Contacts of the helix formed by residues 124 - 136 (chain A) in PDB entry 2K27
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 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A VAL 3.9 0.6 + - - -
123A PRO* 1.3 74.6 - - - +
125A VAL* 1.3 64.3 + - - +
126A SER* 3.8 12.6 - - - -
127A SER* 3.0 32.3 + - - -
128A ILE* 3.1 14.1 + - - +
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Residues in contact with VAL 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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104A ALA* 4.1 22.5 - - + +
105A TRP* 4.1 29.4 - - + +
108A ARG* 5.1 12.0 - - - +
123A PRO 3.6 2.4 + - - -
124A SER* 1.3 70.1 - - - +
126A SER* 1.3 66.7 + - - +
128A ILE* 3.2 24.4 - - + +
129A ASN* 3.4 11.4 + - - +
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Residues in contact with SER 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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124A SER* 3.8 12.0 - - - -
125A VAL* 1.3 84.0 - - - +
127A SER* 1.3 65.7 + - - +
129A ASN* 3.6 16.3 - - - +
130A ARG* 4.1 4.7 + - - +
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Residues in contact with SER 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 5.8 5.2 - - - -
123A PRO* 5.4 3.8 - - - -
124A SER* 3.0 27.7 + - - -
126A SER* 1.3 76.7 + - - +
128A ILE* 1.3 67.5 + - - +
129A ASN 3.1 1.3 - - - -
130A ARG* 3.0 39.3 + - - +
131A ILE* 3.5 4.3 - - - +
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Residues in contact with ILE 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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89A VAL* 4.5 10.8 - - + +
92A ILE* 3.6 50.2 - - + +
96A LYS* 4.8 1.8 + - - +
104A ALA* 3.3 40.6 - - + +
108A ARG* 4.9 4.5 - - + -
123A PRO* 3.9 17.9 - - + +
124A SER 3.1 9.8 + - - +
125A VAL* 3.2 26.9 - - - +
127A SER* 1.3 74.1 - - - +
129A ASN* 1.3 61.9 + - - +
131A ILE* 3.2 26.9 + - + +
132A ILE* 3.6 10.2 + - - +
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Residues in contact with ASN 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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104A ALA* 5.4 1.8 - - + -
125A VAL 3.4 9.6 + - - +
126A SER* 3.6 16.2 - - - +
128A ILE* 1.3 81.4 - - - +
130A ARG* 1.3 63.5 + - - +
132A ILE* 3.1 37.1 + - - +
133A ARG* 3.4 14.0 + - - +
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Residues in contact with ARG 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 SER 4.1 3.8 + - - +
127A SER* 3.0 30.7 + - - +
129A ASN* 1.3 79.1 + - - +
131A ILE* 1.3 69.4 + - + +
133A ARG* 3.1 54.9 + - - +
134A THR* 3.8 5.4 - - - +
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Residues in contact with ILE 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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89A VAL* 3.5 34.8 - - + +
93A GLY* 5.0 16.6 - - - -
96A LYS* 6.3 0.2 - - - +
127A SER 3.5 13.7 - - - +
128A ILE* 3.4 19.1 - - + +
129A ASN 3.1 0.6 - - - -
130A ARG* 1.3 85.8 - - + +
132A ILE* 1.3 64.6 + - + +
134A THR* 2.8 29.1 + - - +
135A LYS* 3.3 24.9 - - + +
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Residues in contact with ILE 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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96A LYS* 3.4 44.9 - - + +
104A ALA* 4.2 20.0 - - + +
128A ILE 3.6 8.5 - - - +
129A ASN* 3.1 27.5 + - - +
131A ILE* 1.3 76.1 - - + +
133A ARG* 1.3 64.2 + - - +
135A LYS* 2.9 23.7 + - + +
136A VAL* 3.1 21.3 + - + +
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Residues in contact with ARG 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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129A ASN* 3.4 11.7 + - - +
130A ARG* 3.1 57.3 + - - +
132A ILE* 1.3 77.7 - - - +
134A THR* 1.3 78.9 + - - +
135A LYS 3.1 1.2 + - - -
136A VAL 3.7 10.3 - - - -
137A GLN* 3.0 46.9 + - + +
140A PHE* 5.7 9.9 - - + -
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Residues in contact with THR 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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130A ARG 3.8 10.1 - - - +
131A ILE* 2.8 17.2 + - - +
133A ARG* 1.3 99.2 - - - +
135A LYS* 1.3 82.4 + - - +
137A GLN* 5.1 1.6 - - - -
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Residues in contact with LYS 135 (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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93A GLY* 6.5 0.7 - - - -
97A ARG* 6.4 2.9 - - - +
131A ILE* 3.3 34.6 - - + +
132A ILE* 2.9 10.1 + - + +
133A ARG 3.8 0.2 - - - -
134A THR* 1.3 98.2 + - - +
136A VAL* 1.3 71.9 + - + +
137A GLN 4.1 0.7 - - - -
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Residues in contact with VAL 136 (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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132A ILE* 3.1 18.2 + - + +
133A ARG* 3.3 10.1 + - - -
135A LYS* 1.3 88.8 - - + +
137A GLN* 1.3 62.1 + - - +
138A GLN* 5.7 3.4 - - - +
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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