Contacts of the helix formed by residues 253 - 258 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132C TYR* 4.3 10.8 + - - +
139C MET* 3.8 16.2 - - + -
252C GLY* 1.3 74.1 - - - -
254C PRO* 1.3 74.8 - - + +
255C ASP* 2.9 55.5 + - + +
256C ASN* 3.2 18.3 + - - +
257C TYR* 4.6 5.1 - - - -
268C SER* 2.9 27.7 + - - -
270C VAL* 3.5 34.1 + - + +
271C PRO 5.2 1.7 + - - +
272C GLU* 6.5 1.1 - - - -
185D HIS* 4.9 7.5 - + - -
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Residues in contact with PRO 254 (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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252C GLY 4.3 3.8 - - - +
253C HIS* 1.3 91.7 - - + +
255C ASP* 1.3 64.7 + - - +
256C ASN 2.9 1.7 + - - -
257C TYR* 3.0 24.1 + - + +
182D LYS 3.6 20.0 - - - +
183D ALA* 3.6 22.4 - - - +
184D ARG* 3.8 6.3 - - - +
185D HIS* 3.5 46.9 - - + +
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Residues in contact with ASP 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C GLN* 3.7 8.5 + - + +
139C MET* 3.5 20.8 - - + +
253C HIS* 2.9 28.7 + - + +
254C PRO* 1.3 78.0 - - - +
256C ASN* 1.3 55.8 + - - +
257C TYR 2.9 6.1 + - - -
258C ILE* 3.1 45.0 + - + +
266C PRO* 3.5 17.0 - - - +
268C SER* 2.7 28.0 + - - +
183D ALA 4.7 3.8 - - - +
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Residues in contact with ASN 256 (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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62C PHE* 3.9 12.5 - - - -
79C ARG* 5.1 4.1 + - - +
132C TYR* 3.7 33.7 - - - +
135C VAL* 3.8 24.6 - - - +
137C GLY* 3.4 7.8 - - - -
139C MET* 3.3 8.3 + - + +
140C SER* 3.1 41.9 + - - -
253C HIS 3.2 13.1 + - - +
254C PRO 2.9 2.6 + - - -
255C ASP* 1.3 75.0 - - - +
257C TYR* 1.3 66.3 + - + +
258C ILE 3.5 0.9 - - - -
501C HEC 4.4 4.2 + - - -
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Residues in contact with TYR 257 (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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62C PHE* 3.3 18.6 - + - -
66C GLU* 3.8 16.6 - - - -
69C MET* 4.3 3.2 - - + +
79C ARG* 4.4 17.5 + - - -
80C TYR* 3.2 7.8 + - - -
249C ASN* 2.8 31.6 + - + -
253C HIS 4.6 7.0 - - - -
254C PRO* 3.0 12.9 + - + +
255C ASP 2.9 0.8 + - - -
256C ASN* 1.3 81.8 - - + +
258C ILE* 1.3 61.4 - - - +
259C PRO* 4.2 1.7 - - - +
179D LEU* 3.8 35.0 - - + +
182D LYS* 3.1 58.5 + - + -
183D ALA* 4.0 16.5 - - + +
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Residues in contact with ILE 258 (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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62C PHE* 3.8 1.6 - - - -
137C GLY* 3.3 2.4 - - - -
138C GLN* 2.9 30.9 + - + +
255C ASP* 3.4 39.3 - - + +
257C TYR* 1.3 82.4 - - - +
259C PRO* 1.3 84.5 - - + +
261C ASN* 6.4 0.7 - - + -
266C PRO* 5.7 1.6 - - + -
183D ALA* 3.9 17.0 - - + +
184D ARG* 4.3 16.8 - - - +
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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