Contacts of the strand formed by residues 516 - 522 (chain A) in PDB entry 4X63
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 GLN 516 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471A PHE* 3.3 5.2 - - - -
472A LEU* 2.9 30.8 + - - +
513A SER* 4.7 0.6 + - - -
514A ALA* 3.5 12.2 + - + +
515A PRO* 1.3 73.7 - - - +
517A PRO* 1.4 78.6 - - + +
538A LEU* 4.2 20.9 - - + +
539A GLU 2.8 30.8 + - - +
540A PHE* 3.4 27.9 - - + +
541A PRO* 4.2 7.3 - - - +
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Residues in contact with PRO 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 THR* 3.8 18.6 - - + -
470A SER 3.4 6.5 - - - +
471A PHE* 3.4 20.1 - - + -
515A PRO 4.7 0.2 - - - +
516A GLN* 1.4 91.1 - - + +
518A CYS* 1.3 59.7 + - - +
520A THR* 5.4 1.6 - - - +
536A CYS* 4.5 1.0 - - - -
538A LEU* 3.4 19.9 - - + +
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Residues in contact with CYS 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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440A PHE* 4.3 4.0 - - + -
469A THR* 4.5 0.4 - - - +
470A SER* 2.6 24.6 + - - +
472A LEU* 3.8 33.7 - - + -
516A GLN 4.7 0.2 - - - +
517A PRO* 1.3 76.9 - - - +
519A PHE* 1.3 100.6 + - - +
520A THR* 5.3 1.1 - - - -
536A CYS* 3.7 23.5 - - - +
538A LEU* 4.5 3.4 - - + -
602A PHE* 4.1 8.1 - - - -
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Residues in contact with PHE 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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440A PHE* 4.5 4.3 - + - -
441A ALA* 5.8 0.2 - - - +
442A ASP* 4.1 15.3 - - - +
468A TYR 3.9 0.2 - - - +
469A THR* 3.2 4.0 - - - -
470A SER* 2.8 41.1 + - - +
518A CYS* 1.3 100.2 - - - +
520A THR* 1.3 63.8 + - - +
521A PHE* 4.4 11.4 - - + -
534A ARG* 3.3 31.4 - - + +
535A TYR 4.2 0.4 - - - -
536A CYS* 3.6 23.6 - - + -
602A PHE* 3.7 26.2 - - + -
604A ARG* 3.8 29.2 - - + -
613A TYR* 4.0 24.9 - + - -
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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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467A GLU* 4.1 20.6 - - - +
468A TYR 3.4 5.8 - - - +
469A THR* 2.8 31.3 + - - +
517A PRO* 5.4 1.7 - - - +
518A CYS 4.4 1.1 + - - -
519A PHE* 1.3 74.9 - - - +
521A PHE* 1.3 64.5 + - - +
522A SER* 5.0 2.5 - - - +
534A ARG* 2.7 33.6 + - - +
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Residues in contact with PHE 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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442A ASP* 3.6 32.5 - - + -
447A PRO* 3.7 24.9 - - + -
467A GLU* 3.2 27.8 - - - +
468A TYR* 3.2 33.5 + + + -
519A PHE* 4.4 9.6 - - + -
520A THR* 1.3 79.2 - - - +
522A SER* 1.3 61.5 + - - +
523A HIS* 4.2 9.8 - + - +
532A ASN* 3.4 47.6 - - - -
534A ARG* 3.3 31.4 - - - +
604A ARG* 3.8 11.7 - - - -
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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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466A GLY 3.5 5.6 - - - -
467A GLU* 3.8 16.3 + - - +
520A THR* 5.0 2.4 - - - +
521A PHE* 1.3 74.8 + - - +
523A HIS* 1.3 75.5 + - - +
524A PRO 3.8 8.1 - - - -
525A ASN* 3.6 22.1 + - - +
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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