Contacts of the helix formed by residues 526 - 537 (chain A) in PDB entry 3NG8
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 526 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518A ILE* 4.5 3.6 - - - -
524A ASN 4.0 1.6 + - - -
525A LEU* 1.4 71.3 - - - +
527A LEU* 1.4 57.9 + - - +
528A ALA* 3.4 8.7 + - - +
529A ASP* 3.0 40.1 + - - +
530A VAL* 2.9 31.9 + - - +
532B GLN* 6.0 0.2 - - - -
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Residues in contact with LEU 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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470A GLU* 3.8 31.0 - - + +
471A TYR* 3.7 22.4 - - - +
472A GLY* 3.8 15.9 - - - +
516A PHE* 4.1 22.2 - - + +
517A ARG* 4.1 9.9 - - + -
518A ILE* 4.0 23.4 - - + +
526A SER* 1.4 68.9 - - - +
528A ALA* 1.4 56.2 + - - +
530A VAL* 3.5 3.8 - - + +
531A THR* 2.7 41.5 + - - +
554A VAL* 4.0 15.0 - - + -
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Residues in contact with ALA 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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526A SER* 3.4 7.2 + - - +
527A LEU* 1.4 77.6 - - - +
529A ASP* 1.3 60.1 + - - +
531A THR* 3.2 6.9 + - - -
532A GLN* 2.8 34.2 + - - +
554A VAL* 4.1 9.7 - - + +
532B GLN* 4.1 35.2 - - + +
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Residues in contact with ASP 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A ASN 5.5 0.3 - - - +
525A LEU* 4.5 15.5 - - + +
526A SER* 3.0 38.4 + - - +
528A ALA* 1.3 79.1 - - - +
530A VAL* 1.3 57.8 + - - +
532A GLN* 3.8 11.9 - - - +
533A GLN* 3.0 36.2 + - + +
532B GLN* 4.2 19.8 + - - +
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Residues in contact with VAL 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A LEU* 3.8 11.9 - - + +
497A VAL* 5.0 10.5 - - + -
499A MET* 5.1 0.7 - - + -
504A PHE* 4.3 14.6 - - + -
516A PHE* 3.8 26.2 - - + -
518A ILE* 3.9 22.9 - - + -
525A LEU* 4.0 23.1 - - + -
526A SER 2.9 21.1 + - - +
527A LEU* 3.5 17.9 - - + +
529A ASP* 1.3 76.6 - - - +
531A THR* 1.3 58.5 + - - +
533A GLN* 3.3 8.2 + - - +
534A ALA* 2.9 26.0 + - - +
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Residues in contact with THR 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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472A GLY* 4.1 3.8 - - - -
473A TYR 4.1 8.3 - - - +
474A ILE* 5.5 0.2 - - + -
516A PHE* 4.0 26.0 - - + -
527A LEU 2.7 26.9 + - - +
528A ALA* 3.2 12.1 + - - -
530A VAL* 1.3 72.6 - - - +
532A GLN* 1.3 65.8 + - - +
534A ALA* 3.3 9.1 + - + +
535A GLY 3.0 17.3 + - - -
552A THR* 3.3 14.0 + - - -
553A GLY* 3.3 36.1 + - - +
554A VAL* 3.9 7.5 - - + +
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Residues in contact with GLN 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 ALA 2.8 21.4 + - - +
529A ASP* 3.8 16.7 - - - +
531A THR* 1.3 71.6 + - - +
533A GLN* 1.3 78.9 + - - +
535A GLY* 3.0 4.7 + - - -
536A LEU* 2.9 33.8 + - + +
552A THR* 5.2 0.9 - - - -
526B SER* 5.4 0.6 + - - -
528B ALA* 3.5 33.9 - - + +
529B ASP* 5.4 3.4 + - - -
532B GLN* 4.4 11.1 + - - -
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Residues in contact with GLN 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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493A LEU* 4.1 3.4 - - + -
496A HIS* 2.9 28.8 + - + -
497A VAL* 3.8 27.6 - - + +
525A LEU* 6.2 2.0 - - + -
529A ASP* 3.0 24.3 + - + +
530A VAL 3.7 4.7 - - - +
532A GLN* 1.3 86.9 + - - +
534A ALA* 1.3 63.6 + - - +
536A LEU* 3.1 28.8 + - - +
537A VAL* 2.9 27.4 + - - +
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Residues in contact with ALA 534 (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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474A ILE* 4.0 27.6 - - + -
493A LEU* 3.7 17.9 - - + +
530A VAL 2.9 14.4 + - - +
531A THR* 3.4 12.6 - - - +
533A GLN* 1.3 76.8 - - - +
535A GLY* 1.3 60.2 + - - +
537A VAL* 3.5 0.4 + - - -
538A LYS* 3.2 19.1 + - - +
541A LEU* 3.5 17.0 - - + +
549A ILE* 5.1 0.3 - - - +
552A THR* 4.1 11.0 - - + +
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Residues in contact with GLY 535 (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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531A THR 3.0 13.2 + - - -
532A GLN* 3.0 5.1 + - - -
534A ALA* 1.3 77.6 - - - +
536A LEU* 1.3 62.7 + - - +
538A LYS* 3.2 27.6 - - - +
549A ILE* 5.7 0.4 - - - -
552A THR* 4.0 15.0 + - - -
470B GLU* 4.5 11.3 - - - +
554B VAL* 6.5 0.9 - - - -
556B GLN* 5.0 8.7 - - - -
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Residues in contact with LEU 536 (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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496A HIS* 5.8 0.4 - - + -
532A GLN* 2.9 26.6 + - + +
533A GLN* 3.1 42.8 + - - +
535A GLY* 1.3 77.2 - - - +
537A VAL* 1.3 62.4 + - + +
538A LYS* 3.5 4.5 + - - +
539A SER* 4.9 1.2 + - - -
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Residues in contact with VAL 537 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ILE* 5.4 2.7 - - + -
493A LEU* 4.5 8.3 - - + -
496A HIS* 3.3 50.3 - - + +
533A GLN 2.9 20.9 + - - +
534A ALA* 3.6 7.9 - - - +
535A GLY 3.3 0.2 - - - -
536A LEU* 1.3 78.2 - - + +
538A LYS* 1.3 62.7 + - - +
539A SER 3.2 3.4 - - - -
540A GLU* 3.0 24.3 + - + +
541A LEU* 2.9 32.8 + - + +
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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