Contacts of the helix formed by residues 127 - 133 (chain A) in PDB entry 1KEK
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 HIS 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ALA* 3.9 10.8 - - + -
126A ASP* 1.3 80.0 - - - +
128A GLN* 1.3 64.8 + - - +
129A ASP 3.1 2.5 - - - -
130A ILE* 3.4 16.1 + - + -
131A TYR* 3.0 48.7 + - + -
170A PHE* 4.3 12.0 - + - -
172A ASP* 2.7 29.0 + - - -
276A MET* 3.3 50.7 - - + +
277A GLY* 4.5 0.6 - - - -
329A ARG* 2.8 34.6 + - + +
363A TYR* 4.4 0.4 - - - -
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Residues in contact with GLN 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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115A ALA* 3.5 3.3 - - - +
116A ILE* 4.0 28.8 + - + +
126A ASP* 2.8 36.6 + - - +
127A HIS* 1.3 76.8 - - - +
129A ASP* 1.3 62.0 + - - +
131A TYR* 3.8 1.9 + - - +
132A ALA* 3.3 19.9 + - - +
330A THR* 3.3 27.7 + - - +
331A LYS 4.4 5.4 + - - +
365A LEU* 4.6 3.7 - - - +
98B TYR* 4.5 7.4 + - + -
135B GLN* 5.7 0.5 - - - +
225B TYR* 2.8 26.3 + - - -
229B ARG* 3.1 39.2 - - - +
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Residues in contact with ASP 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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86A ALA* 3.7 2.1 - - - -
87A SER* 2.7 40.2 + - - +
90A LEU* 3.6 14.4 - - + +
91A LEU* 4.9 1.4 - - + +
111A VAL* 4.0 3.2 - - - +
112A THR 3.6 2.1 - - - +
113A ALA* 3.3 19.1 - - - +
114A ARG 2.8 38.4 + - - +
116A ILE* 3.8 11.4 - - + +
126A ASP 3.4 2.4 - - - +
128A GLN* 1.3 78.2 - - - +
130A ILE* 1.3 83.6 + - - +
132A ALA* 3.0 20.1 + - - +
133A ALA* 3.5 3.5 + - - +
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Residues in contact with ILE 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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90A LEU* 4.0 7.0 - - + -
111A VAL* 3.8 25.6 - - + -
113A ALA* 3.8 8.7 - - + -
127A HIS* 3.6 24.2 - - + +
129A ASP* 1.3 91.8 + - - +
131A TYR* 1.3 83.0 + - + +
133A ALA* 3.1 13.2 + - - +
134A ARG 3.4 2.3 + - - -
140A MET* 3.3 38.2 - - + +
168A MET* 4.0 8.1 - - - -
170A PHE* 3.6 40.4 - - + -
276A MET* 4.5 2.2 - - + -
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Residues in contact with TYR 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 HIS* 3.0 39.9 + - + +
128A GLN 4.3 2.2 - - - +
130A ILE* 1.3 81.0 - - + +
132A ALA* 1.3 62.2 + - - +
133A ALA 3.2 0.9 + - - -
134A ARG* 3.0 42.4 + - - +
135A GLN* 4.0 0.2 + - - -
276A MET* 3.4 26.1 - - + +
305A TYR* 3.5 38.4 - + - -
328A ASP* 2.8 24.9 + - - -
329A ARG 4.5 2.7 - - - -
330A THR* 3.3 36.1 - - + +
332A GLU* 4.1 6.3 - - - +
339A PRO* 3.6 16.4 - - + -
340A LEU* 3.5 10.7 - - - +
135B GLN* 3.9 0.6 - - - +
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Residues in contact with ALA 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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91A LEU* 3.7 23.1 - - + -
94A ILE* 3.6 13.8 - - + +
116A ILE* 5.7 0.2 - - + -
128A GLN 3.3 10.4 + - - +
129A ASP 3.0 13.4 + - - +
131A TYR* 1.3 76.4 - - - +
133A ALA* 1.3 55.6 + - - +
135A GLN* 2.8 16.4 + - - -
94B ILE* 5.8 1.3 - - + -
98B TYR* 3.5 22.9 - - + +
132B ALA 4.7 6.4 - - - +
135B GLN* 4.2 14.3 - - + +
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Residues in contact with ALA 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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90A LEU* 4.4 4.0 - - + -
94A ILE* 4.1 8.1 - - + -
97A MET* 3.8 30.1 - - + +
129A ASP 3.5 4.9 + - - +
130A ILE 3.1 9.9 + - - +
131A TYR 3.1 0.4 - - - -
132A ALA* 1.3 79.4 - - - +
134A ARG* 1.3 60.1 + - - +
135A GLN* 3.2 4.8 + - - +
136A THR* 2.9 31.8 + - + -
138A PHE* 5.3 1.4 + - - +
140A MET* 4.5 4.6 - - - +
168A MET* 4.3 10.8 - - + -
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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