Contacts of the helix formed by residues 521 - 533 (chain A) in PDB entry 6QHD
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 SER 521 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518A ARG* 5.9 1.0 - - - +
519A GLY 4.2 0.2 - - - -
520A LEU* 1.3 70.9 - - - +
522A ILE* 1.3 56.8 + - - +
523A GLU* 2.4 35.1 + - - -
524A GLN* 2.6 25.3 + - - +
525A LEU* 2.7 33.7 + - - +
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Residues in contact with ILE 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 LEU 3.6 3.8 + - - -
521A SER* 1.3 70.5 - - - +
523A GLU* 1.3 68.9 + - - +
525A LEU* 3.6 16.2 - - + +
526A THR* 2.4 52.3 + - - +
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Residues in contact with GLU 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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521A SER* 2.4 29.4 + - - +
522A ILE* 1.3 87.2 - - - +
524A GLN* 1.3 67.4 + - + +
526A THR* 3.1 17.0 + - - -
527A THR* 3.3 13.1 + - - -
586A MET* 5.0 15.5 - - + -
593A ARG* 6.1 2.2 - - - +
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Residues in contact with GLN 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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518A ARG* 5.3 5.5 - - - -
519A GLY 4.0 3.5 - - - +
520A LEU* 3.2 19.3 - - + +
521A SER* 2.6 47.1 + - - +
523A GLU* 1.3 75.6 - - + +
525A LEU* 1.3 64.0 + - - +
527A THR* 3.4 6.6 + - - -
528A LEU 4.0 0.2 + - - -
580A TRP* 3.7 18.4 - - - -
585A ILE 3.6 14.5 + - - -
586A MET* 2.8 46.2 + - + +
588A PHE* 3.3 37.9 - - + +
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Residues in contact with LEU 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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501A TRP* 3.5 31.8 - - + +
505A ALA* 3.4 38.1 - - + +
508A LEU* 5.3 1.1 - - + -
509A SER* 5.2 1.8 - - - -
520A LEU* 4.0 28.0 - - + +
521A SER 2.7 20.3 + - - +
522A ILE* 3.6 19.1 - - + +
524A GLN* 1.3 74.9 - - - +
526A THR* 1.3 68.6 + - - +
528A LEU* 2.9 33.1 + - + +
529A ALA 3.2 6.4 + - - -
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Residues in contact with THR 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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501A TRP* 5.6 0.2 + - - -
522A ILE* 2.4 38.1 + - - +
523A GLU* 3.1 8.2 + - - -
525A LEU* 1.3 79.6 - - - +
527A THR* 1.3 66.7 + - - +
529A ALA* 2.9 27.3 + - + +
530A GLU* 3.2 8.4 + - + +
539A TYR* 4.9 22.2 - - + -
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Residues in contact with THR 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 GLU 3.3 10.4 + - - -
524A GLN* 3.4 7.3 + - - -
526A THR* 1.3 77.4 - - - +
528A LEU* 1.3 61.5 + - + +
530A GLU* 3.5 8.0 + - - +
531A LYS* 3.5 16.5 + - - +
588A PHE* 2.6 26.7 + - + -
589A ILE* 3.1 42.8 - - - +
590A SER* 3.4 10.9 + - - +
612A GLU* 5.8 3.4 - - - +
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Residues in contact with LEU 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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501A TRP* 4.5 6.7 - - + -
508A LEU* 5.3 6.3 - - + -
520A LEU* 4.5 13.5 - - + -
524A GLN 4.3 0.2 - - - +
525A LEU* 2.9 21.7 + - + +
527A THR* 1.3 74.1 - - + +
529A ALA* 1.3 66.3 + - - +
531A LYS* 3.1 19.9 + - + +
532A LEU* 3.2 15.8 + - - +
561A PHE* 4.6 18.4 - - + -
564A TRP* 4.1 22.2 - - + -
565A LEU* 5.1 12.8 - - + -
588A PHE* 3.4 58.3 - - + -
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Residues in contact with ALA 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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501A TRP* 3.4 42.8 - - + +
525A LEU 3.2 2.2 + - - -
526A THR* 2.9 20.2 + - + +
528A LEU* 1.3 78.7 - - - +
530A GLU* 1.3 61.5 + - - +
532A LEU* 3.4 4.2 + - - +
533A LEU* 3.3 27.8 - - + +
539A TYR* 4.0 21.2 - - + -
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Residues in contact with GLU 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 THR* 3.2 7.1 + - + +
527A THR* 3.8 10.2 - - - +
528A LEU 3.3 0.4 - - - -
529A ALA* 1.3 78.2 - - - +
531A LYS* 1.3 61.6 + - - +
533A LEU 3.1 1.2 + - - -
534A GLY* 2.8 30.1 + - - +
535A PRO* 3.3 45.4 - - + +
539A TYR* 4.5 15.8 + - + -
590A SER* 5.1 14.5 + - - -
592A GLU* 4.6 11.6 - - - +
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Residues in contact with LYS 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 THR 3.5 6.4 + - - +
528A LEU* 3.1 18.5 + - + +
530A GLU* 1.3 79.4 - - - +
532A LEU* 1.3 63.7 + - + +
533A LEU* 4.6 1.0 - - - -
554A MET* 2.8 50.4 - - + +
557A LYS* 3.8 16.0 - - - +
561A PHE* 5.0 5.8 - - + -
564A TRP* 4.0 30.9 - - + -
612A GLU* 3.6 35.7 - - - +
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Residues in contact with LEU 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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501A TRP* 4.3 12.1 - - + -
504A VAL* 5.2 1.3 - - + -
528A LEU 3.2 9.5 + - - +
529A ALA* 3.8 3.6 - - - +
530A GLU 3.3 0.6 - - - -
531A LYS* 1.3 81.2 - - + +
533A LEU* 1.3 80.9 + - + +
544A ILE* 3.5 39.5 - - + -
548A LYS* 4.1 26.4 - - + +
549A PHE* 4.9 2.0 - - + -
554A MET* 5.9 3.1 - - + -
561A PHE* 3.6 53.2 - - + -
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Residues in contact with LEU 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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501A TRP* 5.7 3.4 - - + -
529A ALA* 3.3 18.2 - - + +
530A GLU 3.1 3.9 + - - -
531A LYS 4.8 1.5 - - - +
532A LEU* 1.3 98.9 - - + +
534A GLY* 1.3 66.8 + - - +
539A TYR* 5.5 6.7 - - + -
542A CYS* 4.6 25.1 - - + -
543A GLN 4.4 6.7 - - - +
544A ILE* 4.1 18.8 - - + -
548A LYS* 3.8 27.1 - - + +
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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