Contacts of the helix formed by residues 433 - 441 (chain B) in PDB entry 2A72
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 ASP 433 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429B LEU* 3.0 14.4 + - + +
430B MET* 3.4 1.8 + - - -
431B LYS 3.6 0.2 - - - -
432B SER* 1.3 81.8 - - - +
434B SER* 1.3 71.8 + - - +
435B TYR 3.4 1.1 - - - -
436B PRO* 3.2 3.2 - - - +
437B ARG* 2.7 67.3 + - - +
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Residues in contact with SER 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A PHE* 3.5 18.9 - - - -
351A LEU* 3.7 31.0 - - - +
356A SER* 4.4 8.5 + - - -
359A ASN* 4.8 8.3 + - - +
430B MET* 3.4 26.4 + - - +
433B ASP* 1.3 83.6 + - - +
435B TYR* 1.3 62.9 + - - +
437B ARG* 3.5 6.9 + - - +
438B PHE* 3.1 17.2 + - - +
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Residues in contact with TYR 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A TRP 2.6 30.2 + - - -
331A GLY* 3.3 12.0 + - - -
333A GLY* 3.0 23.7 + - - -
334A MET* 3.6 41.1 - - + -
337A ALA* 4.1 10.1 - - + -
347A PHE* 3.6 19.7 - + + -
430B MET 2.9 21.4 + - - +
431B LYS* 4.6 7.2 - - + -
434B SER* 1.3 71.7 - - - +
436B PRO* 1.4 72.5 - - + +
438B PHE* 3.0 19.7 + + - +
439B ILE* 3.0 35.4 + - + +
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Residues in contact with PRO 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B MET 3.5 3.4 - - - +
431B LYS 3.4 24.0 - - - +
432B SER* 3.7 17.3 - - - +
433B ASP 3.2 9.2 - - - +
435B TYR* 1.4 99.7 - - + +
437B ARG* 1.3 59.4 + - + +
439B ILE* 3.5 5.5 + - + +
440B ARG* 3.2 51.1 + - - +
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Residues in contact with ARG 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A PHE* 3.6 16.3 - - + -
351A LEU* 6.1 0.9 - - - -
354A GLU* 4.5 14.0 + - - +
433B ASP* 2.7 51.0 + - - +
434B SER* 3.6 6.5 - - - +
436B PRO* 1.3 73.6 - - + +
438B PHE* 1.3 60.7 + - - +
440B ARG* 3.3 10.1 + - - +
441B SER* 3.0 28.1 + - - -
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Residues in contact with PHE 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A TRP* 4.3 12.6 - + + -
337A ALA* 4.9 7.6 - - + -
343A GLY 4.4 2.7 - - - -
346A GLN* 3.7 28.0 - - + -
347A PHE* 3.7 44.6 - + + -
350A PHE* 3.6 30.5 - + + -
434B SER 3.1 12.9 + - - +
435B TYR* 3.0 14.2 + + - +
437B ARG* 1.3 75.2 - - - +
439B ILE* 1.3 71.0 + - + +
441B SER* 2.6 29.4 + - - -
443B ALA* 5.3 3.6 - - + -
444B TYR* 3.3 42.0 - + + +
447B LEU* 5.4 1.1 - - + -
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Residues in contact with ILE 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A TRP 3.9 7.9 - - - +
331A GLY* 3.9 15.0 - - - +
435B TYR* 3.0 54.0 + - + +
436B PRO* 3.9 7.4 - - + +
438B PHE* 1.3 82.2 - - + +
440B ARG* 1.3 64.7 + - + +
441B SER 3.6 0.2 + - - -
444B TYR* 3.3 43.7 - - + -
445B GLN* 3.4 11.9 + - - +
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Residues in contact with ARG 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436B PRO* 3.2 45.8 + - - +
437B ARG* 3.7 8.5 - - - +
438B PHE 3.2 0.2 - - - -
439B ILE* 1.3 81.6 - - + +
441B SER* 1.3 64.1 + - - +
442B SER 3.8 0.5 + - - -
445B GLN* 4.8 7.0 - - - +
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Residues in contact with SER 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A PHE* 3.3 40.3 - - - -
437B ARG 3.0 5.2 + - - -
438B PHE* 2.6 24.9 + - - -
439B ILE 3.3 0.2 - - - -
440B ARG* 1.3 81.2 - - - +
442B SER* 1.3 65.2 + - - +
443B ALA* 3.7 4.7 + - - +
444B TYR* 3.2 15.4 + - - +
445B GLN* 3.1 22.1 + - - +
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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