Contacts of the helix formed by residues 528 - 536 (chain A) in PDB entry 1B0P
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 SER 528 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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526A LEU 3.6 1.6 + - - -
527A PRO* 1.3 71.8 - - - +
529A GLY* 1.3 64.9 + - - +
531A LYS* 3.0 16.2 + - - +
532A ARG* 2.9 44.8 + - - -
625A ALA* 4.0 13.5 - - - -
626A PRO* 3.8 23.8 - - - -
627A ALA* 3.8 16.6 - - - +
628A GLU 4.9 1.1 + - - -
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Residues in contact with GLY 529 (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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527A PRO* 3.1 4.9 - - - +
528A SER* 1.3 82.3 + - - +
530A ILE* 1.3 60.5 + - - +
532A ARG* 3.7 10.8 + - - +
533A THR* 2.9 30.1 + - - -
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Residues in contact with ILE 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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495A VAL* 3.2 45.3 - - + +
498A TYR 5.0 2.7 - - - +
500A ILE* 4.6 13.7 - - + +
501A LEU* 3.8 19.7 - - + +
510A PHE* 4.3 7.6 - - + -
526A LEU* 3.9 14.1 - - + -
527A PRO* 2.8 22.6 + - + +
529A GLY* 1.3 77.8 - - - +
531A LYS* 1.3 58.7 + - - +
533A THR* 3.6 4.9 + - - -
534A ILE* 2.9 53.2 + - + +
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Residues in contact with LYS 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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523A ASP* 2.9 39.5 + - - +
526A LEU* 3.5 32.7 + - + +
527A PRO 3.2 4.9 + - - +
528A SER* 3.0 19.5 + - - +
530A ILE* 1.3 74.7 - - - +
532A ARG* 1.3 64.1 + - - +
534A ILE* 3.3 2.6 + - - +
535A ALA* 2.9 26.2 + - - +
622A TRP* 3.4 60.3 - - + +
625A ALA* 4.0 14.9 - - + +
626A PRO* 6.0 2.0 - - - +
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Residues in contact with ARG 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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528A SER* 2.9 39.0 + - - +
529A GLY* 3.9 9.4 - - - +
531A LYS* 1.3 76.4 - - - +
533A THR* 1.3 59.7 + - - +
535A ALA 3.2 0.3 + - - -
536A ASN* 2.8 45.6 + - - +
622A TRP 3.0 26.2 + - - -
623A LYS 3.1 22.7 + - - +
624A ASP* 4.9 1.8 - - - +
625A ALA* 2.9 29.4 + - - +
627A ALA* 4.7 8.3 - - - +
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Residues in contact with THR 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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501A LEU* 4.0 34.6 - - + +
504A ILE* 4.6 2.9 - - + -
529A GLY 2.9 21.1 + - - -
530A ILE* 3.8 4.5 - - - -
532A ARG* 1.3 77.1 - - - +
534A ILE* 1.3 56.7 + - - +
536A ASN* 4.9 2.0 - - - -
537A LYS* 2.8 66.5 + - + +
539A LEU* 4.7 1.3 - - + -
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Residues in contact with ILE 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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501A LEU* 4.0 14.4 - - + -
510A PHE* 4.0 9.6 - - + -
526A LEU* 4.1 4.7 - - + -
530A ILE* 2.9 38.8 + - + +
531A LYS 3.6 4.3 - - - +
533A THR* 1.3 75.5 - - - +
535A ALA* 1.3 58.5 + - - +
538A LYS 3.4 1.2 + - - -
539A LEU* 3.0 42.8 + - + +
541A PHE* 3.9 26.0 - - + -
618A TYR* 3.4 40.3 + - + -
622A TRP* 3.9 18.6 - - + -
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Residues in contact with ALA 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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531A LYS 2.9 16.3 + - - +
532A ARG 3.8 1.8 - - - +
534A ILE* 1.3 76.5 - - - +
536A ASN* 1.3 62.6 + - - +
538A LYS* 3.4 14.0 + - - +
618A TYR* 3.7 18.0 - - + -
619A PRO 4.6 2.2 - - - +
620A ASP* 4.6 1.3 - - - +
622A TRP* 3.7 9.6 - - + -
623A LYS* 3.3 50.6 + - + +
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Residues in contact with ASN 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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506A ASP* 4.5 6.2 - - - +
532A ARG* 2.8 42.6 + - - +
533A THR* 4.3 2.5 - - - +
535A ALA* 1.3 69.8 - - - +
537A LYS* 1.3 62.1 + - + +
538A LYS* 3.0 19.2 + - - +
623A LYS* 3.4 37.4 + - - +
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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