Contacts of the helix formed by residues 267 - 275 (chain E) in PDB entry 1KR2
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 LEU 267 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55E TYR* 3.8 31.2 - - + +
56E LYS 4.4 2.9 - - - +
57E LYS* 3.6 43.1 - - + -
58E LYS 5.2 0.2 - - - +
168E LEU* 4.2 22.4 - - + -
265E VAL 3.6 3.8 + - - -
266E ILE* 1.3 72.3 - - - +
268E ALA* 1.3 67.7 + - - +
269E PRO* 3.9 8.3 - - + -
270E LEU* 2.9 36.1 + - + +
271E GLN 3.0 10.4 + - - -
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Residues in contact with ALA 268 (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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54E ALA 3.3 26.2 - - - +
55E TYR 3.0 13.0 + - - +
56E LYS* 4.6 2.2 - - + +
92E TRP* 3.7 23.3 - - + -
266E ILE 3.4 4.6 + - - -
267E LEU* 1.3 69.2 - - - +
269E PRO* 1.3 70.2 - - + +
271E GLN* 3.1 7.9 + - - +
272E ARG* 2.9 27.2 + - - +
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Residues in contact with PRO 269 (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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55E TYR* 3.7 20.6 - - + -
92E TRP* 3.2 46.4 - - + -
167E ASN 3.9 0.4 - - - -
168E LEU* 3.8 27.6 - - + +
267E LEU* 3.4 9.0 - - + -
268E ALA* 1.3 93.7 - - + +
270E LEU* 1.3 56.2 + - - +
272E ARG* 3.8 1.5 - - + -
273E ASN* 2.8 42.2 + - - +
813E TAD 4.0 6.1 - - + -
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Residues in contact with LEU 270 (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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165E VAL* 4.8 6.7 - - + -
166E PRO 3.5 25.1 - - - +
167E ASN* 3.6 17.7 - - + +
168E LEU* 3.8 17.0 - - + +
266E ILE* 3.8 12.8 - - + -
267E LEU* 2.9 36.0 + - + +
269E PRO* 1.3 78.9 - - - +
271E GLN* 1.3 63.1 + - - +
273E ASN 3.9 0.2 - - - -
274E THR* 2.9 33.9 + - - +
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Residues in contact with GLN 271 (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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266E ILE* 3.8 29.9 - - + +
267E LEU 3.0 11.7 + - - +
268E ALA* 3.3 12.1 - - - +
270E LEU* 1.3 78.9 - - - +
272E ARG* 1.3 64.8 + - + +
274E THR* 3.3 4.1 + - - -
275E ALA* 3.3 29.3 + - - +
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Residues in contact with ARG 272 (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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91E GLU* 4.1 18.2 + - - +
92E TRP* 2.7 55.6 + - + +
93E LYS* 6.0 0.2 - - - +
94E GLU* 3.0 37.9 + - - -
97E LYS* 4.6 5.8 - - - +
268E ALA* 2.9 19.9 + - - +
269E PRO* 3.9 4.3 - - + +
271E GLN* 1.3 75.7 - - + +
273E ASN* 1.3 66.5 + - - +
275E ALA* 3.4 20.5 + - - +
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Residues in contact with ASN 273 (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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92E TRP* 5.7 1.2 - - - -
94E GLU* 4.9 3.6 - - - +
167E ASN* 2.8 42.9 + - - +
168E LEU 3.6 17.8 + - - -
169E TRP* 4.1 6.8 - - - +
170E LYS* 3.7 27.2 - - - +
269E PRO* 2.8 22.7 + - - +
272E ARG* 1.3 81.0 - - - +
274E THR* 1.3 62.2 + - - +
275E ALA 3.3 3.0 - - - +
813E TAD 4.8 2.6 + - - -
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Residues in contact with THR 274 (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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167E ASN* 3.8 24.5 + - - +
270E LEU* 2.9 22.7 + - - +
271E GLN* 3.9 4.7 - - - -
273E ASN* 1.3 77.8 - - - +
275E ALA* 1.3 61.3 + - - +
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Residues in contact with ALA 275 (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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271E GLN* 3.3 26.3 + - - +
272E ARG* 3.4 14.6 + - - +
273E ASN 3.3 3.6 - - - +
274E THR* 1.3 81.0 - - - +
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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