Contacts of the helix formed by residues 524 - 537 (chain A) in PDB entry 3V4O
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 LYS 524 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523A LYS* 1.3 75.0 - - - +
525A ILE* 1.3 69.4 + - - +
526A THR* 3.9 21.0 + - - +
527A VAL* 2.9 31.4 + - + +
528A LEU 3.0 8.0 + - - -
554A LEU* 2.9 36.1 + - + -
555A SER* 3.3 13.3 + - - +
556A GLU 3.4 19.1 - - - -
557A LYS* 4.2 29.0 + - + +
558A ARG 3.1 22.7 - - - +
559A ALA* 4.2 1.0 - - - +
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Residues in contact with ILE 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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456A LEU* 4.6 13.7 - - + -
458A VAL* 4.5 14.8 - - + -
460A LEU* 5.7 2.0 - - + -
487A VAL* 3.8 14.1 - - + -
519A LEU* 4.8 2.5 - - + -
523A LYS 3.3 4.9 + - - -
524A LYS* 1.3 70.7 - - - +
526A THR* 1.3 59.4 + - - +
528A LEU* 3.3 15.2 + - + -
529A LEU* 2.9 56.8 + - + +
554A LEU* 3.7 24.7 - - + -
558A ARG 3.1 9.6 + - - +
559A ALA* 4.2 2.0 - - - +
560A LEU* 3.6 40.8 - - + +
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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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487A VAL* 3.9 13.2 - - - +
524A LYS* 3.1 25.4 + - - +
525A ILE* 1.3 80.6 - - - +
527A VAL* 1.3 63.4 + - + +
529A LEU* 3.4 5.5 + - - +
530A ASP* 3.1 21.4 + - + +
550A ILE* 4.0 12.4 - - + +
552A SER* 3.0 35.3 + - - +
554A LEU* 4.2 0.5 - - - +
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Residues in contact with VAL 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A LYS* 4.2 22.4 - - + -
524A LYS* 2.9 31.4 + - + +
526A THR* 1.3 77.4 - - + +
528A LEU* 1.3 66.9 + - - +
530A ASP* 3.2 9.2 + - + +
531A GLU* 3.1 28.3 + - + +
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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
----------------------------------------------------------
515A LEU* 4.4 10.8 - - + -
518A ARG* 3.4 41.7 - - + +
519A LEU* 3.8 24.2 - - + +
521A GLU* 3.9 20.9 - - + +
523A LYS* 4.4 13.0 - - + +
524A LYS 3.0 11.5 + - - +
525A ILE* 3.3 20.4 + - + +
527A VAL* 1.3 78.4 - - - +
529A LEU* 1.3 66.7 + - + +
531A GLU* 3.3 15.0 + - - +
532A VAL* 3.1 25.4 + - + +
560A LEU* 5.2 4.9 - - + +
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Residues in contact with LEU 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LEU* 4.4 15.9 - - + -
487A VAL* 3.7 28.5 - - + -
488A PHE 4.6 1.6 - - - +
489A GLY* 4.2 22.4 - - - +
511A PHE* 5.1 4.7 - - + -
515A LEU* 4.0 26.9 - - + -
525A ILE* 2.9 39.3 + - + +
526A THR 3.8 1.6 - - - +
528A LEU* 1.3 77.8 - - + +
530A ASP* 1.3 57.6 + - - +
532A VAL* 3.3 7.7 + - + +
533A ALA* 2.8 27.5 + - - +
548A LEU* 3.8 7.7 - - + +
550A ILE* 3.5 19.8 - - + +
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Residues in contact with ASP 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A THR* 3.1 15.2 + - + +
527A VAL* 3.4 13.5 - - + +
529A LEU* 1.3 77.4 - - - +
531A GLU* 1.3 61.2 + - - +
533A ALA* 3.2 9.3 + - - +
534A GLU* 3.1 30.4 + - - +
550A ILE* 3.3 16.2 - - + +
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Residues in contact with GLU 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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518A ARG* 3.6 27.6 + - - +
521A GLU* 2.5 29.7 - - - +
523A LYS* 3.0 31.9 + - - +
527A VAL* 3.1 22.0 + - + +
528A LEU* 3.5 11.6 - - - +
530A ASP* 1.3 71.7 - - - +
532A VAL* 1.3 60.4 + - - +
534A GLU* 3.1 13.8 + - - +
535A ASP* 3.0 32.1 + - - +
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Residues in contact with VAL 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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511A PHE* 4.6 3.8 - - + +
514A PHE* 3.9 10.3 - - + +
515A LEU* 3.8 39.7 - - + +
518A ARG* 3.6 27.6 - - + -
528A LEU* 3.1 22.0 + - + +
529A LEU* 3.3 9.4 + - + +
531A GLU* 1.3 77.5 - - - +
533A ALA* 1.3 60.8 + - - +
535A ASP* 3.3 8.3 + - - +
536A MET* 3.0 24.5 + - + +
548A LEU* 3.4 18.8 - - + -
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Residues in contact with ALA 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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529A LEU 2.8 14.1 + - - +
530A ASP* 3.4 17.5 - - - +
531A GLU 3.2 0.4 - - - -
532A VAL* 1.3 75.4 - - - +
534A GLU* 1.3 61.5 + - - +
536A MET* 3.5 2.9 + - - +
537A GLY* 3.1 19.2 + - - -
548A LEU* 3.6 34.9 + - + +
550A ILE* 4.8 3.4 - - + -
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Residues in contact with GLU 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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518A ARG* 6.0 0.2 - - - +
530A ASP* 3.1 21.0 + - - +
531A GLU* 3.1 15.0 + - - +
533A ALA* 1.3 75.1 - - - +
535A ASP* 1.3 68.6 + - - +
537A GLY* 3.1 13.2 + - - -
538A LYS* 3.7 21.3 + - - +
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Residues in contact with ASP 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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514A PHE* 3.6 34.8 - - + +
517A ASP* 5.7 1.6 - - - +
518A ARG* 2.7 52.3 + - - +
531A GLU 3.0 15.7 + - - +
532A VAL* 3.7 7.1 - - - +
534A GLU* 1.3 76.4 - - - +
536A MET* 1.3 63.5 + - - +
538A LYS* 3.1 34.2 + - - +
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Residues in contact with MET 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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491A ALA 4.3 2.7 - - - +
510A ILE* 4.0 19.5 - - + +
511A PHE* 4.0 31.6 - - + -
514A PHE* 3.8 17.0 - - + -
532A VAL* 3.0 17.3 + - + +
533A ALA* 3.8 5.2 - - - +
535A ASP* 1.3 78.1 - - - +
537A GLY* 1.3 61.9 + - - +
538A LYS 3.1 0.2 - - - -
539A CYS* 3.0 19.6 + - - +
542A THR* 4.2 7.2 + - - +
546A GLN* 3.9 27.5 - - - +
547A ALA* 4.2 3.6 - - - -
548A LEU* 3.7 46.9 - - + +
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Residues in contact with GLY 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A ALA 3.1 15.0 + - - -
534A GLU* 3.1 7.8 + - - -
536A MET* 1.3 77.8 - - - +
538A LYS* 1.3 57.4 + - - +
539A CYS 3.3 1.8 - - - -
543A LYS* 3.4 26.4 + - - +
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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