Contacts of the helix formed by residues 482 - 494 (chain A) in PDB entry 3V4R
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 LEU 482 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480A LYS* 2.7 12.4 + - + -
481A THR* 1.3 75.9 - - - +
483A GLU* 1.4 58.5 + - + +
484A ARG 3.1 2.0 - - - +
485A ILE* 3.2 5.1 + - - +
486A GLU* 2.8 39.9 + - + +
481B THR* 4.1 25.6 - - + -
482B LEU* 3.7 31.0 - - + -
485B ILE* 4.4 14.2 - - + +
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Residues in contact with GLU 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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479A ILE* 4.8 8.1 - - + -
480A LYS* 3.1 23.3 + - + +
482A LEU* 1.4 81.3 - - + +
484A ARG* 1.4 56.1 + - - +
486A GLU* 3.8 6.1 - - - +
487A ILE* 3.0 44.3 + - + +
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Residues in contact with ARG 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A THR* 3.9 17.5 + - - +
72A GLN* 5.0 7.3 - - - +
475A LEU* 6.4 1.8 - - + -
479A ILE* 5.0 10.9 - - + +
480A LYS 3.0 15.8 + - - +
481A THR* 3.2 34.7 + - - +
482A LEU 4.5 1.3 - - - +
483A GLU* 1.4 73.4 - - - +
485A ILE* 1.4 74.1 - - - +
487A ILE* 2.8 31.7 + - + +
488A ILE* 3.0 16.3 + - + +
506A ARG* 4.9 9.4 - - + -
507A GLU* 3.1 49.6 + - - +
508A GLY* 4.2 4.0 - - - +
509A LEU* 6.1 4.3 - - + -
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Residues in contact with ILE 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 THR* 3.5 27.8 - - + +
482A LEU* 3.2 8.4 + - - +
484A ARG* 1.4 101.2 - - - +
486A GLU* 1.4 56.4 + - - +
488A ILE* 3.9 6.3 + - - +
489A ARG* 3.2 26.0 + - + +
482B LEU* 3.6 28.9 - - + -
485B ILE* 4.6 12.3 - - + -
486B GLU* 4.2 17.9 - - + +
489B ARG* 3.6 29.0 + - - +
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Residues in contact with GLU 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A LEU* 2.8 24.5 + - + +
483A GLU* 3.8 7.9 - - - +
485A ILE* 1.4 69.9 - - - +
487A ILE* 1.3 58.7 + - + +
489A ARG* 3.4 28.3 + - - +
490A ASP* 2.7 40.5 + - - +
485B ILE* 5.3 5.8 - - + -
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Residues in contact with ILE 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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473A ASN* 3.6 33.9 - - + +
474A TYR 5.6 0.2 - - - +
475A LEU* 3.5 33.0 - - + -
483A GLU* 3.0 30.2 + - + +
484A ARG* 2.8 16.3 + - + +
486A GLU* 1.3 70.7 - - + +
488A ILE* 1.4 64.8 + - - +
490A ASP* 3.6 6.3 + - - +
491A LEU* 3.2 24.4 + - - +
496A TYR* 4.4 13.1 - - + +
499A LEU* 4.2 10.7 - - + +
509A LEU* 5.1 4.0 - - + -
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Residues in contact with ILE 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 ARG* 3.0 16.4 + - + +
485A ILE* 4.1 6.7 - - - +
487A ILE* 1.4 79.3 - - + +
489A ARG* 1.4 56.8 + - - +
491A LEU* 3.8 7.2 - - - +
492A ARG* 3.0 36.9 + - + +
507A GLU 6.0 0.4 - - - +
508A GLY* 4.3 20.4 - - - +
509A LEU* 5.2 11.0 - - + -
511A ILE* 5.0 8.3 - - + +
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Residues in contact with ARG 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 ILE* 3.2 20.3 + - + +
486A GLU* 3.4 19.4 + - - +
487A ILE 3.3 0.2 - - - -
488A ILE* 1.4 76.0 - - - +
490A ASP* 1.3 85.1 + - - +
492A ARG* 3.3 8.6 + - - +
493A LEU* 2.9 48.8 + - + +
485B ILE* 3.5 34.3 + - - +
488B ILE* 6.2 3.4 - - - +
489B ARG* 3.8 38.1 - - + +
492B ARG* 6.3 0.4 - - - +
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Residues in contact with ASP 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 GLU* 2.7 23.3 + - - +
487A ILE* 4.1 1.1 - - - +
489A ARG* 1.3 100.1 + - - +
491A LEU* 1.3 59.3 + - - +
493A LEU* 3.7 6.9 - - - +
494A GLY 2.8 8.5 + - - -
495A LYS* 2.7 52.0 + - + +
496A TYR* 3.7 24.8 + - + -
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Residues in contact with LEU 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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447A ARG* 2.8 42.1 + - + -
448A VAL 4.5 0.7 - - - +
449A LEU* 3.8 26.2 - - + -
487A ILE 3.2 18.2 + - - +
488A ILE* 3.8 6.3 - - - +
490A ASP* 1.3 74.9 - - - +
492A ARG* 1.4 56.2 + - - +
494A GLY 3.3 3.6 + - - -
496A TYR* 3.4 30.9 - - + +
497A ASP 3.9 20.0 - - - +
498A VAL 4.0 4.5 - - - +
499A LEU* 3.8 26.7 - - + +
509A LEU* 5.7 1.8 - - + -
511A ILE* 3.8 23.3 - - + -
514A VAL* 4.1 4.5 - - + -
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Residues in contact with ARG 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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447A ARG* 3.3 14.2 + - - -
488A ILE* 3.0 22.8 + - - +
489A ARG* 3.4 11.7 - - - +
491A LEU* 1.4 77.3 - - - +
493A LEU* 1.3 62.3 + - + +
494A GLY 3.3 0.3 + - - -
511A ILE* 3.9 25.3 - - + +
512A PRO* 3.8 25.3 - - - +
513A GLU* 2.7 52.8 + - - +
588A ILE* 5.2 5.1 - - - +
489B ARG* 6.2 4.3 - - - +
493B LEU* 5.3 17.3 - - + +
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Residues in contact with LEU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ARG* 4.3 3.5 + - - -
489A ARG* 2.9 48.9 + - + +
490A ASP* 4.2 7.6 - - - +
492A ARG* 1.3 72.8 - - + +
494A GLY* 1.3 58.7 + - - +
495A LYS* 3.7 2.7 - - + +
489B ARG* 5.3 4.3 - - + +
492B ARG* 3.6 68.1 + - + +
493B LEU* 4.7 6.5 - - + +
589B ASN 4.4 14.8 - - - +
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Residues in contact with GLY 494 (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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447A ARG* 3.9 16.4 - - - -
471A LYS* 5.2 1.2 - - - +
490A ASP 2.8 7.7 + - - -
491A LEU 3.3 8.5 + - - -
492A ARG 3.2 4.0 - - - -
493A LEU* 1.3 78.7 - - - +
495A LYS* 1.4 58.2 + - - -
496A TYR 3.1 13.1 + - - +
497A ASP* 4.1 10.5 - - - +
589B ASN 6.0 1.1 - - - -
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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