Contacts of the helix formed by residues 443 - 450 (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 ASP 443 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ARG* 4.4 4.5 - - - +
442A LEU* 1.3 78.0 - - - +
444A TYR* 1.3 68.3 + - - +
445A MET* 3.2 5.2 - - - +
446A ARG* 2.9 45.5 + - - +
447A ILE* 3.5 2.6 + - - +
219C ILE* 5.3 4.0 - - + -
220C PRO* 3.1 32.6 - - + +
223C SER* 4.8 0.9 + - - -
224C TYR* 2.7 41.8 + - + +
295D ILE* 4.9 11.2 - - + -
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Residues in contact with TYR 444 (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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245A GLY* 3.5 6.0 - - - -
246A SER* 3.8 14.6 - - - -
247A GLU* 3.2 37.9 + - + +
249A ARG* 4.0 0.6 - - - +
429A ASP* 3.4 10.6 + - - -
430A ILE* 2.7 55.2 + - + -
432A ILE* 3.8 17.5 - - + -
442A LEU 3.6 2.2 + - - -
443A ASP* 1.3 70.2 - - - +
445A MET* 1.3 55.1 + - + +
447A ILE* 3.0 6.4 + - - +
448A ARG* 2.6 53.5 + - + +
224C TYR* 5.1 0.2 + - - -
294D GLY* 6.1 4.5 - - - -
28H ALA* 5.8 2.7 - - + -
29H VAL 4.9 4.0 - - - +
30H SER* 3.5 27.4 - - - -
31H PRO* 4.3 15.5 - - + -
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Residues in contact with MET 445 (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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443A ASP* 3.0 14.4 + - - +
444A TYR* 1.3 80.3 - - + +
446A ARG* 1.3 51.3 + - - +
448A ARG* 3.6 19.5 - - + +
449A SER* 2.5 43.6 + - - +
223C SER* 4.2 13.9 - - - +
224C TYR* 3.6 9.1 + - + +
290D PHE* 4.0 27.1 - - + -
291D LYS* 3.8 39.3 - - - +
294D GLY* 5.7 2.7 - - - +
31H PRO* 3.9 31.0 - - + -
32H TYR* 4.3 10.8 - - + +
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Residues in contact with ARG 446 (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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340A ASP* 5.3 0.6 + - - +
442A LEU* 3.1 38.3 - - + +
443A ASP* 2.9 39.2 + - - +
445A MET* 1.3 70.3 - - - +
447A ILE* 1.3 65.4 + - + +
449A SER* 3.0 17.3 + - - -
450A ASP* 3.3 17.2 + - - +
4C ARG* 3.5 15.6 - - - +
18C ILE* 3.1 30.5 + - - +
19C ASP* 2.6 31.1 + - - -
220C PRO* 3.8 8.6 - - + +
222C HIS* 4.2 24.2 + - - +
223C SER* 5.1 6.0 + - - -
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Residues in contact with ILE 447 (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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262A LEU* 3.7 13.5 - - + -
343A ILE* 3.7 15.5 - - + -
347A LEU* 3.5 31.3 - - + +
430A ILE* 3.6 21.1 - - + -
432A ILE* 3.6 19.7 - - + -
441A LEU* 4.3 24.0 - - + -
442A LEU* 3.4 27.6 - - + +
443A ASP 3.8 8.3 - - - +
444A TYR 3.0 4.9 + - - +
446A ARG* 1.3 74.2 - - + +
448A ARG* 1.3 63.3 + - - +
450A ASP* 3.0 15.6 + - - -
451A MET* 3.9 2.4 + - - +
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Residues in contact with ARG 448 (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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427A ASP* 2.6 54.3 + - - +
428A GLN 3.2 18.4 + - - +
429A ASP* 2.9 44.4 + - - +
430A ILE* 4.1 9.5 - - - +
444A TYR* 2.6 43.8 + - + +
445A MET* 3.7 12.8 - - + +
447A ILE* 1.3 73.0 - - - +
449A SER* 1.3 60.6 + - - +
451A MET* 3.4 14.3 - - - +
452A SER* 5.1 0.9 + - - -
53E ARG* 3.5 5.9 - - - +
32H TYR* 3.3 41.4 + - + +
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Residues in contact with SER 449 (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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348A LYS* 5.5 0.3 + - - -
445A MET* 2.5 29.8 + - - +
446A ARG* 3.0 9.9 + - - -
448A ARG* 1.3 76.5 - - - +
450A ASP* 1.3 59.3 + - - +
451A MET 3.0 9.4 + - - -
452A SER* 3.5 19.6 + - - +
223C SER* 5.0 4.7 + - - -
291D LYS* 5.8 1.9 + - - -
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Residues in contact with ASP 450 (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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343A ILE* 5.1 2.6 - - - +
344A HIS* 3.3 37.6 + - - +
347A LEU* 3.6 27.2 - - + +
348A LYS* 3.3 22.0 + - - +
351A ASN* 3.2 22.7 + - - +
446A ARG* 3.3 12.3 + - - +
447A ILE* 3.0 13.4 + - - +
449A SER* 1.3 74.0 - - - +
451A MET* 1.3 56.0 + - - +
452A SER 3.0 9.8 + - - -
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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