Contacts of the helix formed by residues 304 - 309 (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 VAL 304 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300N LEU 4.8 2.0 - - - +
301N VAL* 3.1 30.1 - - + +
303N LEU* 1.3 78.6 - - + +
305N LEU* 1.3 56.7 + - - +
306N PRO* 3.3 0.4 - - - +
307N PHE* 2.9 32.9 + - + +
308N THR* 3.3 32.0 + - + +
363N PHE* 4.4 3.6 - - + +
364N LEU* 3.9 19.1 - - + -
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Residues in contact with LEU 305 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101N LEU* 4.0 31.6 - - + +
106N TYR* 3.4 39.6 - - + +
114N TRP* 4.9 5.8 - - + +
301N VAL 4.0 1.4 + - - -
302N LEU* 3.6 12.4 + - - +
303N LEU 3.3 0.2 - - - -
304N VAL* 1.3 78.2 - - - +
306N PRO* 1.3 65.4 - - + +
307N PHE 3.1 1.3 + - - -
308N THR* 3.6 14.8 - - - +
309N ASP 3.3 17.3 + - - -
362N TYR* 5.4 0.9 - - + -
363N PHE* 3.9 32.3 - - + -
367N VAL* 4.4 23.6 - - + -
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Residues in contact with PRO 306 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106N TYR* 3.3 39.5 - - + +
107N ARG* 4.9 5.4 - - + +
111N VAL* 3.9 26.0 - - + -
114N TRP* 4.5 5.2 - - + -
115N ASN* 5.4 0.2 - - - +
302N LEU 4.3 2.0 - - - +
303N LEU* 3.1 20.6 - - - +
304N VAL 3.3 1.6 - - - -
305N LEU* 1.3 93.4 - - + +
307N PHE* 1.3 72.9 + - + +
309N ASP* 4.5 8.6 - - + +
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Residues in contact with PHE 307 (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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111N VAL* 5.2 11.7 - - + -
115N ASN* 6.3 0.2 - - - -
303N LEU 3.9 16.4 - - - -
304N VAL* 2.9 18.1 + - + +
306N PRO* 1.3 97.3 - - + +
308N THR* 1.3 65.8 + - + +
309N ASP 3.5 3.4 + - - +
310N ARG* 4.0 19.6 + - - -
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Residues in contact with THR 308 (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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304N VAL* 3.3 26.3 + - + +
305N LEU* 3.6 21.8 + - - +
307N PHE* 1.3 79.5 - - + +
309N ASP* 1.3 60.3 + - - +
310N ARG* 3.1 6.5 + - - +
363N PHE 2.9 25.0 + - - +
364N LEU* 4.6 8.5 - - + +
367N VAL* 4.1 1.3 - - - -
368N PRO* 3.1 41.9 - - + +
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Residues in contact with ASP 309 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104N GLY* 5.2 0.2 - - - -
106N TYR* 2.7 27.9 + - + +
107N ARG* 3.0 31.6 + - + -
305N LEU* 3.3 18.3 + - + +
306N PRO 4.5 9.1 - - - +
307N PHE 3.5 2.2 - - - +
308N THR* 1.3 73.1 + - - +
310N ARG* 1.3 60.2 + - - +
311N SER* 3.1 27.2 + - - +
315N GLY 5.6 1.0 + - - -
319N LYS* 4.3 5.4 + - - -
367N VAL* 3.6 17.2 - - + +
371N SER* 4.1 4.2 - - - -
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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