Contacts of the helix formed by residues 430 - 437 (chain A) in PDB entry 5U3Y
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 HIS 430 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A GLN* 2.8 21.7 + - + +
251A CYS* 6.5 0.4 - - - -
254A VAL* 3.7 31.4 - - + +
428A SER 4.2 0.2 - - - -
429A LEU* 1.3 74.4 - - - +
431A PRO* 1.3 82.3 - - + +
432A LEU* 3.0 40.9 + - + +
433A LEU* 3.1 16.9 + - + +
434A GLN* 3.0 18.0 + - - +
506A PEG 4.9 1.1 - - - -
274B PHE* 4.8 10.9 - + - -
365B MET* 5.5 2.0 - - + -
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Residues in contact with PRO 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A LEU 3.4 0.2 - - - -
430A HIS* 1.3 101.0 - - + +
432A LEU* 1.3 61.9 + - - +
434A GLN* 3.1 17.8 + - - +
435A GLU* 3.0 25.8 + - - +
506A PEG 3.8 22.2 - - - +
365B MET* 3.8 25.1 - - + +
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Residues in contact with LEU 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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254A VAL* 4.3 14.8 - - + -
257A VAL* 3.8 27.4 - - + -
430A HIS* 3.0 19.5 + - + +
431A PRO* 1.3 77.8 - - - +
433A LEU* 1.3 61.4 + - + +
435A GLU* 3.2 5.5 + - - +
436A ILE* 3.1 24.7 + - + +
507A B7G 3.7 21.5 - - + -
274B PHE* 3.6 34.3 - - + -
276B ASN* 3.6 25.1 - - - +
365B MET* 3.5 19.4 - - + -
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Residues in contact with LEU 433 (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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250A GLN* 3.7 27.8 - - + +
253A THR* 3.7 16.6 - - - +
254A VAL* 3.9 21.1 - - + +
257A VAL* 5.1 4.3 - - + -
287A HIS* 4.3 7.2 - - + -
429A LEU* 3.9 13.7 - - + -
430A HIS* 3.1 9.9 + - + +
432A LEU* 1.3 74.3 - - + +
434A GLN* 1.3 65.9 + - - +
436A ILE* 3.1 21.3 + - + +
437A TYR* 3.0 36.0 + - + -
502A 7U7 3.3 38.8 - - + +
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Residues in contact with GLN 434 (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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429A LEU* 2.5 43.0 + - + +
430A HIS 3.0 15.3 + - - +
431A PRO* 3.1 15.4 + - - +
433A LEU* 1.3 76.9 - - - +
435A GLU* 1.3 60.1 + - - +
437A TYR* 3.3 5.0 + - - +
438A LYS* 3.0 28.5 + - - +
506A PEG 3.2 34.7 + - - -
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Residues in contact with GLU 435 (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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283A LYS* 3.8 0.7 + - - -
431A PRO 3.0 13.5 + - - +
432A LEU 3.2 7.2 + - - +
434A GLN* 1.3 79.0 - - - +
436A ILE* 1.3 62.4 + - - +
438A LYS* 3.2 35.4 + - - +
507A B7G 2.8 52.6 + - - +
276B ASN* 3.9 17.3 - - - +
363B GLY 4.7 14.2 - - - +
364B LEU 5.4 0.3 - - - +
365B MET* 3.9 19.2 - - - +
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Residues in contact with ILE 436 (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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257A VAL* 4.5 8.7 - - + -
283A LYS* 3.2 46.9 + - - +
286A VAL* 4.0 21.8 - - + -
287A HIS* 3.8 28.0 - - + +
432A LEU* 3.1 19.2 + - + +
433A LEU* 3.1 19.3 + - + +
435A GLU* 1.3 77.1 - - - +
437A TYR* 1.3 58.9 + - + +
438A LYS 3.2 0.4 + - - -
439A ASP* 4.8 0.9 + - - +
503A PGO 3.3 22.0 - - + +
507A B7G 3.6 25.1 - - + -
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Residues in contact with TYR 437 (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 HIS* 2.8 37.6 + + - -
410A VAL* 6.2 1.3 - - + -
413A HIS* 3.1 14.1 - + - -
414A ALA* 4.1 28.0 - - + -
417A MET* 3.9 24.7 - - + -
429A LEU* 4.4 13.0 - - + -
433A LEU* 3.0 31.5 + - + +
434A GLN* 3.4 6.3 - - - +
436A ILE* 1.3 73.0 - - - +
438A LYS* 1.3 63.2 + - - +
439A ASP* 3.2 10.0 + - - +
502A 7U7 2.8 20.9 + - - -
503A PGO 3.4 24.0 - - - -
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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