Contacts of the strand formed by residues 534 - 542 (chain A) in PDB entry 3IJE
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 GLN 534 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478A CYS* 3.2 0.6 - - - -
479A LEU 3.1 23.7 + - - +
525A MET* 3.1 27.5 - - + +
526A THR* 2.9 32.3 + - - +
527A ILE* 3.2 21.5 - - + -
532A LEU* 2.7 12.2 + - + +
533A MET* 1.3 70.3 - - - +
535A CYS* 1.3 64.8 - - - +
536A GLU* 3.8 16.6 + - - -
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Residues in contact with CYS 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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476A ARG* 4.0 26.7 - - + -
477A PHE 3.2 9.4 - - - -
478A CYS* 2.0 43.5 - - - -
525A MET* 3.7 3.9 - - - +
533A MET 3.5 3.0 + - - +
534A GLN* 1.3 74.6 - - - +
536A GLU* 1.3 77.3 + - - +
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Residues in contact with GLU 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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476A ARG* 3.9 1.1 - - - -
477A PHE* 3.4 61.0 + - + +
523A LYS* 4.5 19.7 - - + +
525A MET* 3.4 16.9 - - + +
534A GLN* 3.8 11.1 + - - -
535A CYS* 1.3 89.0 - - - +
537A GLU* 1.3 64.9 + - - +
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Residues in contact with GLU 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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450A TYR* 5.6 5.2 - - - -
474A ASN* 2.8 36.0 + - - +
475A VAL 3.6 2.5 - - - -
476A ARG* 3.4 42.4 + - + +
536A GLU* 1.3 77.3 - - - +
538A LEU* 1.3 71.5 + - - +
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Residues in contact with LEU 538 (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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474A ASN* 3.3 4.6 - - - +
475A VAL* 2.7 47.3 + - + +
477A PHE* 4.4 20.0 - - + -
497A LEU* 4.5 5.8 - - + -
513A PHE* 4.4 30.3 - - + -
515A TYR* 5.9 6.1 - - + -
521A HIS* 3.3 45.1 - - + +
537A GLU* 1.3 80.8 - - - +
539A ILE* 1.3 63.1 + - + +
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Residues in contact with ILE 539 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461A CYS* 5.8 0.7 - - + -
472A CYS* 5.3 10.3 - - + -
473A PHE 3.4 10.5 - - - +
474A ASN* 3.2 34.5 - - + +
513A PHE* 4.0 2.0 - - - +
514A LEU* 3.0 54.7 + - + +
515A TYR* 3.7 20.4 - - + -
538A LEU* 1.3 75.7 - - + +
540A ALA* 1.3 59.8 + - - +
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Residues in contact with ALA 540 (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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472A CYS* 4.0 2.2 - - - -
473A PHE* 2.8 65.9 + - + +
475A VAL* 4.3 3.6 - - + -
499A LEU* 3.9 9.9 - - + -
512A LEU 3.1 15.3 - - - +
513A PHE* 3.7 23.1 - - + +
514A LEU* 5.4 0.2 - - - -
538A LEU 3.9 1.4 + - - -
539A ILE* 1.3 74.7 - - - +
541A TYR* 1.3 54.6 + - - +
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Residues in contact with TYR 541 (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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463A LEU* 4.3 15.0 - - + +
470A VAL* 3.5 36.6 - - + -
471A SER 3.9 0.2 - - - -
472A CYS* 3.7 12.1 - - + +
473A PHE* 4.4 2.7 - - - -
511A ALA* 3.5 6.2 - - - +
512A LEU* 2.7 72.3 + - + +
513A PHE 3.4 22.2 - - - -
514A LEU* 3.8 19.7 - - + -
517A ARG* 3.5 29.2 - - + +
539A ILE 4.3 0.2 - - - -
540A ALA* 1.3 75.0 - - - +
542A LEU* 1.3 77.1 + - - +
543A ARG* 4.7 7.0 - - + -
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Residues in contact with LEU 542 (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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454A LEU* 4.0 31.0 - - + -
456A GLN* 3.9 27.6 - - + -
470A VAL* 4.3 10.7 - - - +
471A SER* 3.1 29.6 + - - +
510A ARG* 3.0 29.4 - - + +
511A ALA* 4.3 4.9 - - + -
541A TYR* 1.3 87.0 - - - +
543A ARG* 1.3 71.8 + - - +
548A PHE* 4.6 7.9 - - + -
555A ILE* 3.7 25.1 - - + -
592A ILE* 4.2 9.9 - - + -
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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