Contacts of the helix formed by residues 518 - 533 (chain A) in PDB entry 3ODX
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 ARG 518 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A ASN* 2.9 58.4 + - - +
460A ILE 5.6 0.2 - - - -
462A PRO* 3.7 21.7 - - + +
514A ARG 3.7 2.6 + - - +
515A PHE 3.6 2.7 + - - +
516A CYS 3.1 0.4 - - - -
517A SER* 1.3 80.9 - - - +
519A GLN* 1.3 53.6 + - - +
520A SER 3.4 1.3 - - - -
521A PHE* 2.7 32.4 + - + +
522A ALA* 2.5 36.9 + - + -
609A MET* 3.7 33.6 - - + +
613A LEU* 3.9 23.2 - - - +
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Residues in contact with GLN 519 (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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515A PHE* 3.8 7.3 + - + -
516A CYS* 3.2 23.1 + - - +
517A SER 3.4 0.9 - - - +
518A ARG* 1.3 71.5 - - - +
520A SER* 1.3 68.7 + - - +
522A ALA* 3.0 8.2 + - - +
523A LEU* 2.8 37.0 + - + +
558A ILE* 4.0 22.0 - - + +
559A PRO* 3.0 34.2 + - + +
562A MET* 3.8 28.4 + - - +
606A VAL* 6.2 0.7 - - + -
610A GLU* 5.5 2.0 - - - +
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Residues in contact with SER 520 (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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517A SER 4.6 2.0 + - - -
518A ARG 3.2 1.4 + - - -
519A GLN* 1.3 79.3 + - - +
521A PHE* 1.3 65.2 + - - +
523A LEU* 3.4 8.1 + - - +
524A GLU* 3.1 27.5 + - - +
610A GLU* 2.9 39.2 + - - -
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Residues in contact with PHE 521 (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 GLU* 5.0 1.8 - - + -
459A ASN* 3.9 41.7 - - + -
460A ILE* 4.3 5.2 - - + -
517A SER 5.2 0.6 + - - +
518A ARG* 2.7 33.3 + - + +
520A SER* 1.3 77.0 - - - +
522A ALA* 1.3 68.8 + - - +
524A GLU* 3.3 13.5 + - - +
525A GLN* 3.0 61.6 + - + +
613A LEU* 3.5 38.7 - - + +
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Residues in contact with ALA 522 (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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460A ILE* 3.4 38.3 - - + +
518A ARG 2.5 17.6 + - - +
519A GLN* 3.3 11.7 - - - +
521A PHE* 1.3 79.2 - - - +
523A LEU* 1.3 61.9 + - - +
525A GLN* 3.4 3.0 - - - +
526A LEU* 3.0 29.0 + - - +
558A ILE* 4.3 15.7 - - + -
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Residues in contact with LEU 523 (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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519A GLN* 2.8 33.9 + - + +
520A SER* 3.8 6.7 - - - +
522A ALA* 1.3 74.8 - - - +
524A GLU* 1.3 61.5 + - - +
526A LEU* 2.9 10.7 + - + +
527A LYS* 2.8 28.7 + - - +
555A LYS* 4.0 36.3 - - + +
558A ILE* 4.0 26.9 - - + -
559A PRO* 5.3 4.3 - - + -
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Residues in contact with GLU 524 (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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520A SER* 3.1 14.7 + - - +
521A PHE* 3.3 27.8 + - - +
523A LEU* 1.3 75.6 - - - +
525A GLN* 1.3 72.0 + - - +
527A LYS* 3.7 8.2 - - - +
528A ALA* 2.8 33.1 + - - +
613A LEU* 5.3 3.8 - - - +
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Residues in contact with GLN 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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452A PHE* 4.2 13.3 - - + -
456A GLU* 5.0 6.3 + - - -
460A ILE* 3.7 18.1 - - + +
521A PHE* 3.0 57.3 + - + +
522A ALA 3.4 8.5 - - - +
524A GLU* 1.3 89.0 - - - +
526A LEU* 1.3 62.5 + - - +
528A ALA* 3.7 7.3 + - - +
529A LYS* 3.3 25.6 + - - +
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Residues in contact with LEU 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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446A MET* 4.6 9.9 - - + -
452A PHE* 4.5 4.9 - - + -
460A ILE* 3.9 25.8 - - + -
461A PHE* 4.8 2.9 - - + -
522A ALA 3.0 18.1 + - - +
523A LEU* 2.9 10.3 + - + +
525A GLN* 1.3 73.7 - - - +
527A LYS* 1.3 66.6 + - - +
529A LYS* 3.3 1.4 + - - -
530A GLN* 3.0 40.6 + - - +
536A PHE* 3.6 22.7 - - + -
554A LEU* 3.7 21.5 - - + -
558A ILE* 3.5 30.3 - - + -
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Residues in contact with LYS 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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523A LEU 2.8 15.6 + - - +
524A GLU* 3.7 8.3 - - - +
526A LEU* 1.3 77.1 - - - +
528A ALA* 1.3 63.8 + - - +
530A GLN* 3.1 15.3 + - + +
531A ARG* 2.9 61.2 + - + +
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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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524A GLU 2.8 21.0 + - - +
525A GLN* 3.7 9.2 - - - +
527A LYS* 1.3 73.4 - - - +
529A LYS* 1.3 53.7 + - + +
531A ARG* 3.0 17.4 + - - +
532A LYS* 2.7 42.0 + - + +
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Residues in contact with LYS 529 (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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451A PHE* 3.9 20.9 + - - +
452A PHE* 3.5 41.5 - - + -
525A GLN 3.3 10.0 + - - +
527A LYS 3.3 0.4 - - - -
528A ALA* 1.3 80.6 - - + +
530A GLN* 1.3 56.9 + - - +
532A LYS* 4.3 21.8 - - - +
533A ASP* 2.7 57.2 + - - +
536A PHE* 3.4 41.0 - - + -
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Residues in contact with GLN 530 (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 LEU* 3.0 27.7 + - - +
527A LYS* 3.7 15.6 - - - +
529A LYS* 1.3 77.0 - - - +
531A ARG* 1.3 65.7 + - + +
532A LYS 3.3 0.7 + - - -
533A ASP 3.8 5.5 + - - +
534A PRO* 4.6 0.7 - - - +
536A PHE* 3.3 18.8 - - + -
537A CYS* 3.5 37.1 - - + +
540A VAL* 3.4 38.3 - - + +
544A GLU* 5.3 1.0 + - - -
554A LEU* 4.8 5.7 - - - +
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Residues in contact with ARG 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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527A LYS* 2.9 48.4 + - + +
528A ALA* 3.8 21.3 - - - +
530A GLN* 1.3 79.1 - - + +
532A LYS* 1.3 59.6 + - - +
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Residues in contact with LYS 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* 2.7 19.4 + - + +
529A LYS* 4.2 27.4 - - - +
531A ARG* 1.3 81.0 - - - +
533A ASP* 1.3 67.1 + - - +
534A PRO* 3.7 7.9 - - - +
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Residues in contact with ASP 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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451A PHE* 4.5 1.4 - - - -
529A LYS* 2.7 42.7 + - - +
530A GLN 3.8 4.0 - - - +
531A ARG 3.8 0.4 - - - -
532A LYS* 1.3 82.8 - - - +
534A PRO* 1.3 66.8 - - - +
535A ARG* 3.0 27.8 + - - +
536A PHE* 3.1 18.2 + - - +
537A CYS 3.0 22.3 + - - -
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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