Contacts of the helix formed by residues 425 - 432 (chain A) in PDB entry 2YD0
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 ASN 425 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A ILE* 4.6 13.7 - - + -
424A GLU* 1.3 82.5 - - + +
426A PRO* 1.3 72.0 - - + +
427A ALA* 3.1 11.0 + - - +
428A GLN* 2.9 37.6 + - - +
429A ILE* 2.8 29.5 + - - +
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Residues in contact with PRO 426 (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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52A ILE* 5.3 7.2 - - + -
129A GLU* 3.9 29.4 - - - +
184A PRO* 5.0 0.3 - - - +
185A THR* 3.9 15.7 - - + +
188A ARG* 4.5 7.0 - - - +
424A GLU 4.6 0.7 - - - +
425A ASN* 1.3 90.9 - - + +
427A ALA* 1.3 57.3 + - - +
429A ILE* 3.3 12.1 + - + +
430A ARG* 2.8 59.7 + - - +
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Residues in contact with ALA 427 (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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425A ASN* 3.1 8.1 + - - +
426A PRO* 1.3 77.3 - - - +
428A GLN* 1.3 63.1 + - - +
430A ARG* 3.3 6.2 + - - +
431A GLU* 3.0 31.4 + - + +
866A LEU* 3.7 36.6 - - + +
867A GLY 3.7 6.5 + - - +
905A LEU* 5.6 1.8 - - + -
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Residues in contact with GLN 428 (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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422A PRO 5.6 0.7 - - - -
423A VAL* 3.8 21.5 - - + +
424A GLU* 2.8 33.9 + - - +
425A ASN* 2.9 36.7 + - - +
427A ALA* 1.3 73.6 - - - +
429A ILE* 1.3 66.7 + - - +
431A GLU* 3.1 27.8 + - - +
432A MET* 3.4 12.1 + - - +
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Residues in contact with ILE 429 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A PRO* 3.5 26.9 - - + -
185A THR* 4.1 15.3 - - + -
368A TRP* 4.1 8.1 - - + -
369A TRP* 3.5 47.6 - - + +
423A VAL* 3.8 20.4 - - + -
424A GLU 3.9 11.9 - - - +
425A ASN 2.8 25.9 + - - +
426A PRO* 3.6 7.2 - - + +
428A GLN* 1.3 75.7 - - - +
430A ARG* 1.3 62.0 - - - +
432A MET* 3.1 21.3 + - - +
433A PHE* 3.7 5.5 - - + -
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Residues in contact with ARG 430 (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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129A GLU* 5.5 2.2 + - - -
184A PRO* 4.2 20.2 - - + +
185A THR* 3.9 12.7 + - - -
426A PRO* 2.8 42.2 + - - +
427A ALA* 3.5 15.3 - - - +
428A GLN 3.3 0.2 - - - -
429A ILE* 1.3 74.6 - - - +
431A GLU* 1.3 57.5 + - - +
433A PHE* 3.0 34.0 + - + +
865A GLU* 3.0 48.1 + - - +
866A LEU* 2.4 38.2 + - - +
867A GLY 3.5 14.6 - - - +
868A SER* 4.3 11.6 - - - +
869A SER 5.2 1.7 + - - -
1950A BES 6.0 3.6 - - + -
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Residues in contact with GLU 431 (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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417A HIS* 4.7 1.6 + - - -
427A ALA* 3.0 23.5 + - - +
428A GLN* 3.1 16.9 + - - +
430A ARG* 1.3 70.6 - - - +
432A MET* 1.3 64.6 + - - +
433A PHE* 3.1 3.2 + - - -
434A ASP* 3.3 25.3 - - - +
867A GLY* 3.6 17.5 - - - +
904A GLN 4.5 2.2 - - - +
905A LEU* 3.6 17.8 - - - +
906A ARG* 2.9 45.0 + - + +
907A CYS* 4.8 0.9 + - - -
1947A K 3.4 19.2 - - - -
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Residues in contact with MET 432 (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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369A TRP* 3.9 22.7 - - + +
370A ASN 3.9 7.4 - - - +
372A LEU* 3.4 20.5 - - + +
373A TRP 5.5 0.2 - - - +
417A HIS* 4.3 11.0 - - + -
419A VAL 3.7 23.3 - - - +
421A THR* 3.8 21.1 - - + +
423A VAL* 3.7 34.3 - - + -
428A GLN 3.4 1.3 + - - +
429A ILE* 3.1 16.0 + - - +
431A GLU* 1.3 75.5 - - - +
433A PHE* 1.3 58.2 + - - +
434A ASP* 2.9 8.5 + - - +
437A SER* 2.6 41.2 + - - +
1947A K 4.4 6.3 - - - -
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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