Contacts of the helix formed by residues 267 - 275 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55C TYR* 3.6 34.8 - - + +
56C LYS 4.5 2.9 - - - +
57C LYS* 3.4 41.7 - - + -
168C LEU* 4.0 23.1 - - + -
265C VAL 3.7 2.6 + - - -
266C ILE* 1.3 73.9 - - - +
268C ALA* 1.3 67.7 + - - +
269C PRO* 3.7 11.2 - - + -
270C LEU* 3.0 32.4 + - + +
271C GLN 3.0 10.0 + - - -
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Residues in contact with ALA 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ALA 3.6 23.6 - - - +
55C TYR 3.0 11.7 + - - +
56C LYS* 4.6 1.5 - - - +
92C TRP* 3.8 27.6 - - + -
266C ILE 3.4 3.6 + - - -
267C LEU* 1.3 70.7 - - - +
269C PRO* 1.4 65.9 - - + +
271C GLN* 3.3 5.2 + - - +
272C ARG* 2.8 34.8 + - - +
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Residues in contact with PRO 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C TYR* 3.6 14.4 - - + -
92C TRP* 3.4 39.7 - - + -
167C ASN 4.1 0.2 - - - -
168C LEU* 3.5 31.9 - - + +
267C LEU* 3.3 15.5 - - + -
268C ALA* 1.4 94.7 - - + +
270C LEU* 1.3 57.2 + - - +
272C ARG* 3.6 3.0 - - + -
273C ASN* 2.7 42.0 + - - +
811C TAD 4.1 7.2 - - + -
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Residues in contact with LEU 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C VAL* 4.9 6.7 - - + -
166C PRO 3.6 23.6 - - - +
167C ASN* 3.7 5.6 - - + -
168C LEU* 3.6 31.2 - - + +
266C ILE* 3.6 15.3 - - + -
267C LEU* 3.0 31.2 + - + +
269C PRO* 1.3 76.9 - - - +
271C GLN* 1.3 63.2 + - - +
273C ASN* 4.3 0.2 - - - +
274C THR* 2.9 34.2 + - - +
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Residues in contact with GLN 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C ILE* 3.3 43.3 + - + +
267C LEU 3.0 12.0 + - - +
268C ALA* 3.7 8.5 - - - +
270C LEU* 1.3 75.1 - - - +
272C ARG* 1.3 62.1 + - - +
274C THR* 4.9 3.4 - - - +
275C ALA* 3.2 47.5 + - + +
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Residues in contact with ARG 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C GLU* 4.2 16.6 + - - +
92C TRP* 3.0 51.8 + - - +
94C GLU* 2.8 43.3 + - - -
97C LYS* 4.6 5.7 - - - +
268C ALA* 2.8 21.5 + - - +
269C PRO* 3.9 3.6 - - + +
271C GLN* 1.3 80.2 - - - +
273C ASN* 1.3 67.4 + - - +
275C ALA 3.9 12.8 - - - -
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Residues in contact with ASN 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C TRP* 5.9 1.0 - - - -
94C GLU* 5.0 4.7 - - - +
167C ASN* 2.7 41.0 + - + +
168C LEU 3.5 16.2 + - - -
169C TRP 4.1 1.8 - - - +
170C LYS* 3.6 34.4 - - + +
269C PRO* 2.7 23.0 + - - +
272C ARG* 1.3 84.5 - - - +
274C THR* 1.3 65.0 + - - +
275C ALA 4.8 1.4 - - - +
811C TAD 4.9 2.0 + - - -
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Residues in contact with THR 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C ASN* 3.5 29.0 + - - +
270C LEU* 2.9 21.7 + - - +
271C GLN* 4.3 3.6 - - - +
273C ASN* 1.3 80.5 - - - +
275C ALA* 1.3 65.5 + - + +
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Residues in contact with ALA 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C GLN* 3.2 32.8 + - - +
272C ARG* 3.9 15.9 - - - -
273C ASN 4.8 1.1 - - - +
274C THR* 1.3 85.3 - - + +
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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