Contacts of the helix formed by residues 3260 - 3265 (chain D) in PDB entry 1KY5
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 THR3260 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2404C LYS* 4.4 13.0 - - + +
2405C LEU 4.0 20.4 - - - +
2406C THR* 4.3 15.7 - - + +
3241D THR* 4.1 1.8 - - - -
3259D THR* 1.3 82.1 + - - +
3261D MET* 1.3 63.6 + - - +
3262D ASP* 3.7 13.9 + - - +
3263D GLU* 3.4 22.3 + - - +
3264D ALA* 3.0 24.3 + - - +
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Residues in contact with MET3261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2406C THR* 5.0 3.2 + - - +
3216D VAL* 3.8 23.3 - - + +
3218D ALA* 4.2 11.9 - - + +
3241D THR* 3.9 14.6 - - + +
3260D THR* 1.3 71.9 - - - +
3262D ASP* 1.3 61.3 + - - +
3264D ALA* 4.3 1.1 - - - -
3265D CYS* 2.8 36.9 + - - -
3271D PHE* 3.8 27.6 - - + -
3272D VAL 6.0 0.9 - - - +
3280D ILE* 3.6 33.9 - - + +
3281D ILE* 4.0 24.7 - - + -
3285D HIS* 3.7 21.5 - - + +
3289D MET* 5.9 0.2 - - - -
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Residues in contact with ASP3262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3260D THR* 3.1 12.9 - - - +
3261D MET* 1.3 79.0 - - - +
3263D GLU* 1.3 59.2 + - + +
3265D CYS* 3.0 17.9 - - - -
3266D LYS* 4.0 12.9 + - - -
3284D ARG* 2.5 36.8 + - - -
3285D HIS* 2.7 26.8 + - - -
3288D GLN* 5.0 0.2 - - - +
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Residues in contact with GLU3263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2404C LYS* 6.0 6.5 - - + -
3259D THR* 4.8 12.1 - - + +
3260D THR* 3.2 16.8 + - - +
3261D MET 3.1 0.2 - - - -
3262D ASP* 1.3 83.4 - - + +
3264D ALA* 1.3 63.2 + - - +
3265D CYS 3.4 0.2 - - - -
3266D LYS* 3.1 48.8 + - - +
3267D GLU* 4.4 2.4 + - - +
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Residues in contact with ALA3264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3216D VAL* 4.1 26.0 - - + +
3239D ILE* 4.1 27.4 - - + -
3241D THR* 4.9 1.3 - - + -
3259D THR* 4.2 2.9 - - - +
3260D THR 3.0 17.4 + - - +
3261D MET* 4.1 3.6 - - - +
3263D GLU* 1.3 73.9 - - - +
3265D CYS* 1.3 57.2 + - - +
3266D LYS 2.9 5.4 - - - -
3267D GLU* 2.8 24.0 + - - +
3268D GLY 3.2 10.6 + - - -
3271D PHE* 4.2 2.6 - - - -
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Residues in contact with CYS3265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3261D MET* 2.8 31.7 + - - +
3262D ASP* 3.0 20.2 - - - -
3264D ALA* 1.3 72.9 - - - +
3266D LYS* 1.3 60.8 + - - +
3267D GLU 3.4 0.2 - - - -
3268D GLY 4.6 1.2 + - - +
3271D PHE* 3.5 28.6 - - + -
3284D ARG 5.1 0.2 - - - -
3285D HIS* 3.3 46.0 - - + +
3288D GLN* 3.7 14.3 - - - +
3289D MET* 3.4 25.3 - - + -
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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