Contacts of the helix formed by residues 116 - 128 (chain A) in PDB entry 4CQM
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 SER 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A HIS 3.3 6.6 + - - -
115A MET* 1.3 81.3 - - - +
117A GLU* 1.3 64.1 + - - +
118A ASP* 3.8 6.2 + - - +
119A ASP* 3.0 33.2 + - - -
120A TRP* 3.3 17.5 + - - +
132D PHE* 4.9 1.0 - - - -
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Residues in contact with GLU 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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116A SER* 1.3 73.3 - - - +
118A ASP* 1.3 62.1 + - - +
120A TRP* 3.3 7.2 + - - +
121A ASP* 2.9 46.4 + - - +
78D GLU* 5.3 4.2 - - - +
79D ALA* 3.4 32.1 + - + +
129D LYS* 2.9 30.2 + - - +
132D PHE* 5.5 4.5 - - - -
133D LEU* 5.3 3.1 - - + -
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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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116A SER* 3.3 6.3 + - - +
117A GLU* 1.3 79.3 - - - +
119A ASP* 1.3 65.9 + - - +
121A ASP* 4.1 13.6 - - - +
122A LYS* 3.0 40.7 + - - +
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Residues in contact with ASP 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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108A GLN* 3.3 37.5 + - + +
109A ASP 5.9 0.2 - - - -
110A GLU* 4.4 14.2 - - + +
114A HIS 4.9 0.5 - - - +
115A MET* 3.8 11.4 - - + -
116A SER* 3.0 36.4 + - - +
118A ASP* 1.3 77.8 - - - +
120A TRP* 1.3 60.9 + - - +
122A LYS* 3.5 9.7 + - - +
123A VAL* 3.3 14.2 - - - +
168A ASN* 3.0 17.0 + - - -
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Residues in contact with TRP 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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115A MET* 4.2 2.4 - - - +
116A SER 3.3 5.8 + - - +
117A GLU* 3.5 7.2 - - + +
118A ASP 3.2 0.2 - - - -
119A ASP* 1.3 79.4 - - - +
121A ASP* 1.3 90.1 + - - +
123A VAL* 3.3 4.3 + - - +
124A ILE* 3.1 43.9 + - + +
167A THR* 3.8 11.7 - - + -
168A ASN* 3.6 39.4 - - + +
171A ALA* 3.6 19.7 - - + -
124D ILE* 6.1 0.6 - - + +
128D LEU* 3.7 23.1 - - + -
129D LYS* 3.5 35.7 - - + +
132D PHE* 3.7 59.5 - + + -
179D LEU* 3.9 7.6 - - + -
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Residues in contact with ASP 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 GLU* 2.9 41.1 + - - +
118A ASP* 3.3 14.3 + - - +
120A TRP* 1.3 94.1 + - - +
122A LYS* 1.3 57.8 + - - +
124A ILE* 3.3 4.9 + - - +
125A ALA* 2.9 32.5 + - - +
129D LYS* 3.3 22.6 + - - +
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Residues in contact with LYS 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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106A ILE* 3.7 14.2 - - + +
108A GLN* 3.5 34.7 + - + +
118A ASP* 3.0 34.8 + - - +
119A ASP* 3.5 15.8 + - - +
121A ASP* 1.3 77.1 - - - +
123A VAL* 1.3 68.0 + - + +
125A ALA* 4.0 4.4 - - - +
126A VAL* 3.2 31.4 + - + +
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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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106A ILE* 4.0 12.3 - - + +
107A THR 4.5 2.0 - - - -
108A GLN* 3.7 26.0 - - + +
119A ASP 3.3 17.3 - - - +
120A TRP 3.3 6.8 + - - +
121A ASP 3.2 0.6 - - - -
122A LYS* 1.3 77.7 - - + +
124A ILE* 1.3 59.3 + - - +
127A ASN* 2.9 51.1 + - - +
168A ASN* 3.4 41.7 - - + +
169A TYR* 3.9 6.1 - - + -
172A SER* 3.8 3.6 - - - +
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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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120A TRP* 3.1 54.6 + - + +
121A ASP* 3.8 5.8 - - - +
123A VAL* 1.3 76.8 - - - +
125A ALA* 1.3 51.1 + - - +
128A LEU* 3.0 26.2 + - + -
129A LYS* 2.7 35.7 + - + +
168A ASN 3.7 20.4 - - - +
172A SER* 3.8 18.4 - - - +
120D TRP* 6.0 0.4 - - - +
124D ILE* 4.2 20.4 - - + -
128D LEU* 4.2 7.6 - - + -
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Residues in contact with ALA 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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77A SER* 3.3 23.8 - - - -
121A ASP 2.9 17.8 + - - +
122A LYS* 4.0 6.3 - - - +
124A ILE* 1.3 78.9 - - - +
126A VAL* 1.3 53.0 + - + +
129A LYS* 3.3 19.4 - - + +
130A GLY 2.6 28.4 + - - -
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Residues in contact with VAL 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 ASP* 5.1 4.0 - - - +
76A VAL* 3.9 13.3 - - + +
77A SER* 4.1 16.8 - - - +
104A ALA* 4.0 7.5 - - + +
105A GLY* 3.8 20.2 - - - +
106A ILE* 3.8 24.2 - - + +
122A LYS* 3.2 19.9 + - + +
125A ALA* 1.3 76.8 - - + +
127A ASN* 1.3 78.2 + - - +
130A GLY* 3.2 17.7 - - - -
131A THR 3.8 1.0 + - - -
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Residues in contact with ASN 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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104A ALA 4.5 5.6 - - - +
105A GLY* 3.3 5.7 - - - -
106A ILE* 2.8 47.7 + - - +
123A VAL* 2.9 25.4 + - - +
126A VAL* 1.3 77.5 - - - +
128A LEU* 1.3 55.6 + - - +
131A THR* 2.5 29.3 + - - -
169A TYR* 3.6 23.6 - - - -
172A SER* 3.6 15.2 + - - +
173A LYS* 3.8 17.0 + - + +
176A VAL* 3.5 9.1 - - - +
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Residues in contact with LEU 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 ILE* 3.0 22.7 + - + +
127A ASN* 1.3 77.7 - - - +
129A LYS* 1.3 65.3 + - - +
130A GLY 3.2 0.7 - - - -
131A THR* 3.2 4.9 + - - -
132A PHE* 3.0 21.3 + - - +
171A ALA 4.5 2.7 - - - +
172A SER* 3.7 21.5 - - - +
175A GLY* 3.5 35.0 - - - +
176A VAL* 3.6 7.0 - - - +
179A LEU* 3.9 13.5 - - + -
120D TRP* 3.7 15.9 - - + -
124D ILE* 4.3 8.3 - - + -
128D LEU* 3.8 29.2 - - + -
171D ALA* 4.1 3.1 - - + +
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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