Contacts of the strand formed by residues 530 - 534 (chain A) in PDB entry 1PMS
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 ALA 530 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470A VAL* 4.6 8.5 - - + -
520A ASP* 3.6 10.7 - - - +
521A LYS* 4.8 5.4 + - - +
528A LYS 2.9 13.1 + - - +
529A HIS* 1.3 75.8 - - - +
531A PHE* 1.3 86.6 + - - +
542A ILE* 5.1 1.3 - - + -
543A PHE 2.9 15.3 - - - +
544A SER* 2.6 30.7 - - - +
551A LYS* 4.3 0.2 - - - -
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Residues in contact with PHE 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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518A ILE* 3.6 13.7 - - + -
519A ASN 3.4 11.7 - - - +
520A ASP* 3.8 12.1 - - - +
521A LYS* 5.7 0.4 - - - +
529A HIS* 4.0 4.7 - + - -
530A ALA* 1.3 92.9 - - - +
532A GLU* 1.3 62.6 + - - +
533A ILE 4.0 0.7 - - - -
542A ILE* 3.0 21.2 - - - +
543A PHE* 3.2 34.2 + + + -
544A SER* 5.1 0.4 - - - -
545A ALA 5.1 0.4 - - - -
551A LYS* 2.7 61.7 - - + -
552A ASN* 3.1 15.7 - - - -
555A MET* 3.0 43.5 - - + -
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Residues in contact with GLU 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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517A GLN 3.9 0.9 - - - +
519A ASN* 3.2 48.2 + - + +
520A ASP 4.3 4.0 - - - +
521A LYS* 4.3 32.1 + - + +
531A PHE* 1.3 76.7 - - - +
533A ILE* 1.3 63.6 + - - +
534A ILE* 4.5 12.4 - - + +
540A SER* 6.0 0.2 - - - -
542A ILE* 3.3 32.4 - - + +
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Residues in contact with ILE 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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485A MET* 6.3 1.3 - - + -
513A MET* 4.9 2.0 - - + -
516A VAL* 3.5 32.1 - - + -
517A GLN 3.0 9.9 - - - +
518A ILE* 3.0 27.4 - - + +
531A PHE 4.0 0.2 - - - -
532A GLU* 1.3 76.3 - - - +
534A ILE* 1.3 67.6 + - - +
540A SER* 3.3 5.9 - - - -
541A VAL* 2.6 57.7 + - + +
543A PHE* 3.3 16.4 - - + -
558A LEU* 3.0 38.1 - - + -
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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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515A LYS 4.8 0.5 - - - +
516A VAL* 3.6 21.7 - - - +
517A GLN* 3.4 8.6 + - + +
519A ASN* 5.7 5.2 - - - +
532A GLU* 4.5 14.1 - - + +
533A ILE* 1.3 89.1 - - - +
535A LEU* 1.3 81.6 + - - +
536A LYS* 5.3 0.2 - - - +
539A ASN 3.4 11.0 - - - +
540A SER* 3.9 12.3 - - - +
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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