Contacts of the strand formed by residues 524 - 531 (chain A) in PDB entry 1ZJA
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 ILE 524 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504A LEU* 4.1 11.4 - - + -
518A LEU* 3.5 22.4 - - + -
523A HIS* 1.3 75.0 - - - +
525A ALA* 1.3 63.0 + - - +
526A GLU 3.7 23.8 - - - +
527A THR* 4.5 0.2 - - - +
537A PRO* 4.1 22.7 - - + +
538A ALA 4.1 12.3 - - - +
539A ALA* 5.2 1.6 - - - -
540A GLY* 2.7 28.2 + - - -
541A ALA* 3.0 27.5 + - + +
544A LEU* 4.5 9.0 - - + -
554A TYR* 4.0 23.3 - - + -
555A LYS 4.1 2.9 - - - +
556A VAL* 4.4 2.2 - - + +
557A LYS* 3.4 4.9 - - - -
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Residues in contact with ALA 525 (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 HIS 3.6 0.2 + - - -
524A ILE* 1.3 76.6 - - - +
526A GLU* 1.3 60.7 + - + +
539A ALA* 4.2 16.8 - - - +
540A GLY 5.1 0.2 - - - +
555A LYS* 2.8 34.7 + - + +
556A VAL 4.0 9.0 - - - +
557A LYS* 4.0 23.8 - - + +
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Residues in contact with GLU 526 (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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524A ILE* 3.7 4.5 - - - +
525A ALA* 1.3 81.3 - - + +
527A THR* 1.3 64.7 + - - +
528A LEU* 4.0 6.7 - - + -
554A TYR* 3.3 9.7 - - - +
555A LYS* 3.0 39.8 + - + +
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Residues in contact with THR 527 (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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524A ILE* 4.5 0.9 - - - +
526A GLU* 1.3 74.4 - - - +
528A LEU* 1.3 65.8 + - - +
529A ILE* 3.9 8.1 - - - +
530A GLU* 3.7 30.1 - - + -
536A ALA* 3.6 19.9 - - + +
537A PRO* 3.3 28.6 + - - +
553A ILE 4.0 2.5 - - - -
554A TYR* 3.4 13.5 - - + -
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Residues in contact with LEU 528 (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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465A ASN* 5.4 1.4 + - - -
469A ILE* 3.7 38.3 - - + +
473A THR* 4.2 8.7 - - - +
476A LEU* 4.9 1.3 - - + -
503A TYR* 3.8 24.0 - - + -
526A GLU* 4.4 7.4 - - + +
527A THR* 1.3 76.4 - - - +
529A ILE* 1.3 65.4 + - - +
553A ILE* 2.9 26.8 + - + +
555A LYS* 3.8 36.1 - - + +
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Residues in contact with ILE 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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352A THR* 5.6 0.7 - - - +
462A PHE* 3.6 32.1 - - + -
465A ASN* 3.0 42.6 - - + +
466A LEU* 3.9 11.9 - - + +
469A ILE* 3.6 17.5 - - + -
527A THR* 3.5 3.6 - - - -
528A LEU* 1.3 80.0 - - - +
530A GLU* 1.3 74.8 + - - +
552A GLY* 3.2 0.8 - - - -
553A ILE* 3.0 54.3 + - + +
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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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462A PHE* 3.8 12.6 - - - -
527A THR* 3.7 11.4 - - + +
529A ILE* 1.3 85.2 - - - +
531A SER* 1.3 62.9 + - - +
533A SER* 2.8 35.5 + - - -
535A ALA 3.6 0.7 - - - +
536A ALA* 3.4 23.6 + - - +
537A PRO* 3.7 6.9 - - - +
544A LEU* 5.3 0.7 - - - +
550A GLN* 3.2 10.3 + - - -
551A SER 3.0 9.9 - - - +
554A TYR* 2.5 36.5 + - - +
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Residues in contact with SER 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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345A ALA 4.7 0.3 + - - -
348A LYS* 3.8 28.7 - - - +
349A ALA 4.3 2.3 + - - -
462A PHE* 3.5 23.1 - - - -
530A GLU* 1.3 73.8 - - - +
532A SER* 1.3 71.9 + - - +
533A SER 3.1 2.2 + - - -
549A TRP 4.3 3.3 + - - -
550A GLN* 3.1 18.2 - - - +
551A SER* 2.7 33.9 + - - -
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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