Contacts of the helix formed by residues 124 - 132 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ASN* 4.2 14.6 - - - +
23A ALA* 3.7 33.2 - - + +
24A MET* 3.7 31.6 - - - -
27A ALA* 4.1 6.6 - - + +
114E TYR* 2.8 33.0 + - + +
115E LEU* 5.1 1.3 - - + -
123E SER* 1.3 71.2 - - - +
125E SER* 1.3 58.3 + - - +
126E ALA 3.2 1.3 - - - -
127E LEU* 2.9 29.1 + - + +
128E ASN 3.7 1.7 + - - -
183E HIS* 4.0 22.0 - - + +
186E ILE* 3.9 20.2 - - + -
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Residues in contact with SER 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E LEU* 3.4 35.5 - - - +
114E TYR 3.7 1.4 + - - -
115E LEU* 2.7 41.4 + - - +
117E LYS* 6.2 1.6 - - - -
123E SER* 3.2 12.1 + - - -
124E ILE* 1.3 78.5 - - - +
126E ALA* 1.3 57.3 + - - +
128E ASN* 2.8 24.3 + - - +
129E LEU* 3.1 12.4 + - - +
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Residues in contact with ALA 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E SER* 4.0 5.7 + - - +
124E ILE 3.2 1.0 - - - -
125E SER* 1.3 78.0 - - - +
127E LEU* 1.3 57.3 + - - +
129E LEU* 3.3 17.1 + - + +
130E MET* 3.0 26.3 + - - +
175E VAL 4.7 2.1 - - - +
178E LYS* 3.8 27.1 - - + +
179E GLY* 3.7 22.6 + - - +
182E ASP* 4.1 13.9 - - + +
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Residues in contact with LEU 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A MET* 3.5 40.4 - - + -
27A ALA* 3.6 12.1 - - + -
124E ILE* 2.9 20.8 + - + +
126E ALA* 1.3 78.7 - - - +
128E ASN* 1.3 56.2 + - - +
130E MET* 3.5 16.0 - - + +
131E ASN* 2.8 42.9 + - - +
179E GLY* 2.9 37.5 - - - +
180E MET* 4.0 4.0 - - - +
183E HIS* 3.8 22.0 - - + +
1698E FER 5.5 1.3 - - - +
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Residues in contact with ASN 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU 3.2 21.2 + - - -
27A ALA* 3.4 19.9 + - + +
33E PRO* 3.5 13.3 + - - +
36E LEU* 3.5 21.1 - - + +
37E LYS* 3.1 29.5 - - - +
40E LEU* 3.7 13.9 - - + +
115E LEU* 6.2 1.1 - - + -
124E ILE 3.7 0.8 + - - -
125E SER* 2.8 13.4 + - - +
127E LEU* 1.3 75.6 - - - +
129E LEU* 1.3 65.2 + - - +
130E MET 3.0 1.3 - - - -
132E GLN* 2.8 39.0 + - - +
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Residues in contact with LEU 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E LYS* 3.7 20.8 - - + +
40E LEU* 3.8 30.1 - - + +
41E GLU* 3.8 31.6 - - + +
125E SER* 3.1 18.8 + - - +
126E ALA* 3.6 15.9 - - + +
128E ASN* 1.3 77.1 - - - +
130E MET* 1.3 61.1 + - - +
133E ASP* 3.6 19.4 + - - +
175E VAL* 3.7 13.1 - - + +
178E LYS* 6.4 0.4 - - + -
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Residues in contact with MET 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E ALA 3.0 16.7 + - - +
127E LEU* 3.5 13.7 - - + +
128E ASN 3.0 0.2 - - - -
129E LEU* 1.3 75.5 - - - +
131E ASN* 1.3 81.2 + - - +
132E GLN 3.2 1.3 - - - -
133E ASP* 3.0 19.6 + - - +
136E LEU* 3.5 18.6 - - + +
172E PHE* 4.8 2.0 - - + -
175E VAL* 3.7 17.0 - - + +
176E PHE* 3.7 45.8 - - + +
179E GLY* 4.5 1.8 - - - -
180E MET* 3.9 18.6 - - - +
1698E FER 3.0 40.6 - - + +
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Residues in contact with ASN 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA* 3.4 24.6 - - - +
28A SER* 3.8 17.1 - - - -
30A SER* 4.3 2.4 + - - +
127E LEU* 2.8 29.1 + - - +
130E MET* 1.3 81.8 - - - +
132E GLN* 1.3 64.0 + - - +
133E ASP 3.3 1.0 + - - -
136E LEU* 4.0 19.5 - - - +
137E MET* 3.7 14.0 + - - +
140E TRP* 5.3 1.7 + - - -
316E ILE* 6.0 0.7 - - - +
319E ILE* 3.7 16.8 - - + +
323E HIS* 5.8 1.0 - - - -
1698E FER 3.1 28.9 + - - +
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Residues in contact with GLN 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA 2.8 29.2 + - - +
28A SER* 3.7 2.4 - - - -
29A ALA 3.7 2.6 + - - -
30A SER* 2.9 38.0 + - - -
141A TYR* 3.5 10.6 - - - -
33E PRO* 3.9 18.6 - - + +
34E MET* 3.7 23.2 - - - +
37E LYS* 3.1 31.1 + - + +
128E ASN* 2.8 40.9 + - - +
131E ASN* 1.3 77.1 - - - +
133E ASP* 1.3 65.2 + - - +
137E MET* 3.7 7.7 - - - +
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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