Contacts of the helix formed by residues 650 - 657 (chain D) in PDB entry 1K0Y
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 THR 650 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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647D ASP* 6.1 0.2 - - - +
649D SER* 1.4 86.4 - - - +
651D PRO* 1.3 74.6 - - - +
652D ASP* 3.8 8.2 + - - +
653D ALA* 3.0 34.4 + - + +
654D VAL* 3.0 16.8 + - - +
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Residues in contact with PRO 651 (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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519C PRO* 4.9 4.7 - - + -
520C ALA* 4.4 27.1 - - + +
633D VAL* 4.0 34.8 - - + -
649D SER 4.7 1.3 - - - +
650D THR* 1.3 86.7 - - + +
652D ASP* 1.4 64.0 + - - +
654D VAL* 3.4 1.4 + - - +
655D MET* 3.0 35.4 + - + +
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Residues in contact with ASP 652 (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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650D THR* 3.1 7.8 + - - +
651D PRO* 1.4 85.2 - - - +
653D ALA* 1.4 61.3 + - - +
655D MET* 4.0 4.3 - - - +
656D GLY* 3.1 21.0 + - - -
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Residues in contact with ALA 653 (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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647D ASP* 3.5 43.4 - - + +
649D SER 4.4 0.2 - - - +
650D THR* 3.0 30.2 + - + +
652D ASP* 1.4 77.1 - - - +
654D VAL* 1.4 56.6 + - - +
656D GLY* 3.5 1.4 + - - -
657D ASN* 3.0 30.0 + - - +
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Residues in contact with VAL 654 (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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629D GLY* 3.4 34.5 - - - +
632D LEU* 3.9 19.1 - - + -
633D VAL* 3.9 13.2 - - + -
639D GLN* 4.8 7.4 - - - +
648D LEU* 3.5 41.7 - - + +
650D THR 3.0 14.3 + - - +
651D PRO 3.7 5.4 - - - +
653D ALA* 1.4 76.0 - - - +
655D MET* 1.4 61.7 + - - +
657D ASN* 3.3 15.9 + - - +
660D VAL* 3.7 11.5 - - + +
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Residues in contact with MET 655 (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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519C PRO* 3.9 32.5 - - + -
625D GLY 4.5 2.9 - - - +
626D GLU* 3.3 50.7 - - - +
629D GLY* 3.6 31.4 - - - +
630D ARG* 3.9 2.0 - - + +
633D VAL* 4.5 2.9 - - + -
651D PRO 3.0 23.5 + - - +
652D ASP* 4.3 4.3 - - - +
654D VAL* 1.4 75.3 - - - +
656D GLY* 1.4 56.7 + - - +
660D VAL* 5.6 0.8 - - - +
661D LYS* 3.2 24.6 - - - +
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Residues in contact with GLY 656 (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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652D ASP 3.1 16.4 + - - -
653D ALA* 3.8 2.0 - - - -
655D MET* 1.4 75.1 - - - +
657D ASN* 1.4 64.3 + - - +
658D PRO* 3.1 11.4 - - - +
661D LYS* 4.2 15.0 + - - -
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Residues in contact with ASN 657 (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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645D PHE 2.7 32.1 + - - +
647D ASP* 3.4 23.8 + - - +
648D LEU* 3.7 7.5 - - - +
653D ALA 3.0 15.7 + - - +
654D VAL* 3.3 12.8 + - - +
656D GLY* 1.4 73.7 - - - +
658D PRO* 1.3 71.6 - - - +
659D LYS* 2.8 29.3 + - - +
660D VAL* 3.2 18.0 + - + +
661D LYS* 3.1 22.9 + - - +
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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