Contacts of the helix formed by residues 529 - 537 (chain A) in PDB entry 1ASZ
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 LEU 529 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A GLN* 3.4 51.4 - - + +
254A VAL* 4.3 19.1 - - + -
255A CYS* 3.5 14.6 - - - -
339A THR* 3.0 27.6 + - - +
340A GLY* 4.4 0.6 - - - -
341A LEU* 4.6 16.2 - - + +
527A ILE 3.9 2.4 + - - -
528A GLY* 1.3 71.4 - - - +
530A GLU* 1.3 68.9 + - - +
532A VAL* 3.6 3.9 + - - +
533A VAL* 3.5 15.2 + - + +
271B HIS* 3.5 30.3 - - + +
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Residues in contact with GLU 530 (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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251A GLN* 3.9 6.1 + - - +
335A MET* 3.4 17.9 - - + -
338A PHE* 2.9 17.9 - - + +
339A THR* 2.9 49.3 + - - +
528A GLY 3.3 0.8 - - - -
529A LEU* 1.3 86.3 - - - +
531A ARG* 1.3 55.5 + - - +
533A VAL* 3.1 11.4 - - - +
534A MET* 2.9 28.6 + - - +
542A ILE* 3.4 26.9 - - + -
545A ALA* 3.4 20.1 - - - +
546A SER* 4.1 5.8 - - - -
701A ATP 5.6 0.7 - - + -
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Residues in contact with ARG 531 (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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333A ARG* 3.4 31.3 - - + +
334A HIS* 2.8 38.2 + - - -
478A GLU* 3.2 25.8 + - - +
479A ILE* 4.2 8.5 - - + -
528A GLY* 3.3 9.0 + - - +
530A GLU* 1.3 73.0 - - - +
532A VAL* 1.3 69.3 + - - +
534A MET* 4.1 6.1 - - - -
535A PHE* 2.9 50.2 + - + -
542A ILE* 4.3 9.0 - - + -
701A ATP 2.5 77.0 + - - +
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Residues in contact with VAL 532 (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 29.4 - - + -
362A PHE* 4.2 9.9 - - + -
365A ILE* 5.2 9.0 - - + -
366A PHE* 5.2 0.9 - - + -
369A LEU* 5.8 1.6 - - + -
474A MET* 4.0 20.8 - - + +
479A ILE* 4.0 21.1 - - + -
527A ILE* 3.4 33.0 - - + -
528A GLY 3.2 5.1 + - - +
529A LEU* 3.9 7.4 - - - +
530A GLU 3.4 0.4 - - - -
531A ARG* 1.3 81.0 - - - +
533A VAL* 1.3 63.0 + - - +
536A TYR* 3.0 26.1 + - + +
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Residues in contact with VAL 533 (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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247A ILE* 4.1 18.2 - - + +
250A ILE* 3.7 29.8 - - + -
251A GLN* 4.1 17.7 - - + +
254A VAL* 5.4 4.3 - - + -
529A LEU* 3.5 12.3 + - + +
530A GLU* 3.1 14.3 + - - +
532A VAL* 1.3 80.5 - - - +
534A MET* 1.3 69.8 + - - +
536A TYR* 4.4 4.7 - - - -
537A LEU* 3.3 26.4 + - + +
539A LEU* 3.9 2.4 - - - +
545A ALA* 3.2 25.8 - - + +
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Residues in contact with MET 534 (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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332A HIS* 3.2 36.3 - - - +
333A ARG* 4.6 2.5 - - - -
477A GLU* 4.6 0.4 - - - +
530A GLU 2.9 18.0 + - - +
531A ARG* 3.5 6.7 - - - +
532A VAL 3.2 0.2 - - - -
533A VAL* 1.3 82.9 - - - +
535A PHE* 1.3 85.6 + - + +
537A LEU* 3.0 0.5 + - - +
538A ASP 2.8 28.1 + - - -
539A LEU* 3.3 15.7 + - + -
540A LYS* 3.7 26.2 - - - +
541A ASN 4.2 11.7 - - - +
542A ILE* 3.3 30.3 - - - +
545A ALA* 4.5 4.9 - - + -
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Residues in contact with PHE 535 (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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333A ARG* 4.7 5.6 - - + -
474A MET* 3.8 29.4 - - + +
475A ARG* 2.6 52.2 + - + +
477A GLU* 2.9 45.8 - - + -
478A GLU 4.0 3.4 - - - -
479A ILE* 3.5 20.0 - - + -
531A ARG* 2.9 54.4 + - + +
532A VAL 4.3 0.4 - - - +
534A MET* 1.3 101.7 - - + +
536A TYR* 1.3 55.3 + - - +
538A ASP* 3.1 7.6 + - - +
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Residues in contact with TYR 536 (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 ILE* 5.4 2.2 - - + -
366A PHE* 3.7 27.8 + + - -
369A LEU* 3.8 26.1 - - + +
370A PRO* 3.6 27.0 - - - +
377A ILE* 3.4 28.0 - - + +
386A VAL* 5.4 1.0 - - - +
387A GLU 5.4 0.3 - - - +
389A PHE* 3.9 30.6 + + + +
474A MET* 3.8 23.0 - - + +
475A ARG* 2.6 22.5 + - - +
532A VAL* 3.0 23.2 + - + +
533A VAL* 3.9 5.8 - - - +
535A PHE* 1.3 75.7 - - - +
537A LEU* 1.3 80.9 + - + +
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Residues in contact with LEU 537 (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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247A ILE* 4.4 8.1 - - + -
250A ILE* 4.1 18.6 - - + -
377A ILE* 3.6 31.2 - - + -
380A VAL* 4.4 22.6 - - + +
384A TYR* 5.0 3.8 - - - +
386A VAL* 3.8 16.5 - - - +
533A VAL* 3.6 27.8 - - + +
534A MET 3.0 3.0 + - - -
536A TYR* 1.3 100.3 - - + +
538A ASP* 1.3 69.3 + - - +
539A LEU* 3.1 28.8 + - + +
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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