Contacts of the strand formed by residues 528 - 535 (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 GLU 528 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A MET* 3.2 34.1 - - + +
519A VAL* 3.7 2.7 - - - -
520A ASP* 2.9 36.5 + - - +
522A ASP* 3.0 15.0 - - - +
526A HIS 4.5 4.3 - - - +
527A ASN* 1.3 73.5 - - - +
529A VAL* 1.3 64.1 + - - +
530A ILE* 4.4 0.2 - - - +
602A CA 2.9 26.3 - - - -
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Residues in contact with VAL 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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459A MET* 4.1 11.3 - - - +
470A LYS* 5.7 5.4 - - - +
517A ALA* 4.7 5.8 - - + -
518A VAL 3.7 5.8 - - - +
519A VAL* 3.9 21.3 - - + -
527A ASN 5.4 1.6 - - - +
528A GLU* 1.3 75.6 - - - +
530A ILE* 1.3 65.7 + - - +
531A GLY* 3.6 23.8 - - - +
532A VAL* 4.2 11.9 - - + -
568A GLU* 5.3 14.8 - - + +
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Residues in contact with ILE 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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430A LEU* 3.4 47.7 - - - +
456A LEU* 4.2 13.0 - - + -
457A LYS* 3.8 21.1 - - + +
459A MET* 3.4 23.2 - - + +
465A SER* 3.8 27.8 - - - -
467A PRO* 4.6 1.8 - - + -
518A VAL* 2.9 31.6 + - + +
519A VAL 4.3 0.2 - - - -
520A ASP* 3.7 18.8 - - + +
528A GLU 3.6 0.2 + - - -
529A VAL* 1.3 76.1 - - - +
531A GLY* 1.3 60.2 + - - +
565A LEU* 4.9 1.6 - - + -
567A GLU* 5.4 0.9 - - - +
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Residues in contact with GLY 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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430A LEU* 4.0 7.6 - - - -
517A ALA* 3.3 4.3 - - - +
518A VAL 3.0 25.6 + - - +
529A VAL* 3.6 2.7 - - - +
530A ILE* 1.3 84.1 - - - +
532A VAL* 1.3 66.6 + - - +
565A LEU* 4.0 17.9 - - - +
566A VAL 3.9 8.7 - - - -
567A GLU* 5.7 0.4 - - - -
568A GLU 5.7 0.4 - - - -
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Residues in contact with VAL 532 (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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515A SER* 3.5 19.5 - - - +
516A ILE 3.1 16.4 - - - +
517A ALA* 3.8 12.8 - - + +
529A VAL* 4.2 7.4 - - + -
531A GLY* 1.3 78.7 - - - +
533A CYS* 1.3 74.6 + - - +
534A ARG* 3.9 18.2 - - - +
564A GLN 3.7 0.7 - - - +
565A LEU* 3.2 6.3 - - - -
566A VAL* 2.7 40.7 + - - +
568A GLU* 4.1 35.2 - - + +
571A LEU* 5.2 4.5 - - + -
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Residues in contact with CYS 533 (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* 4.2 9.2 - - - -
435A PHE* 4.0 21.3 - - - -
514A LEU 4.2 0.3 - - - +
515A SER* 3.7 2.3 - - - -
516A ILE* 2.8 57.4 + - - +
532A VAL* 1.3 78.7 - - - +
534A ARG* 1.3 67.7 + - - +
563A HIS* 4.1 17.7 - - + +
564A GLN 3.8 15.5 - - - +
565A LEU* 4.3 6.3 - - + -
566A VAL* 5.4 2.2 - - - -
571A LEU* 6.2 1.3 - - - -
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Residues in contact with ARG 534 (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 ILE* 4.2 8.8 - - + +
514A LEU 4.0 4.9 - - - +
515A SER* 3.8 20.5 + - - -
532A VAL* 3.9 17.4 - - - +
533A CYS* 1.3 82.3 - - - +
535A VAL* 1.3 66.4 + - - +
538A GLU 5.2 3.1 - - - +
539A ALA* 4.2 24.0 - - + -
540A ALA* 5.0 4.7 - - + +
541A ASP 6.1 0.2 - - - +
544A GLY* 3.8 14.7 - - - -
563A HIS* 4.7 5.0 + - - -
568A GLU* 4.0 10.9 + - - -
571A LEU* 3.2 53.5 - - + +
572A SER* 4.2 1.4 - - - +
573A SER* 3.1 36.6 + - - +
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Residues in contact with VAL 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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435A PHE* 4.6 15.5 - - + -
437A LEU* 4.1 10.5 - - + -
513A GLY* 3.6 1.0 - - - -
514A LEU* 2.9 60.9 + - + +
516A ILE* 5.0 2.2 - - + -
534A ARG* 1.3 78.3 - - - +
536A GLY* 1.3 58.7 + - - +
539A ALA* 4.6 1.6 - - - -
544A GLY 2.9 24.2 - - - +
547A HIS* 3.6 30.7 - - + +
548A TRP* 3.7 6.5 - - + +
563A HIS* 4.2 4.7 - - - +
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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