Contacts of the helix formed by residues 300 - 307 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A GLY 4.1 2.3 + - - +
299A ILE* 1.3 70.9 - - - +
301A LEU* 1.3 63.7 + - - +
302A LEU 3.0 1.4 + - - -
303A ASP* 3.2 27.7 + - - +
304A ASN* 4.3 4.3 + - - +
349A GLN* 3.5 21.7 - - - +
352A ARG* 3.8 25.6 - - - +
358A THR* 4.9 7.2 + - - -
361A GLU* 3.5 28.2 + - + +
121R ASP* 3.5 27.9 + - - +
122R ASN* 5.2 2.1 + - - -
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A PHE* 5.0 6.3 - - + -
299A ILE* 3.3 10.8 - - + +
300A LYS* 1.3 77.9 - - - +
302A LEU* 1.3 63.2 + - - +
304A ASN* 3.1 15.9 + - - +
305A ILE* 3.2 27.8 + - + +
314A PHE* 4.1 30.1 - - + -
316A HIS* 4.7 7.9 - - + +
345A PHE* 3.7 15.3 - - + +
346A THR* 3.6 48.7 - - + +
349A GLN* 3.5 26.1 - - + +
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A TYR* 3.3 35.9 - - + -
294A SER 3.5 25.1 - - - +
295A ARG 3.5 17.5 - - - +
297A GLN* 3.9 22.9 - - + +
299A ILE* 3.0 26.2 + - + +
300A LYS 3.0 0.8 + - - -
301A LEU* 1.3 74.9 - - - +
303A ASP* 1.3 66.9 + - - +
305A ILE* 3.7 17.7 - - + -
306A GLN* 3.3 36.4 + - - +
314A PHE* 4.2 7.6 - - + -
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Residues in contact with ASP 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A ILE 4.7 2.5 - - - +
300A LYS* 3.2 21.0 + - - +
302A LEU* 1.3 78.1 - - - +
304A ASN* 1.3 69.0 + - - +
306A GLN* 4.1 1.8 + - - +
307A GLU* 4.1 16.5 + - - +
117R LYS* 3.1 35.4 + - - -
121R ASP* 4.2 6.2 - - - +
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Residues in contact with ASN 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A LYS 4.7 3.4 + - - +
301A LEU* 3.1 16.6 + - - +
303A ASP* 1.3 86.0 - - - +
305A ILE* 1.3 64.0 + - - +
306A GLN 3.4 0.5 + - - -
307A GLU* 3.7 13.4 + - - +
308A TYR 4.8 1.0 + - - -
310A LEU* 4.1 8.8 - - - +
345A PHE* 3.6 55.2 - - + +
349A GLN* 4.9 6.9 - - - +
1C MET 4.9 2.8 + - - -
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Residues in contact with ILE 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A TYR* 3.3 41.7 - - + +
301A LEU* 3.2 41.3 + - + +
302A LEU* 3.7 21.8 - - + +
304A ASN* 1.3 77.9 - - + +
306A GLN* 1.3 62.7 + - + +
308A TYR 4.1 0.7 + - - -
309A GLN* 3.2 16.7 + - - +
310A LEU* 2.9 45.7 + - + +
311A CYS* 4.1 11.2 - - - -
314A PHE* 4.5 4.5 - - + -
342A LEU* 4.5 14.4 - - + -
345A PHE* 5.2 1.3 - - + -
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Residues in contact with GLN 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A TYR* 3.6 20.8 + - + +
295A ARG* 3.1 57.2 + - - +
302A LEU* 3.3 30.0 + - - +
303A ASP* 4.8 2.0 - - - +
304A ASN 3.3 0.2 - - - -
305A ILE* 1.3 81.0 - - + +
307A GLU* 1.3 64.4 + - - +
308A TYR 3.2 3.2 + - - -
309A GLN* 3.5 17.2 + - - +
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Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ASP 4.1 10.9 + - - +
304A ASN* 3.7 11.0 + - - +
305A ILE 3.5 1.2 - - - -
306A GLN* 1.3 76.8 - - - +
308A TYR* 1.3 89.5 + - + +
1C MET 5.3 4.5 + - - +
7S LYS* 5.9 1.6 + - - +
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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