Contacts of the strand formed by residues 520 - 528 (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 SER 520 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496A GLU* 3.7 8.1 - - - -
497A LEU 3.5 5.2 - - - -
498A LEU* 3.5 19.7 - - - -
513A PHE* 3.7 2.3 - - - -
516A SER* 4.5 2.4 + - - -
518A SER* 3.2 23.6 + - - -
519A PRO* 1.3 83.2 - - - +
521A HIS* 1.3 64.9 + - - +
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Residues in contact with HIS 521 (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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477A PHE* 5.9 0.4 - - - -
496A GLU* 3.0 8.1 + - - +
497A LEU* 2.9 37.1 + - + +
513A PHE* 3.3 25.1 - + + -
516A SER* 4.4 20.0 - - - -
520A SER* 1.3 74.8 - - - +
522A SER* 1.3 84.7 + - - +
523A LYS* 5.0 10.6 - - + +
538A LEU* 3.3 37.6 - - + +
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Residues in contact with SER 522 (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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494A GLN* 3.9 17.4 + - - -
495A VAL 3.5 3.1 - - - -
496A GLU* 2.6 20.9 + - - -
497A LEU* 6.5 0.2 - - - -
521A HIS* 1.3 99.5 + - - +
523A LYS* 1.3 62.6 + - - +
2524A NAG 5.1 11.2 - - - -
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Residues in contact with LYS 523 (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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477A PHE* 4.0 33.2 - - + -
494A GLN* 4.1 2.4 - - - +
495A VAL* 3.1 34.3 + - + +
497A LEU* 6.2 0.9 - - + -
521A HIS* 5.0 8.7 - - + +
522A SER* 1.3 81.6 - - - +
524A ASN* 1.3 88.9 + - - +
525A MET* 3.0 14.4 + - + +
536A GLU* 4.5 21.0 - - + +
2524A NAG 5.8 1.3 - - - -
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Residues in contact with ASN 524 (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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493A PHE 3.8 4.3 - - - +
494A GLN* 2.7 30.9 - - - +
523A LYS* 1.3 87.2 - - - +
525A MET* 1.3 60.6 + - - +
526A THR* 4.3 4.0 + - - +
564A ASP* 5.2 4.3 - - - +
2524A NAG 1.5 71.9 + - - +
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Residues in contact with MET 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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477A PHE* 3.8 27.6 - - + -
479A LEU* 4.6 9.2 - - + -
492A ASN* 3.5 2.3 - - - +
493A PHE* 2.7 49.0 + - + +
495A VAL* 4.1 13.5 - - + -
523A LYS* 3.0 10.8 + - + +
524A ASN* 1.3 71.8 - - - +
526A THR* 1.3 67.0 + - - +
527A ILE* 4.0 11.2 - - + -
534A GLN* 3.1 51.1 - - + +
535A CYS* 3.7 9.2 - - - -
536A GLU* 3.4 25.4 - - - +
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Residues in contact with THR 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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490A LYS* 3.3 33.4 - - + +
491A LEU 3.3 7.0 - - - +
492A ASN* 3.0 26.1 + - - +
524A ASN* 4.6 4.5 + - - +
525A MET* 1.3 78.4 + - - +
527A ILE* 1.3 61.4 + - - +
528A SER* 5.1 0.9 - - - -
534A GLN* 2.9 19.5 + - - +
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Residues in contact with ILE 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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479A LEU* 3.6 42.4 - - + +
481A ALA* 3.2 43.7 - - + +
490A LYS* 3.9 1.6 - - - -
491A LEU* 2.9 32.2 + - + +
493A PHE* 3.5 26.0 - - + -
525A MET* 4.0 11.6 - - + -
526A THR* 1.3 76.0 - - - +
528A SER* 1.3 66.6 + - - +
532A LEU 4.8 3.4 - - - +
534A GLN* 3.2 29.4 - - + +
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Residues in contact with SER 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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481A ALA 4.3 5.4 + - - +
489A ARG* 2.9 21.8 - - - -
490A LYS* 4.4 3.4 - - - -
491A LEU* 4.5 2.7 - - - +
526A THR 5.1 0.7 - - - -
527A ILE* 1.3 82.4 - - - +
529A ARG* 1.3 76.0 + - - +
530A GLY* 2.9 17.2 + - - -
531A GLY 5.0 0.2 + - - -
532A LEU* 4.4 23.8 + - - +
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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