Contacts of the helix formed by residues 122 - 132 (chain A) in PDB entry 4A9H
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 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A PHE* 3.4 13.2 - - - +
101A GLN* 3.4 23.7 - - - +
102A PRO* 3.4 28.7 - - + +
103A VAL 5.3 0.4 - - - +
120A PRO 5.6 0.2 - - - -
121A MET* 1.3 80.4 - - - +
123A MET* 1.3 62.6 + - - +
124A GLY* 2.9 25.1 + - - -
125A THR* 2.5 30.1 + - - -
126A ILE* 3.2 24.0 + - - +
148A MET* 3.8 11.7 - - - -
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Residues in contact with MET 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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87A MET* 3.5 8.5 - - + +
90A LEU* 3.6 38.8 - - + +
91A TRP* 3.8 19.1 - - + -
96A ALA* 3.8 29.8 - - + +
99A PHE* 2.9 33.1 + - + +
100A ARG* 5.3 1.1 - - + +
122A ASP* 1.3 69.2 - - - +
124A GLY* 1.3 60.3 + - - +
126A ILE* 3.8 7.9 - - - -
127A LYS* 2.9 30.5 + - - +
145A PHE* 4.3 9.6 - - + -
148A MET* 3.5 26.7 - - + -
169A LEU* 4.1 14.6 - - + -
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Residues in contact with GLY 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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91A TRP* 3.8 10.5 - - - -
100A ARG 3.3 19.8 + - - -
122A ASP* 2.9 10.0 + - - -
123A MET* 1.3 75.0 - - - +
125A THR* 1.3 59.8 + - - +
127A LYS* 3.4 3.0 + - - +
128A ARG* 2.9 40.2 + - - +
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Residues in contact with THR 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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102A PRO* 4.7 4.7 - - - +
121A MET* 3.8 18.1 - - + -
122A ASP* 2.5 34.3 + - - -
124A GLY* 1.3 77.1 - - - +
126A ILE* 1.3 61.8 + - - +
128A ARG* 3.4 29.1 + - - +
129A ARG* 2.9 56.8 + - + +
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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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87A MET* 3.6 20.2 - - + -
121A MET* 3.9 8.1 - - + -
122A ASP 3.2 20.4 + - - +
123A MET* 4.0 2.9 - - - +
124A GLY 3.3 0.4 - - - -
125A THR* 1.3 75.2 - - - +
127A LYS* 1.3 57.3 + - - +
129A ARG* 3.1 2.9 + - - +
130A LEU* 2.9 30.8 + - + +
135A TYR* 3.7 15.7 - - - +
141A CYS* 3.9 22.9 - - - -
144A ASP* 3.7 21.3 - - + +
145A PHE* 3.5 48.5 - - + +
148A MET* 4.8 3.6 - - + -
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Residues in contact with LYS 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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83A HIS* 5.1 5.6 - - - +
87A MET* 3.6 25.7 - - + +
91A TRP* 3.9 49.2 - - + +
123A MET 2.9 19.5 + - - +
124A GLY* 3.7 5.2 - - - +
126A ILE* 1.3 76.2 - - - +
128A ARG* 1.3 58.3 + - - +
130A LEU* 3.3 7.5 + - - +
131A GLU* 2.9 63.5 + - + +
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Residues in contact with ARG 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 GLY* 2.9 36.1 + - - +
125A THR* 3.6 29.9 + - - +
127A LYS* 1.3 76.3 - - - +
129A ARG* 1.3 57.9 + - + +
131A GLU* 3.2 13.1 + - - +
132A ASN* 2.9 55.0 + - - +
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Residues in contact with ARG 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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119A GLN* 5.6 0.6 + - - -
121A MET* 3.7 11.5 - - - +
125A THR* 2.9 40.1 + - + +
126A ILE 3.5 7.4 - - - +
128A ARG* 1.3 73.6 - - + +
130A LEU* 1.3 64.1 + - - +
132A ASN* 3.4 1.7 + - - -
133A ASN 3.2 3.3 + - - -
134A TYR* 2.8 85.0 + - + -
135A TYR* 3.5 25.4 + - + -
144A ASP* 2.8 33.3 + - - -
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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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79A LEU* 4.0 31.4 - - + +
82A LEU* 4.3 3.8 - - + +
83A HIS* 3.8 39.2 + - + +
87A MET* 4.2 18.4 - - + -
126A ILE* 2.9 34.0 + - + +
127A LYS* 3.6 6.7 - - - +
129A ARG* 1.3 76.3 - - - +
131A GLU* 1.3 62.6 + - - +
132A ASN 3.3 0.7 + - - -
133A ASN* 3.3 17.7 + - - +
135A TYR* 3.8 22.0 - - + -
141A CYS* 4.0 14.8 - - - -
145A PHE* 5.2 0.7 - - + -
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Residues in contact with GLU 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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83A HIS* 3.7 22.5 + - + +
127A LYS* 2.9 57.4 + - - +
128A ARG* 3.7 13.9 + - - +
130A LEU* 1.3 75.0 - - - +
132A ASN* 1.3 66.2 + - - +
133A ASN* 3.4 7.3 + - - +
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Residues in contact with ASN 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 ARG* 2.9 38.5 + - - +
129A ARG* 4.3 3.5 - - - +
130A LEU 3.2 0.4 - - - -
131A GLU* 1.3 85.2 - - - +
133A ASN* 1.3 72.9 + - - +
134A TYR* 3.1 7.0 + - + +
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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