Contacts of the helix formed by residues 253 - 258 (chain N) in PDB entry 1KYO
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 253 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132N TYR* 4.0 18.8 + - - +
139N MET* 3.8 9.8 - - + +
252N GLY* 1.3 74.1 - - - +
254N PRO* 1.4 75.9 - - + +
255N ASP* 2.8 54.8 + - + +
256N ASN* 3.2 17.5 + - - +
257N TYR* 4.6 5.0 + - - -
268N SER* 3.0 25.7 + - - -
270N VAL* 3.5 39.2 + - + +
271N PRO 5.4 0.4 + - - -
185O HIS* 5.1 5.4 - + - -
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Residues in contact with PRO 254 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252N GLY 4.3 4.0 - - - +
253N HIS* 1.4 82.9 - - + +
255N ASP* 1.3 64.0 + - - +
256N ASN 3.0 2.9 - - - -
257N TYR* 2.9 25.4 + - + +
182O LYS 3.6 19.5 - - - +
183O ALA* 3.6 23.5 - - - +
184O ARG* 3.9 11.2 - - - +
185O HIS* 3.5 42.0 - - + +
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Residues in contact with ASP 255 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138N GLN* 3.5 8.8 + - + +
139N MET* 3.4 26.6 - - + +
253N HIS* 2.8 30.2 + - + -
254N PRO* 1.3 77.3 - - - +
256N ASN* 1.3 56.1 + - - +
257N TYR 3.1 4.8 + - - -
258N ILE* 3.2 41.9 + - - +
266N PRO* 3.9 11.1 - - - +
268N SER* 2.6 32.6 + - - -
183O ALA 5.1 1.6 - - - +
185O HIS* 6.5 0.4 - - - -
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Residues in contact with ASN 256 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62N PHE* 3.4 18.2 - - - -
79N ARG* 5.9 0.3 + - - -
132N TYR* 3.8 26.7 - - + +
135N VAL* 3.8 25.1 - - - +
137N GLY* 3.1 12.3 - - - -
138N GLN 4.2 0.7 - - - +
139N MET* 3.2 11.9 + - + +
140N SER* 3.0 39.1 + - - -
253N HIS 3.2 13.2 + - - +
254N PRO 2.9 2.2 + - - -
255N ASP* 1.3 76.5 - - - +
257N TYR* 1.3 61.2 + - + +
258N ILE 3.2 3.6 - - - -
521N HEC 4.3 4.0 + - - -
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Residues in contact with TYR 257 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62N PHE* 3.3 16.7 - + - -
66N GLU* 3.9 21.3 - - - -
69N MET* 4.5 1.4 - - + +
79N ARG* 3.9 22.6 + - - -
80N TYR* 3.5 9.7 + - - -
249N ASN* 2.8 32.1 + - + -
253N HIS 4.9 3.1 - - - -
254N PRO* 2.9 17.3 + - + +
256N ASN* 1.3 81.3 - - + +
258N ILE* 1.3 61.1 + - - +
259N PRO* 4.0 2.1 - - - +
179O LEU* 3.8 26.5 - - + +
182O LYS* 2.9 61.4 + - + -
183O ALA* 4.1 15.2 - - + +
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Residues in contact with ILE 258 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62N PHE* 3.7 1.8 - - - -
137N GLY* 3.3 3.1 - - - -
138N GLN* 2.8 42.3 + - + +
255N ASP* 3.2 32.7 + - - +
257N TYR* 1.3 82.6 - - - +
259N PRO* 1.3 76.6 - - + +
266N PRO* 6.2 0.4 - - + -
183O ALA* 3.9 28.3 - - + +
184O ARG* 4.1 14.1 - - - +
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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