Contacts of the helix formed by residues 480 - 492 (chain A) in PDB entry 4L6V
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 PRO 480 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478A LEU 3.7 4.2 - - - +
479A GLN* 1.3 77.3 - - - +
481A ILE* 1.3 65.5 + - - +
482A PHE* 3.1 5.1 + - + -
483A ALA* 3.3 15.2 + - + +
484A GLN* 3.1 38.6 + - - +
527A LEU* 3.8 23.8 - - + -
528A GLY 3.6 23.3 - - - +
532A PHE* 3.9 23.3 - - + +
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Residues in contact with ILE 481 (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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479A GLN* 2.7 28.9 + - + +
480A PRO* 1.3 70.3 - - - +
482A PHE* 1.3 78.8 + - + +
484A GLN* 3.7 11.3 + - - +
485A TRP* 3.0 28.8 + - + +
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Residues in contact with PHE 482 (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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480A PRO* 3.1 1.7 - - + -
481A ILE* 1.3 94.5 - - + +
483A ALA* 1.3 56.5 + - - +
484A GLN 3.1 1.6 - - - -
485A TRP* 2.9 24.6 + + + +
486A VAL* 2.7 41.2 + - + +
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Residues in contact with ALA 483 (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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480A PRO* 3.3 15.9 + - + +
482A PHE* 1.3 78.1 - - - +
484A GLN* 1.3 61.9 + - - +
486A VAL* 3.4 11.3 + - - +
487A GLN* 3.1 26.5 + - - +
527A LEU* 3.6 24.6 - - + +
535A HIS* 6.3 1.3 - - + +
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Residues in contact with GLN 484 (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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479A GLN* 3.3 31.6 + - - +
480A PRO* 3.1 25.8 + - + +
481A ILE* 3.7 10.2 + - - +
483A ALA* 1.3 76.0 - - - +
485A TRP* 1.3 65.3 + - - +
487A GLN* 3.2 13.7 + - - +
488A HIS* 3.1 21.3 + - - +
527A LEU* 2.7 35.0 - - + +
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Residues in contact with TRP 485 (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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481A ILE* 3.0 20.5 + - + +
482A PHE* 2.9 28.1 + + + +
484A GLN* 1.3 76.3 - - - +
486A VAL* 1.3 69.7 + - + +
488A HIS* 3.3 12.7 + - + +
489A LEU* 3.3 53.4 + - + +
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Residues in contact with VAL 486 (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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482A PHE* 2.7 25.3 + - + +
483A ALA* 3.5 12.8 - - - +
484A GLN 3.2 0.2 - - - -
485A TRP* 1.3 82.3 - - + +
487A GLN* 1.3 62.3 + - + +
489A LEU* 3.2 11.8 + - + +
490A HIS* 2.7 55.2 + - + -
509A PHE* 5.4 5.6 - - + -
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Residues in contact with GLN 487 (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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483A ALA 3.1 15.6 + - - +
484A GLN* 3.2 13.3 + - - +
486A VAL* 1.3 77.3 - - + +
488A HIS* 1.3 63.8 + - - +
490A HIS* 3.1 3.5 + - - +
491A THR* 3.0 30.1 + - - -
508A ALA 4.3 4.2 + - - +
509A PHE* 3.4 44.1 - - + +
524A PRO* 6.1 0.7 - - - +
525A ILE* 3.0 28.3 + - - +
526A THR* 4.7 4.9 - - - +
527A LEU* 3.4 26.5 + - + +
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Residues in contact with HIS 488 (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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484A GLN 3.1 10.0 + - - +
485A TRP* 3.5 18.6 - - + +
486A VAL 3.2 0.4 - - - -
487A GLN* 1.3 79.4 - - - +
489A LEU* 1.3 67.1 + - - +
491A THR* 3.9 4.5 + - - -
492A LEU* 3.2 64.4 + - + +
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Residues in contact with LEU 489 (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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485A TRP* 3.3 56.3 - - + +
486A VAL* 3.5 11.7 - - + +
487A GLN 3.1 0.8 - - - -
488A HIS* 1.3 86.1 - - - +
490A HIS* 1.3 67.5 + - + +
492A LEU* 3.5 5.9 + - + -
493A ALA* 3.2 23.2 + - - +
497A THR* 4.8 1.7 + - - +
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Residues in contact with HIS 490 (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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486A VAL* 2.7 48.5 + - + +
487A GLN 3.1 3.8 + - - +
489A LEU* 1.3 81.4 - - + +
491A THR* 1.3 61.7 + - - +
493A ALA* 3.3 19.1 + - - +
504A THR* 3.1 19.1 + - - +
505A ALA* 6.4 0.9 - - + -
509A PHE* 3.2 53.9 - + + -
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Residues in contact with THR 491 (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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487A GLN 3.0 15.7 + - - -
488A HIS* 4.3 4.5 - - - -
490A HIS* 1.3 76.4 - - - +
492A LEU* 1.3 64.1 + - + +
493A ALA 3.2 4.4 + - - -
494A PRO* 3.4 12.5 - - - +
504A THR* 4.4 8.9 - - + -
509A PHE* 3.1 25.1 + - - +
510A GLY* 3.3 26.5 + - - +
511A GLY* 4.2 5.2 - - - +
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Residues in contact with LEU 492 (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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488A HIS* 3.2 58.1 + - + +
489A LEU* 3.5 7.8 + - + +
490A HIS 3.3 0.2 - - - -
491A THR* 1.3 82.5 - - + +
493A ALA* 1.3 61.3 + - - +
494A PRO* 3.6 8.6 - - - +
496A ALA* 3.9 12.5 - - - +
497A THR* 4.6 1.6 + - - +
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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