Contacts of the helix formed by residues 519 - 532 (chain A) in PDB entry 3RFU
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 ASN 519 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444A ASP* 2.8 39.6 + - - +
518A ASP* 1.3 80.1 - - - +
520A ALA* 1.3 66.5 - - - +
521A PRO* 3.3 10.2 - - - +
522A LEU* 3.0 22.9 + - - +
523A PHE* 2.9 25.0 + - + -
545A THR* 3.1 39.1 + - + +
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Residues in contact with ALA 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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518A ASP* 5.3 1.4 + - - +
519A ASN* 1.3 70.7 - - - +
521A PRO* 1.3 73.7 - - + +
522A LEU 3.0 1.6 + - - -
523A PHE* 3.0 16.6 + - - +
524A GLU* 3.2 29.7 + - - +
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Residues in contact with PRO 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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444A ASP* 3.7 20.0 - - + +
519A ASN* 3.3 11.7 - - - +
520A ALA* 1.3 95.3 - - + +
522A LEU* 1.3 62.6 + - + +
524A GLU* 4.0 7.6 + - + +
525A LYS* 3.3 28.4 + - - +
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Residues in contact with LEU 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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442A VAL* 4.3 27.6 - - + -
443A THR 4.4 7.4 - - - +
444A ASP* 3.6 21.5 - - + +
519A ASN* 3.0 36.3 + - + +
520A ALA 3.0 0.2 + - - -
521A PRO* 1.3 79.1 - - + +
523A PHE* 1.3 62.0 + - + +
525A LYS* 3.6 1.2 + - - -
526A ALA* 3.0 27.3 + - - +
538A PHE* 4.7 2.0 - - + -
545A THR* 3.8 15.5 - - + -
546A VAL 3.7 23.8 - - - +
547A ALA* 3.8 12.6 - - - +
548A LEU* 3.2 16.0 - - + +
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Residues in contact with PHE 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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509A ALA* 4.3 19.1 - - + -
512A MET* 4.7 8.5 - - + -
517A GLY 4.8 2.2 - - - -
518A ASP* 4.1 7.2 - - + -
519A ASN* 2.9 49.9 + - + -
520A ALA* 3.0 8.3 + - - +
522A LEU* 1.3 76.4 - - + +
524A GLU* 1.3 65.4 + - + +
526A ALA* 3.1 5.5 + - - +
527A ASP* 2.9 27.2 + - - +
538A PHE* 3.8 29.6 - + - -
545A THR* 4.2 17.3 - - + -
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Residues in contact with GLU 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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520A ALA* 3.2 28.5 + - - +
521A PRO* 4.3 6.5 - - - +
523A PHE* 1.3 77.2 - - + +
525A LYS* 1.3 63.2 + - + +
527A ASP* 2.6 32.6 - - - +
528A GLU* 3.0 10.5 + - - +
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Residues in contact with LYS 525 (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 ARG* 5.4 10.4 - - - +
442A VAL* 4.9 20.9 - - + -
521A PRO 3.3 20.3 + - - +
522A LEU* 4.0 4.3 - - - +
524A GLU* 1.3 77.8 - - + +
526A ALA* 1.3 57.3 + - - +
528A GLU* 4.2 24.5 + - - +
529A LEU* 3.0 53.4 + - + +
548A LEU* 4.3 9.4 - - + -
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Residues in contact with ALA 526 (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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522A LEU 3.0 19.2 + - - +
523A PHE 3.2 7.4 - - - +
524A GLU 3.1 0.4 - - - -
525A LYS* 1.3 76.5 - - - +
527A ASP* 1.3 61.1 + - - +
530A ARG* 3.0 30.8 + - - +
536A VAL* 3.5 16.5 - - + +
538A PHE* 3.4 32.5 - - + -
548A LEU* 3.9 11.2 - - + -
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Residues in contact with ASP 527 (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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523A PHE 2.9 17.2 + - - +
524A GLU* 2.6 28.8 - - - +
526A ALA* 1.3 74.2 - - - +
528A GLU* 1.3 78.8 + - - +
530A ARG* 3.4 7.4 + - - +
531A GLY* 3.0 18.5 + - - -
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Residues in contact with GLU 528 (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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524A GLU 3.0 11.6 + - - +
525A LYS* 3.6 31.3 + - - +
527A ASP* 1.3 85.0 + - - +
529A LEU* 1.3 64.7 + - + +
531A GLY* 2.7 24.8 + - - -
532A LYS* 3.0 9.6 + - + +
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Residues in contact with LEU 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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440A ARG* 5.4 7.4 - - + +
442A VAL* 4.5 15.5 - - + -
525A LYS* 3.0 33.4 + - + +
528A GLU* 1.3 93.0 - - + +
530A ARG* 1.3 56.7 + - - +
532A LYS* 3.0 32.3 + - + +
533A GLY 3.4 4.9 + - - -
534A ALA* 3.5 16.3 + - + +
536A VAL* 4.4 11.7 - - + -
548A LEU* 5.4 0.7 - - + -
550A VAL* 3.6 30.1 - - + -
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Residues in contact with ARG 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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526A ALA 3.0 21.4 + - - +
527A ASP* 3.6 9.2 - - - +
528A GLU 3.0 0.2 - - - -
529A LEU* 1.3 76.7 - - - +
531A GLY* 1.3 60.3 + - - +
533A GLY 3.2 0.7 + - - -
534A ALA 3.7 2.9 - - - -
535A SER* 3.6 14.6 + - - +
536A VAL* 3.0 50.5 + - + +
537A MET* 5.5 5.7 - - - +
582A ARG* 2.8 58.4 + - - +
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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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527A ASP 3.0 9.1 + - - -
528A GLU 2.7 9.9 + - - -
530A ARG* 1.3 72.8 - - - +
532A LYS* 1.3 58.1 + - - +
533A GLY* 3.0 10.2 + - - -
582A ARG* 4.4 16.6 - - - +
586A ALA* 5.1 1.0 - - - +
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Residues in contact with LYS 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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528A GLU* 3.0 5.6 + - + +
529A LEU* 3.0 29.7 + - + +
531A GLY* 1.3 76.0 - - - +
533A GLY* 1.3 54.4 + - - +
534A ALA* 3.3 11.5 + - + +
552A GLU* 4.6 12.7 + - - +
586A ALA* 3.2 27.5 - - + +
590A THR* 5.3 13.2 - - - -
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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