Contacts of the helix formed by residues 124 - 132 (chain A) in PDB entry 1KYZ
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 ILE 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A TYR* 3.9 28.4 + - + +
115A LEU* 3.8 13.5 - - + -
123A SER* 1.3 69.8 + - - +
125A SER* 1.3 54.6 + - - +
126A ALA 3.0 2.9 - - - -
127A LEU* 2.7 38.0 + - + +
128A ASN* 3.1 7.4 + - - +
182A ASP* 5.6 0.7 - - - -
183A HIS* 5.0 7.0 - - + +
186A ILE* 4.1 31.6 - - + +
20E ASN* 4.6 4.3 - - - +
23E ALA* 4.1 12.1 - - + +
24E MET* 3.8 33.7 - - - -
27E ALA* 4.0 17.3 - - + -
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Residues in contact with SER 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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40A LEU* 3.8 31.0 - - - -
115A LEU* 3.8 11.2 + - - +
117A LYS* 4.6 12.8 - - - +
123A SER* 3.0 22.3 + - - -
124A ILE* 1.3 78.1 - - - +
126A ALA* 1.3 63.5 + - - +
128A ASN* 2.9 27.4 + - - +
129A LEU* 3.0 20.5 + - - +
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Residues in contact with ALA 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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123A SER 3.2 12.7 + - - +
124A ILE 2.9 0.4 + - - -
125A SER* 1.3 82.4 + - - +
127A LEU* 1.3 57.3 + - + +
129A LEU* 3.5 15.1 + - + +
130A MET* 3.0 26.3 + - - +
175A VAL 4.8 1.6 - - - +
178A LYS* 3.7 19.3 - - + +
179A GLY* 3.7 24.4 + - - +
182A ASP* 3.8 12.6 - - + +
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Residues in contact with LEU 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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124A ILE* 2.7 21.7 + - + +
126A ALA* 1.3 77.7 - - + +
128A ASN* 1.3 57.7 + - - +
130A MET* 4.2 13.5 - - - -
131A ASN* 2.8 45.8 + - - +
179A GLY* 3.3 30.3 - - - +
180A MET* 5.1 3.6 - - - -
182A ASP* 6.1 0.4 - - + -
183A HIS* 3.8 34.3 - - + +
366A FER 5.4 5.8 - - - +
24E MET* 3.8 32.3 - - + -
27E ALA* 3.9 11.4 - - + -
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Residues in contact with ASN 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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33A PRO 5.7 0.6 - - - +
36A LEU* 3.4 26.9 - - - +
37A LYS* 4.0 9.5 - - + +
40A LEU* 3.4 21.7 - - + +
115A LEU* 4.1 11.3 - - - +
124A ILE 3.1 18.8 + - - -
125A SER* 2.9 17.6 + - - +
127A LEU* 1.3 76.1 - - - +
129A LEU* 1.3 62.6 + - - +
132A GLN* 2.9 32.6 + - - +
23E ALA 4.8 0.6 + - - -
26E LEU* 3.6 3.3 - - - +
27E ALA* 3.5 33.4 + - - +
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Residues in contact with LEU 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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37A LYS* 4.0 26.4 - - + +
40A LEU* 4.2 17.7 - - + +
41A GLU* 3.6 33.0 - - + +
117A LYS* 6.5 0.9 - - - -
125A SER* 3.0 21.1 + - - +
126A ALA* 3.7 14.1 - - - +
128A ASN* 1.3 79.0 - - - +
130A MET* 1.3 60.1 + - - +
133A ASP* 3.5 21.8 + - - +
175A VAL* 3.7 13.6 - - + +
178A LYS* 6.4 2.7 - - + -
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Residues in contact with MET 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 ALA 3.0 14.5 + - - +
127A LEU* 3.7 12.6 - - - +
128A ASN 3.2 0.2 - - - -
129A LEU* 1.3 75.5 - - - +
131A ASN* 1.3 74.1 + - - +
132A GLN 3.2 1.6 - - - -
133A ASP* 3.0 19.4 + - - +
136A LEU* 3.6 21.4 - - + +
172A PHE* 4.9 1.1 - - + -
175A VAL* 3.7 13.2 - - + +
176A PHE* 2.6 57.2 - - + +
179A GLY* 3.1 27.6 - - - -
180A MET* 3.1 22.7 - - + +
366A FER 4.8 6.7 - - - -
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Residues in contact with ASN 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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127A LEU* 2.8 26.5 + - - +
130A MET* 1.3 84.5 - - - +
132A GLN* 1.3 68.7 + - - +
133A ASP 3.3 0.7 + - - -
136A LEU* 4.2 17.3 - - - +
137A MET* 3.8 13.7 - - - +
140A TRP* 5.3 1.9 + - - -
319A ILE* 3.9 11.4 - - + +
366A FER 3.4 27.1 + - - +
27E ALA* 2.8 33.4 - - - +
28E SER* 3.7 13.6 - - - -
30E SER* 4.4 1.6 + - - +
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Residues in contact with GLN 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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33A PRO* 4.1 17.0 - - + +
34A MET* 3.7 23.9 - - - +
37A LYS* 3.0 34.3 + - + +
128A ASN* 2.9 32.2 + - - +
130A MET 3.2 1.2 - - - -
131A ASN* 1.3 78.0 - - - +
133A ASP* 1.3 63.3 + - - +
134A LYS 3.6 0.5 + - - -
137A MET* 3.8 7.8 - - - +
26E LEU 4.5 1.1 - - - +
27E ALA 3.0 16.8 - - - +
28E SER* 3.6 16.4 - - - +
29E ALA 3.8 0.6 - - - +
30E SER* 2.6 45.0 + - - +
141E TYR* 3.6 9.7 - - - -
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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