Contacts of the helix formed by residues 434 - 440 (chain A) in PDB entry 1Y8B
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 434 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A TYR 5.9 0.4 - - - +
91A LEU* 5.3 6.2 - - - +
92A VAL* 2.5 34.5 + - + +
93A PRO 2.5 33.1 - - - +
94A GLN* 3.4 22.7 + - - +
431A THR* 5.1 2.0 - - - +
432A SER 3.1 2.3 - - - +
433A LEU* 1.3 93.0 + - + +
435A LEU* 1.3 50.4 + - - +
436A ARG* 2.6 8.7 + - - +
437A SER* 2.5 39.0 + - - +
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Residues in contact with LEU 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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424A ILE* 5.4 2.0 - - + -
426A ASP* 4.7 10.3 - - - +
427A GLU* 5.1 0.2 - - - +
431A THR* 3.1 42.8 - - - +
432A SER* 3.7 13.4 + - - +
434A ASN* 1.3 76.0 - - - +
436A ARG* 1.3 61.0 + - - +
437A SER 3.0 1.3 + - - -
438A CYS* 3.9 9.9 - - + +
439A ILE* 3.0 27.1 + - + +
449A ILE* 4.2 37.2 - - + -
488A ASN* 6.1 0.7 - - - +
489A ASN* 3.7 24.9 - - - +
492A SER* 5.5 11.4 - - - -
493A GLY* 5.7 5.4 - - - +
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Residues in contact with ARG 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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94A GLN* 3.6 28.2 - - + +
95A PRO* 3.3 14.9 - - + +
96A GLU* 2.9 52.7 + - - +
97A ARG* 4.2 1.8 - - - +
98A VAL* 4.2 6.1 - - + +
434A ASN* 2.6 8.3 + - - +
435A LEU* 1.3 76.8 - - - +
437A SER* 1.3 56.7 + - - +
439A ILE* 3.1 21.9 - - + +
440A ALA* 3.4 2.6 + - - +
492A SER* 5.3 20.5 + - - +
497A GLY* 4.7 20.6 - - - +
569A PHE* 3.8 27.5 - - - -
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Residues in contact with SER 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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92A VAL* 4.3 9.2 - - - +
93A PRO 3.8 15.7 - - - -
95A PRO* 3.4 22.4 - - - +
395A GLY 5.7 0.9 - - - -
396A PRO* 5.4 12.5 - - - +
399A VAL* 4.2 7.8 - - - +
434A ASN* 2.5 28.1 + - - +
436A ARG* 1.3 71.8 - - - +
438A CYS* 1.3 79.4 + - - +
439A ILE 3.2 1.1 - - - -
440A ALA* 2.8 20.1 + - - +
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Residues in contact with CYS 438 (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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393A MET* 3.0 41.0 - - + +
395A GLY 6.4 0.7 - - - +
399A VAL* 3.9 13.3 - - - +
424A ILE* 3.7 11.5 - - - +
427A GLU* 3.4 17.3 - - - -
431A THR* 3.6 25.4 - - + -
434A ASN 3.6 0.6 + - - -
435A LEU* 3.3 11.6 + - + +
437A SER* 1.3 85.2 + - - +
439A ILE* 1.3 62.1 + - - +
440A ALA 3.2 0.2 + - - -
441A GLN* 3.4 15.2 + - - +
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Residues in contact with ILE 439 (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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98A VAL* 4.7 7.0 - - + -
100A VAL* 5.5 1.8 - - + -
424A ILE* 4.8 7.9 - - - -
435A LEU* 3.0 23.2 + - + +
436A ARG* 3.1 17.3 - - - +
438A CYS* 1.3 74.4 - - - +
440A ALA* 1.3 56.9 + - - +
441A GLN* 2.2 25.1 + - - +
442A ALA* 2.9 10.7 + - - +
446A VAL* 4.0 8.9 - - + +
447A ALA 4.2 9.4 - - - +
449A ILE* 3.6 31.9 - - + -
493A GLY* 5.6 3.6 - - - -
497A GLY 4.0 10.1 - - - +
498A LEU* 3.6 40.8 - - + +
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Residues in contact with ALA 440 (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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95A PRO* 3.4 30.3 - - + -
98A VAL* 3.9 17.9 - - + +
399A VAL* 4.4 6.2 - - + +
403A ASN* 5.2 0.3 + - - -
437A SER* 2.8 16.4 + - - +
439A ILE* 1.3 80.0 - - - +
441A GLN* 1.3 50.6 + - - +
442A ALA* 2.5 18.7 + - - +
443A ARG* 3.8 4.0 + - - +
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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