Contacts of the strand formed by residues 518 - 523 (chain A) in PDB entry 3HO5
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 PHE 518 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A ILE* 5.8 1.6 - - + -
495A PHE* 4.7 0.9 - + - -
510A VAL* 3.7 21.1 - - + -
511A PHE 3.3 2.2 - - - -
512A GLY* 3.8 18.6 - - - -
516A GLY* 3.2 26.4 + - - -
517A ASN* 1.3 74.5 - - - +
519A LEU* 1.3 65.0 + - - +
534A PRO* 3.6 5.2 - - - +
535A LEU* 2.9 54.0 + - + +
537A LEU* 4.1 26.0 - - + -
547A PHE* 4.7 3.4 - + - -
551A ILE* 3.8 20.4 - - + -
554A PHE* 4.0 17.3 - + - -
564A ILE* 3.9 13.9 - - + -
582A ILE* 4.1 20.6 - - + -
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Residues in contact with LEU 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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486A PHE* 3.6 34.5 - - + -
488A ASN* 4.4 23.6 - - + +
491A LEU* 4.4 11.7 - - + -
510A VAL* 3.4 11.8 - - - +
511A PHE* 2.7 34.5 + - + +
517A ASN* 5.1 4.7 - - + +
518A PHE* 1.3 81.1 - - - +
520A THR* 1.3 71.6 + - - +
521A LEU* 5.0 1.3 - - + +
532A GLU* 3.3 32.8 - - + +
533A LYS 3.6 8.1 - - - +
534A PRO* 4.9 9.2 - - + -
535A LEU* 4.1 2.8 - - - +
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Residues in contact with THR 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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505A LEU* 5.3 0.9 - - - +
508A SER* 4.2 20.2 - - - +
509A TYR 3.1 15.8 + - - +
510A VAL* 5.1 2.3 - - - +
519A LEU* 1.3 79.3 + - - +
521A LEU* 1.3 72.1 + - - +
522A GLN* 3.7 14.7 + - + +
531A GLN 2.9 14.7 - - - +
532A GLU* 3.1 3.7 - - - -
533A LYS* 3.0 30.4 + - - +
535A LEU* 3.3 25.8 - - - +
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Residues in contact with LEU 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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451A LEU* 4.9 7.0 - - + -
483A PHE* 4.8 4.9 - - + -
485A PRO* 3.8 33.0 - - + -
486A PHE* 3.4 31.9 - - + -
509A TYR* 3.1 41.1 + - + +
511A PHE* 3.5 30.3 - - + -
519A LEU* 5.0 3.4 - - + -
520A THR* 1.3 77.5 - - - +
522A GLN* 1.3 60.1 + - - +
530A TRP* 3.9 23.9 - - + -
531A GLN 3.9 14.4 - - - +
532A GLU* 4.3 4.0 - - - +
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Residues in contact with GLN 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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520A THR* 4.5 13.4 - - + +
521A LEU* 1.3 75.0 - - - +
523A GLN* 1.3 68.7 + - - +
524A SER 4.0 0.3 + - - -
525A PRO* 6.4 0.2 - - - +
529A GLN 3.9 0.9 - - - +
530A TRP* 3.5 8.0 - - - -
531A GLN* 2.9 37.6 + - + +
533A LYS* 3.9 33.4 + - + +
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Residues in contact with GLN 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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465A ILE* 5.8 0.4 - - - +
467A GLN* 4.7 11.4 + - - +
522A GLN* 1.3 83.2 + - - +
524A SER* 1.3 74.5 + - - +
525A PRO* 3.3 10.3 - - + +
528A LYS* 3.0 53.9 + - + +
529A GLN 3.8 2.9 - - - +
530A TRP* 3.4 45.4 - - + +
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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