Contacts of the helix formed by residues 121 - 134 (chain A) in PDB entry 1INZ
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 VAL 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A ASP* 5.2 6.7 + - - +
119A GLN* 3.2 7.1 - - - +
120A GLY* 1.3 76.9 - - - +
122A ASN* 1.3 93.5 + - + +
123A VAL 2.9 1.6 - - - -
124A ARG* 2.7 38.3 + - + +
125A GLU* 3.1 29.2 + - + +
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Residues in contact with ASN 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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71A TRP* 4.1 21.0 - - + -
75A TYR* 3.1 44.2 + - + -
119A GLN 5.0 1.3 - - - +
121A VAL* 1.3 92.4 - - + +
123A VAL* 1.3 59.5 + - - +
125A GLU* 4.0 3.6 + - - +
126A LYS* 3.2 14.2 + - - +
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Residues in contact with VAL 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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71A TRP* 3.6 26.2 - - + -
74A VAL* 2.8 41.1 - - + -
75A TYR* 3.7 10.3 - - - +
78A MET* 2.8 37.7 - - + +
106A LEU* 4.3 5.3 - - + +
109A PHE* 4.8 12.1 - - + +
120A GLY* 2.9 29.1 - - - +
121A VAL 2.7 4.2 + - - -
122A ASN* 1.3 77.2 - - - +
124A ARG* 1.3 80.8 + - + +
126A LYS 3.1 5.2 + - - -
127A ALA* 3.1 2.3 + - - +
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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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106A LEU 4.1 9.2 - - - +
107A LYS* 2.7 48.1 + - + +
109A PHE 5.3 2.5 - - - +
110A GLN* 5.2 21.6 - - - +
120A GLY 3.7 11.4 - - - +
121A VAL* 2.7 34.8 + - + +
123A VAL* 1.3 82.3 - - + +
125A GLU* 1.3 68.6 + - + +
127A ALA* 3.6 0.3 + - - +
128A LYS* 3.4 18.2 + - - +
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Residues in contact with GLU 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 VAL* 3.1 25.9 + - + +
122A ASN* 4.5 4.0 - - - +
124A ARG* 1.3 80.0 + - + +
126A LYS* 1.3 66.9 + - - +
128A LYS* 3.3 8.9 + - - +
129A GLN* 3.0 29.8 + - - +
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Residues in contact with LYS 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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75A TYR* 3.0 42.4 + - + +
78A MET* 3.5 27.7 - - + +
79A THR* 5.4 7.4 - - - +
82A GLU* 4.1 24.0 + - - -
122A ASN 3.2 16.4 + - - +
123A VAL 3.1 6.9 + - - +
125A GLU* 1.3 78.2 - - - +
127A ALA* 1.3 65.4 + - - +
129A GLN* 2.9 30.0 + - - +
130A LEU* 3.2 7.7 + - - +
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Residues in contact with ALA 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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78A MET* 2.8 23.8 - - + -
103A VAL* 3.1 19.2 - - - +
106A LEU* 3.0 38.4 - - + -
107A LYS 4.0 2.2 - - - +
123A VAL 3.1 4.9 + - - +
124A ARG 4.0 3.1 - - - +
126A LYS* 1.3 75.6 - - - +
128A LYS* 1.3 63.7 + - - +
129A GLN 3.2 0.3 + - - -
130A LEU* 3.3 8.1 + - - +
131A VAL* 3.2 20.3 + - - +
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Residues in contact with LYS 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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104A GLN* 4.9 11.7 - - - +
107A LYS* 3.7 31.8 - - + +
124A ARG 3.4 11.7 + - - +
125A GLU* 3.5 13.5 - - - +
126A LYS 3.2 0.2 - - - -
127A ALA* 1.3 78.9 - - - +
129A GLN* 1.3 63.4 + - - +
131A VAL* 3.4 7.5 + - - +
132A ALA* 2.9 36.1 + - + +
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Residues in contact with GLN 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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82A GLU* 4.5 11.2 - - - +
125A GLU* 3.0 16.2 + - - +
126A LYS* 2.9 23.4 + - - +
128A LYS* 1.3 75.9 - - - +
130A LEU* 1.3 69.1 + - - +
132A ALA* 2.7 19.9 + - - +
133A LEU* 3.0 37.4 + - + +
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Residues in contact with LEU 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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78A MET* 3.0 47.6 - - + +
81A MET* 3.6 25.6 - - + +
82A GLU* 3.4 27.2 + - + +
85A ILE* 3.0 37.7 - - + -
96A CYS* 4.2 1.8 - - - -
103A VAL* 3.7 7.6 - - + -
126A LYS* 3.2 6.0 + - + +
127A ALA 3.3 9.8 + - - +
129A GLN* 1.3 79.3 - - - +
131A VAL* 1.3 60.2 + - - +
133A LEU* 4.3 2.9 - - - +
134A LEU* 2.6 43.0 + - + +
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Residues in contact with VAL 131 (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 CYS* 5.5 1.6 - - - -
100A MET* 3.3 33.4 - - + -
103A VAL* 3.2 29.8 - - + +
104A GLN* 3.2 32.1 - - + +
127A ALA 3.2 17.7 - - - +
128A LYS* 3.7 6.3 - - - +
129A GLN 3.0 0.4 - - - -
130A LEU* 1.3 74.4 - - - +
132A ALA* 1.3 66.7 + - - +
134A LEU* 3.9 5.7 - - + +
135A ARG* 3.1 26.6 + - + +
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Residues in contact with ALA 132 (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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128A LYS* 2.9 33.9 + - + +
129A GLN* 2.7 22.7 + - + +
131A VAL* 1.3 72.2 - - - +
133A LEU* 1.3 62.6 + - + +
135A ARG 2.7 33.3 - - - +
136A ASP* 3.0 11.7 + - - +
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Residues in contact with LEU 133 (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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82A GLU* 5.2 11.9 - - + +
86A LYS* 5.8 7.6 - - + +
129A GLN* 3.0 45.3 + - + +
130A LEU* 4.3 4.0 - - - +
132A ALA* 1.3 82.5 - - + +
134A LEU* 1.3 62.3 + - + +
135A ARG* 2.7 7.3 + - - -
136A ASP* 3.9 7.8 + - - +
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Residues in contact with LEU 134 (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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82A GLU* 6.4 0.2 - - + -
85A ILE* 3.3 41.1 - - + -
93A SER* 3.9 16.8 - - - +
96A CYS* 3.0 43.7 - - + -
97A LYS* 5.2 10.6 - - + +
130A LEU* 2.6 30.7 + - + +
131A VAL* 4.0 4.9 - - - +
133A LEU* 1.3 80.0 - - + +
135A ARG* 1.3 67.3 + - + +
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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