Contacts of the strand formed by residues 513 - 520 (chain A) in PDB entry 3HN8
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 GLY 513 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473A LEU* 3.3 9.6 - - - +
474A ILE* 2.5 43.1 + - - -
512A VAL* 1.3 77.9 - - - +
514A LEU* 1.3 57.2 + - - -
535A VAL 3.6 10.5 - - - -
536A GLY* 4.3 3.8 - - - -
537A PRO* 4.7 1.8 - - - -
548A TRP* 4.0 12.1 - - - -
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Residues in contact with LEU 514 (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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437A LEU* 4.7 6.5 - - + -
446A LEU* 4.7 11.9 - - + -
448A VAL* 3.6 34.5 - - + -
471A ALA* 4.4 4.9 - - + -
472A SER 3.3 16.2 - - - +
473A LEU* 4.2 5.4 - - + -
474A ILE* 4.1 3.8 - - - +
502A PHE* 4.5 6.7 - - + -
513A GLY* 1.3 76.2 - - - +
515A SER* 1.3 60.2 + - - +
516A ILE* 3.6 21.4 + - + +
534A ARG* 3.9 1.8 - - - +
535A VAL* 2.9 57.6 + - + +
548A TRP* 3.2 28.3 - - + +
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Residues in contact with SER 515 (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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470A LYS 3.3 4.0 - - - +
472A SER* 2.9 37.7 + - - -
474A ILE* 3.4 26.6 - - - +
514A LEU* 1.3 71.5 - - - +
516A ILE* 1.3 61.6 + - - +
517A ALA* 5.0 1.4 - - - +
532A VAL* 3.5 22.2 - - - +
533A CYS 3.7 4.9 - - - -
534A ARG* 3.8 18.0 + - - +
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Residues in contact with ILE 516 (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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433A LEU* 3.5 15.0 - - + -
435A PHE* 4.1 23.6 - - + -
448A VAL* 4.1 10.3 - - + -
450A ILE* 4.0 7.9 - - + -
469A VAL* 3.4 31.4 - - + -
470A LYS 3.5 4.5 - - - +
471A ALA* 3.6 22.4 - - + -
514A LEU* 3.6 30.7 - - + +
515A SER* 1.3 73.0 - - - +
517A ALA* 1.3 59.0 + - - +
532A VAL* 3.1 4.2 - - - +
533A CYS* 2.8 45.8 + - - +
535A VAL* 5.0 2.5 - - + -
565A LEU* 5.7 0.2 - - - -
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Residues in contact with ALA 517 (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 VAL* 4.4 2.5 - - - -
470A LYS* 2.9 40.0 + - + +
515A SER* 5.0 2.2 - - - +
516A ILE* 1.3 79.0 - - - +
518A VAL* 1.3 64.0 + - - +
519A VAL* 3.5 13.6 - - + +
529A VAL* 4.7 5.2 - - + -
531A GLY 3.3 14.1 - - - +
532A VAL* 3.8 17.7 - - + +
565A LEU* 5.3 0.7 - - - -
568A GLU* 6.0 0.2 - - - +
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Residues in contact with VAL 518 (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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433A LEU* 3.9 29.6 - - + +
453A ALA* 4.9 2.0 - - + -
456A LEU* 3.7 31.9 - - + -
467A PRO* 4.1 7.9 - - + -
468A TYR 3.5 9.0 - - - +
469A VAL* 4.4 8.7 - - + +
496A TYR* 5.3 0.7 - - + +
517A ALA* 1.3 71.1 - - - +
519A VAL* 1.3 64.3 + - - +
529A VAL* 3.7 1.2 - - - +
530A ILE* 2.9 35.6 + - + -
531A GLY 3.0 12.5 + - - +
565A LEU* 3.6 31.9 - - + +
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Residues in contact with VAL 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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467A PRO* 3.2 4.0 - - - +
468A TYR* 2.8 83.6 + - + +
470A LYS* 4.6 13.9 - - + +
517A ALA* 3.5 17.0 - - + +
518A VAL* 1.3 80.3 - - - +
520A ASP* 1.3 66.3 + - - +
527A ASN* 3.9 7.4 - - + +
528A GLU 3.5 21.1 - - - +
529A VAL* 3.9 17.0 - - + +
530A ILE* 4.1 2.5 - - - +
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Residues in contact with ASP 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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459A MET* 3.4 29.6 - - + +
460A ASP* 3.2 5.0 - - - +
465A SER* 4.1 0.9 - - - -
466A ASP 2.7 34.4 + - - -
519A VAL* 1.3 70.6 - - - +
521A TYR* 1.3 75.4 + - - +
522A ASP* 2.8 5.5 - - - +
527A ASN* 3.5 4.3 - - - +
528A GLU* 2.9 38.5 + - + +
530A ILE* 3.7 11.1 - - + +
602A CA 2.5 30.1 - - - -
605A CA 3.0 4.3 - - - -
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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