Contacts of the helix formed by residues 523 - 533 (chain B) in PDB entry 3Q6N
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 523 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442B SER* 3.3 14.4 + - - -
443B LYS* 3.1 31.3 + - - +
446B LYS* 2.9 23.9 + - - +
495B THR* 5.9 0.3 - - - -
496B GLY 5.3 1.2 - - - +
521B MET 4.8 0.5 - - - +
522B ILE* 1.3 87.5 - - + +
524B PRO* 1.3 70.0 - - + +
525B ILE* 3.3 12.3 - - + +
526B ASP* 2.9 35.7 + - - +
527B GLU 4.1 0.7 + - - -
609B ASN* 5.3 3.6 + - - -
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Residues in contact with PRO 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B LYS* 5.7 0.2 - - - +
522B ILE 4.6 1.3 - - - +
523B GLU* 1.3 80.7 - - + +
525B ILE* 1.3 71.9 + - + +
526B ASP 2.9 6.3 + - - -
527B GLU* 3.0 22.0 + - + +
528B TYR* 3.8 3.1 + - - +
609B ASN* 5.4 7.0 - - - +
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Residues in contact with ILE 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B LYS* 3.8 52.5 - - + +
446B LYS* 4.4 17.9 - - + -
447B LEU* 4.5 20.4 - - + +
523B GLU* 3.8 15.0 - - + +
524B PRO* 1.3 94.5 - - + +
526B ASP* 1.3 52.5 + - - +
528B TYR* 3.1 18.6 + - + +
529B CYS* 2.6 36.1 + - - +
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Residues in contact with ASP 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B LYS* 3.2 32.6 + - - +
465B TYR* 3.5 14.1 + - - -
495B THR* 4.6 3.8 - - + -
521B MET* 3.4 29.2 - - + +
522B ILE 3.2 9.5 + - - -
523B GLU* 2.9 39.5 + - - +
524B PRO 2.9 0.6 - - - -
525B ILE* 1.3 76.5 - - - +
527B GLU* 1.3 63.0 + - - +
529B CYS* 2.9 5.5 + - - +
530B VAL* 2.9 29.8 + - - +
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Residues in contact with GLU 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B TYR* 5.9 0.2 - - - -
495B THR* 2.7 27.3 + - - +
523B GLU 4.1 0.4 + - - -
524B PRO* 3.0 11.9 + - + +
526B ASP* 1.3 79.8 - - - +
528B TYR* 1.3 62.6 + - - +
530B VAL* 3.5 18.8 + - - +
531B GLN* 3.8 11.6 + - - +
607B THR* 3.1 43.2 + - - +
609B ASN* 3.4 27.4 - - - +
610B MET* 3.8 26.9 - - + +
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Residues in contact with TYR 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446B LYS 5.6 0.2 - - - -
447B LEU* 4.3 21.5 - - + -
450B HIS* 3.1 76.6 + + + -
451B GLU* 3.4 11.1 + - - -
524B PRO 3.8 1.7 + - - +
525B ILE* 3.1 27.0 + - + +
527B GLU* 1.3 79.3 - - - +
529B CYS* 1.3 63.0 + - + +
531B GLN* 3.4 27.6 - - - +
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Residues in contact with CYS 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446B LYS* 4.0 41.7 - - + +
449B ILE* 4.1 27.0 - - - +
450B HIS* 4.9 4.0 - - - -
463B LEU* 4.8 1.3 - - - -
465B TYR* 4.3 13.7 - - - -
525B ILE 2.6 19.2 + - - +
526B ASP* 2.9 9.1 + - - +
528B TYR* 1.3 74.2 - - - +
530B VAL* 1.3 63.8 + - + +
532B GLN* 3.2 16.5 + - - +
533B LEU* 3.2 18.5 + - - +
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Residues in contact with VAL 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B TYR* 3.8 39.5 + - + +
495B THR* 4.5 3.6 - - + -
521B MET* 3.3 38.4 - - + -
526B ASP 2.9 19.7 + - - +
527B GLU* 3.5 15.9 - - - +
529B CYS* 1.3 71.3 - - - +
531B GLN* 1.3 66.2 + - - +
532B GLN 3.2 0.2 - - - -
533B LEU* 3.5 22.7 - - + +
534B LYS* 5.1 1.0 - - - +
541B LEU* 4.4 11.2 - - + -
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Residues in contact with GLN 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B HIS* 3.1 25.4 + - - -
527B GLU 3.8 7.2 + - - +
528B TYR* 3.4 27.4 + - - +
529B CYS 3.2 0.4 - - - -
530B VAL* 1.3 82.5 - - - +
532B GLN* 1.3 72.0 + - + +
534B LYS* 3.8 20.3 - - - +
610B MET* 5.6 6.1 - - - +
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Residues in contact with GLN 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B ILE 3.7 6.7 - - - +
450B HIS* 3.7 39.9 + - + +
456B ARG* 3.3 48.6 + - - +
529B CYS 3.2 7.3 + - - +
531B GLN* 1.3 94.2 + - - +
533B LEU* 1.3 62.2 + - - +
534B LYS* 3.0 28.6 + - - +
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Residues in contact with LEU 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B ILE* 3.9 16.7 - - + +
456B ARG* 4.7 7.6 - - + +
460B SER* 3.8 24.5 - - - -
463B LEU* 3.8 25.6 - - + -
465B TYR* 4.7 5.6 - - - +
477B LEU* 4.3 13.0 - - + -
521B MET* 5.2 2.0 - - + -
529B CYS* 3.2 22.9 + - - +
530B VAL* 3.5 18.7 + - + +
531B GLN 3.6 0.2 - - - -
532B GLN* 1.3 74.9 - - - +
534B LYS* 1.3 59.5 + - - +
535B GLU 3.9 17.7 - - - +
536B PHE* 5.5 0.2 - - + -
541B LEU* 3.4 34.8 - - + +
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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