 68.8 + - + -
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Residues in contact with CYS 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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11A THR* 4.1 7.2 + - + -
12A PRO* 5.5 1.6 - - - -
118A ASP* 3.0 17.6 + - - +
119A ASN* 3.3 14.8 - - - +
121A GLN* 1.3 77.6 - - - +
123A GLU* 1.3 59.4 + - - +
125A PHE* 5.2 0.2 - - - -
126A GLN 3.2 2.1 + - - -
127A VAL* 3.1 54.4 + - + +
128A LEU* 3.5 34.2 + - - -
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Residues in contact with GLU 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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11A THR* 2.6 36.2 + - - +
14A VAL* 3.8 9.5 - - - +
95A LEU 4.7 0.2 - - - +
96A ARG* 2.8 55.5 + - - +
97A THR 3.2 37.6 + - - +
99A THR* 4.6 9.4 - - - +
102A LEU* 3.6 22.2 - - + -
119A ASN 3.1 7.1 + - - +
120A ILE* 3.7 6.5 - - + +
122A CYS* 1.3 74.1 - - - +
124A ILE* 1.3 61.1 + - - +
126A GLN* 2.9 17.4 + - - +
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Residues in contact with ILE 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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96A ARG* 5.3 0.4 - - - +
99A THR* 4.1 28.9 - - + +
120A ILE* 3.0 17.8 + - + +
121A GLN* 3.6 17.0 - - + +
123A GLU* 1.3 77.4 - - - +
125A PHE* 1.3 80.1 + - + +
126A GLN* 3.2 11.8 + - - +
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Residues in contact with PHE 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 GLN* 2.8 52.9 + - + +
124A ILE* 1.3 94.7 - - + +
126A GLN* 1.3 70.2 + - - +
127A VAL* 3.2 19.7 + - + +
130A GLU* 4.5 10.2 - - - +
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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