Contacts of the strand formed by residues 518 - 524 (chain A) in PDB entry 3N8E
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 518 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470A GLN 3.8 0.2 - - - +
471A VAL* 3.3 2.6 - - - +
472A PHE* 2.8 50.4 + - + +
473A SER* 4.5 7.6 - - - -
474A THR* 5.2 0.4 - - + +
482A VAL* 4.1 22.9 - - + -
484A ILE* 5.1 0.4 - - + -
505A LEU* 3.8 34.5 - - + -
508A ILE* 4.0 10.8 - - + -
516A PRO* 4.0 15.0 - - + +
517A GLN* 1.4 75.5 - - - +
519A GLU* 1.3 62.3 + - - +
520A VAL* 3.4 19.4 + - + -
534A ALA* 4.3 6.5 - - + -
535A LYS 3.4 3.4 - - - +
536A ASP* 4.0 22.4 - - - +
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Residues in contact with GLU 519 (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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469A SER* 3.9 22.8 - - - -
470A GLN 3.8 5.8 + - - +
471A VAL* 3.8 23.3 - - + +
517A GLN 3.8 1.8 + - - -
518A ILE* 1.3 70.3 - - - +
520A VAL* 1.3 60.4 + - - +
521A THR* 4.0 14.3 + - - +
533A SER* 3.7 2.3 + - - +
534A ALA* 3.4 2.6 - - - -
535A LYS* 2.8 48.1 + - + +
537A LYS* 3.9 28.7 + - + +
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Residues in contact with VAL 520 (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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447A ILE* 4.1 19.7 - - + -
457A LEU* 4.0 14.4 - - + +
468A LYS 3.9 1.0 - - - +
469A SER* 3.4 2.8 - - - -
470A GLN 2.9 29.0 + - - -
472A PHE* 3.8 24.9 - - + -
484A ILE* 4.1 24.7 - - + -
518A ILE* 3.4 8.7 + - + -
519A GLU* 1.3 75.4 - - - +
521A THR* 1.3 61.7 + - - +
522A PHE* 4.5 3.1 - - + -
532A VAL* 3.8 24.9 - - + -
533A SER 3.2 3.6 - - - +
534A ALA* 4.2 7.9 - - + -
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Residues in contact with THR 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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467A LYS* 3.6 27.8 - - + -
468A LYS 3.5 3.4 - - - +
469A SER* 3.2 22.5 + - - +
519A GLU* 4.0 12.6 + - - +
520A VAL* 1.3 73.3 - - - +
522A PHE* 1.3 64.7 + - - +
523A ASP* 3.7 18.6 + - - +
531A HIS 3.4 1.9 - - - +
532A VAL* 3.2 5.6 - - - -
533A SER* 3.0 44.8 + - - -
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Residues in contact with PHE 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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445A LEU* 3.7 23.6 - - + -
446A GLY* 3.4 30.7 - - - -
447A ILE* 3.6 22.2 - - + -
457A LEU* 3.8 23.1 - - + -
458A ILE* 3.5 31.8 - - + +
466A THR 3.8 0.9 - - - +
467A LYS* 3.2 8.0 - - - +
468A LYS 2.8 33.7 + - - +
486A VAL* 3.6 24.2 - - + -
520A VAL* 4.5 0.9 - - + -
521A THR* 1.3 71.1 - - - +
523A ASP* 1.3 61.1 + - - +
524A ILE* 5.2 1.6 - - + -
530A VAL* 4.3 11.4 - - + -
531A HIS 3.4 2.7 - - - -
532A VAL* 3.7 23.3 - - + -
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Residues in contact with ASP 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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466A THR 3.6 3.3 - - - +
467A LYS* 3.4 26.6 - - - +
521A THR* 3.7 18.1 + - - +
522A PHE* 1.3 72.4 - - - +
524A ILE* 1.3 61.3 + - - +
525A ASP 4.0 0.7 - - - +
530A VAL* 3.6 1.2 - - - -
531A HIS* 2.7 61.3 + - + +
533A SER* 5.4 2.1 + - - -
544A GLN* 4.9 4.3 - - - +
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Residues in contact with ILE 524 (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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441A THR* 3.8 17.0 - - + -
445A LEU* 3.5 31.2 - - + -
458A ILE* 3.7 23.1 - - + -
464A ILE* 3.8 13.7 - - + -
465A PRO* 3.2 8.3 - - - +
466A THR* 2.9 38.1 + - + +
522A PHE* 5.2 2.7 - - + -
523A ASP* 1.3 78.4 - - - +
525A ASP* 1.3 69.4 + - - +
528A GLY* 3.7 25.8 - - - +
529A ILE 3.4 3.6 - - - +
530A VAL* 4.3 12.8 - - + -
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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