Contacts of the helix formed by residues 300 - 307 (chain L) 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 LYS 300 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121G ASP* 3.5 32.3 + - - +
122G ASN* 5.1 3.8 + - - -
298L GLY 4.2 1.9 - - - +
299L ILE* 1.3 72.1 - - - +
301L LEU* 1.3 62.0 + - - +
303L ASP* 3.1 31.3 + - - +
304L ASN* 4.0 5.2 + - - +
349L GLN* 4.2 17.5 - - - +
352L ARG* 3.6 32.3 - - - +
358L THR* 4.7 10.3 - - - -
361L GLU* 3.6 23.5 + - + +
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Residues in contact with LEU 301 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284L PHE* 5.2 6.1 - - + +
299L ILE* 3.0 12.3 + - + +
300L LYS* 1.3 78.0 - - - +
302L LEU* 1.3 58.7 + - - +
303L ASP 2.9 5.9 + - - -
304L ASN* 3.0 17.2 + - - +
305L ILE* 3.1 30.8 + - + +
314L PHE* 3.7 34.5 - - + -
316L HIS* 4.7 4.0 - - - +
342L LEU* 6.2 0.4 - - + -
345L PHE* 3.7 8.7 - - + -
346L THR* 3.7 42.0 - - + +
349L GLN* 3.7 35.4 - - + +
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Residues in contact with LEU 302 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287L TYR* 3.2 43.5 - - + -
294L SER 3.7 22.2 - - - +
295L ARG 4.7 4.3 - - - +
297L GLN* 3.8 19.5 - - + +
299L ILE* 2.8 40.5 + - + +
301L LEU* 1.3 76.0 - - - +
303L ASP* 1.3 61.9 + - - +
305L ILE* 3.9 14.4 - - + -
306L GLN* 3.0 35.3 + - - +
314L PHE* 3.9 10.3 - - + -
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Residues in contact with ASP 303 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G LYS* 3.4 25.2 + - - -
121G ASP* 4.2 12.5 - - - +
299L ILE 4.8 2.2 - - - +
300L LYS* 3.1 21.7 + - - +
301L LEU 2.9 1.2 + - - -
302L LEU* 1.3 77.7 - - - +
304L ASN* 1.3 68.3 + - - +
305L ILE 3.3 0.5 + - - -
306L GLN* 3.4 10.3 + - - +
307L GLU* 3.8 12.5 + - - +
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Residues in contact with ASN 304 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300L LYS 4.1 8.2 - - - +
301L LEU* 3.0 9.0 + - + +
303L ASP* 1.3 82.5 - - - +
305L ILE* 1.3 60.2 + - - +
307L GLU* 4.3 7.8 + - - +
308L TYR 5.1 0.3 + - - -
310L LEU* 4.0 4.9 - - - +
345L PHE* 3.6 61.7 - - + +
349L GLN* 4.1 16.1 - - - +
1N MET 4.6 5.0 + - - -
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Residues in contact with ILE 305 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287L TYR* 3.3 41.1 - - + +
301L LEU* 3.1 41.2 + - + +
302L LEU* 3.9 21.8 - - + -
303L ASP 3.3 0.2 - - - -
304L ASN* 1.3 80.7 - - + +
306L GLN* 1.3 61.0 + - + +
307L GLU 3.5 0.2 - - - -
308L TYR 4.7 0.2 - - - -
309L GLN* 3.3 14.4 + - - +
310L LEU* 3.1 46.9 + - + +
311L CYS* 4.2 12.3 - - - -
314L PHE* 5.0 2.7 - - + -
342L LEU* 4.9 11.7 - - + -
345L PHE* 5.0 2.5 - - + -
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Residues in contact with GLN 306 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287L TYR* 3.5 24.3 + - - +
295L ARG* 2.8 65.0 + - - +
302L LEU* 3.0 25.2 + - - +
303L ASP* 3.4 4.8 + - - +
305L ILE* 1.3 83.7 - - + +
307L GLU* 1.3 65.5 + - - +
308L TYR 3.3 1.2 + - - -
309L GLN* 3.5 17.9 + - - +
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Residues in contact with GLU 307 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303L ASP 3.8 11.1 + - - +
304L ASN* 4.7 6.3 - - - +
305L ILE 3.5 1.4 - - - -
306L GLN* 1.3 79.4 - - - +
308L TYR* 1.3 87.9 + - + +
1N MET 4.8 5.4 + - - +
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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