Contacts of the helix formed by residues 512 - 528 (chain A) in PDB entry 3B60
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 ASP 512 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511A LEU* 1.3 68.4 - - - +
513A THR* 1.3 59.2 + - - +
514A GLU* 3.1 14.4 - - - +
515A SER* 2.6 36.9 + - - +
516A GLU 2.6 32.9 + - - -
376B GLY 3.1 7.4 - - - +
377B ARG* 2.8 38.9 + - - +
378B SER* 3.2 26.2 - - - +
537B HIS* 3.3 14.5 + - - -
575B LEU* 4.1 10.8 - - - +
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Residues in contact with THR 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A LEU 2.9 10.0 + - - -
512A ASP* 1.3 68.5 + - - +
514A GLU* 1.3 73.8 + - - +
516A GLU* 3.1 20.0 + - - +
517A ARG* 3.0 23.0 + - - +
538A ARG* 4.9 3.4 - - - +
537B HIS* 4.9 8.7 + - - +
539B LEU* 4.9 8.1 - - + -
575B LEU* 3.4 48.0 - - + +
578B MET* 3.7 24.5 + - + +
579B GLN* 3.9 7.2 + - - -
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Residues in contact with GLU 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A TYR* 4.0 15.5 + - - -
512A ASP* 3.1 10.8 + - - +
513A THR* 1.3 83.6 - - - +
515A SER* 1.3 63.9 + - - +
517A ARG* 3.3 3.6 + - - +
518A ALA* 3.0 21.1 + - + +
377B ARG* 3.1 41.4 + - - -
574B GLN* 3.5 13.8 - - - +
575B LEU* 3.9 13.2 - - + -
578B MET* 3.7 31.1 - - + +
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Residues in contact with SER 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A TYR* 3.9 32.2 + - - -
488A ARG* 5.1 4.8 + - - -
511A LEU* 4.8 9.6 - - - -
512A ASP* 2.6 39.6 + - - +
514A GLU* 1.3 71.6 + - - +
516A GLU* 1.3 68.8 + - - +
518A ALA* 3.0 17.1 + - - +
519A ILE* 3.0 17.7 + - - +
377B ARG* 5.3 1.4 - - - +
378B SER* 4.6 4.2 + - - -
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Residues in contact with GLU 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A THR* 3.0 35.5 - - + +
511A LEU* 4.2 16.5 - - + +
512A ASP 2.6 13.6 + - - +
513A THR* 3.1 27.0 + - - +
515A SER* 1.3 71.9 - - - +
517A ARG* 1.3 60.0 + - - +
519A ILE* 2.7 29.1 + - - +
520A GLN* 3.0 8.9 + - - +
538A ARG* 3.7 28.4 + - - +
540A SER* 5.1 8.5 + - - -
541A THR* 3.7 28.0 - - + +
578B MET 5.5 0.7 - - - +
579B GLN 5.8 0.5 - - - +
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Residues in contact with ARG 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A THR 3.0 8.4 + - - +
514A GLU 3.7 7.2 - - - +
516A GLU* 1.3 83.7 - - + +
518A ALA* 1.3 62.3 + - - +
520A GLN* 3.2 17.1 - - + +
521A ALA* 3.0 22.9 + - - +
540A SER* 5.8 2.5 - - - +
541A THR* 5.6 1.1 - - + -
577B LYS* 4.2 18.6 - - - +
578B MET* 3.8 38.1 + - + +
580B PHE 3.1 25.4 + - - -
581B GLY* 3.6 22.3 + - - -
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Residues in contact with ALA 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A TYR* 3.4 34.5 - - + -
514A GLU* 3.0 14.5 + - + +
515A SER 3.0 13.5 - - - +
516A GLU 2.8 0.4 + - - -
517A ARG* 1.3 73.8 - - - +
519A ILE* 1.3 63.3 - - - +
521A ALA* 3.3 8.5 + - - +
522A ALA* 3.1 19.5 + - - +
578B MET* 5.5 0.2 - - - +
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Residues in contact with ILE 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A MET 5.4 1.1 - - - +
457A ALA* 4.2 25.6 - - - +
458A TYR* 4.2 8.7 - - + -
488A ARG* 4.4 14.6 - - + -
491A ILE* 4.4 27.4 - - + -
495A LEU* 6.3 0.2 - - + -
511A LEU* 3.7 30.7 - - + -
515A SER* 3.0 12.6 + - - +
516A GLU 2.7 11.4 + - - +
518A ALA* 1.3 71.4 - - - +
520A GLN* 1.3 50.4 + - - +
522A ALA* 2.6 16.6 + - + +
523A LEU* 2.6 57.9 + - + -
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Residues in contact with GLN 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A GLU 3.0 6.7 + - - +
517A ARG* 3.2 26.2 - - + +
519A ILE* 1.3 75.2 - - - +
521A ALA* 1.3 63.2 + - - +
523A LEU* 3.1 25.3 + - - +
524A ASP* 2.9 44.1 + - - +
527A GLN* 5.1 2.6 + - - +
534A VAL* 6.1 1.8 - - - +
540A SER 5.5 1.6 - - - +
541A THR* 3.6 48.6 + - + +
542A ILE* 5.4 0.3 - - - -
544A GLN* 4.1 17.8 + - - +
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Residues in contact with ALA 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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517A ARG 3.0 12.6 + - - +
518A ALA* 3.5 10.8 - - - +
519A ILE 3.1 0.2 - - - -
520A GLN* 1.3 76.8 - - - +
522A ALA* 1.3 65.2 + - - +
524A ASP* 3.2 9.8 + - - +
525A GLU* 3.0 22.1 + - - +
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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
----------------------------------------------------------
456A MET* 3.8 32.5 - - + +
495A LEU* 5.8 1.8 - - + -
518A ALA 3.1 8.8 + - - +
519A ILE* 2.6 21.7 + - + +
521A ALA* 1.3 73.9 - - - +
523A LEU* 1.3 63.6 + - - +
525A GLU* 3.1 16.8 + - - +
526A LEU* 3.2 12.1 + - - +
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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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491A ILE* 5.5 3.8 - - + -
495A LEU* 4.6 23.6 - - + -
502A LEU* 5.1 4.7 - - + -
504A LEU* 3.7 32.8 - - + -
519A ILE* 2.6 34.9 + - + +
520A GLN* 3.1 32.3 + - - +
522A ALA* 1.3 71.7 - - - +
524A ASP* 1.3 65.8 + - - +
526A LEU* 2.8 17.3 + - - -
527A GLN* 2.8 35.7 + - + +
534A VAL* 5.6 5.8 - - + -
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Residues in contact with ASP 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 GLN* 2.9 28.1 + - - +
521A ALA* 3.4 11.5 - - - +
523A LEU* 1.3 75.0 - - - +
525A GLU* 1.3 62.9 + - - +
527A GLN* 3.3 21.1 + - - -
528A LYS* 3.1 40.3 + - + +
544A GLN* 3.1 32.6 + - - +
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Residues in contact with GLU 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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521A ALA 3.0 11.9 + - - +
522A ALA* 3.3 12.6 - - - +
523A LEU 3.0 0.2 + - - -
524A ASP* 1.3 78.5 - - - +
526A LEU* 1.3 67.0 + - - +
528A LYS* 3.7 9.8 - - - +
529A ASN* 5.1 3.3 + - - -
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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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452A GLU* 5.4 7.9 - - - +
456A MET* 5.9 2.7 - - + -
495A LEU* 4.2 39.7 - - + +
498A ASP* 4.7 12.3 - - - +
502A LEU* 5.6 6.3 - - + -
522A ALA 3.2 5.7 + - - +
523A LEU* 2.8 12.7 + - - +
525A GLU* 1.3 80.4 - - - +
527A GLN* 1.3 58.8 + - + +
528A LYS 2.6 16.9 + - - -
529A ASN* 3.2 17.9 + - - +
530A ARG* 4.0 37.7 + - + +
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Residues in contact with GLN 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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369A GLY 3.8 5.2 - - - +
371A THR* 2.7 42.1 + - - +
502A LEU* 5.5 5.2 - - + -
520A GLN* 5.1 2.8 + - - -
523A LEU* 2.8 52.9 + - + +
524A ASP* 3.3 26.8 + - - +
526A LEU* 1.3 78.5 - - + +
528A LYS* 1.3 64.2 + - - +
529A ASN 2.9 2.3 + - - -
530A ARG* 3.1 23.0 - - - +
532A SER* 3.1 24.4 + - - +
534A VAL* 6.3 1.4 - - - +
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Residues in contact with LYS 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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369A GLY* 4.2 9.4 - - - +
524A ASP* 3.1 28.4 + - + +
525A GLU* 3.7 11.9 - - - +
526A LEU 2.6 6.0 + - - +
527A GLN* 1.3 73.8 - - - +
529A ASN* 1.3 67.1 + - - +
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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
------------------------------------------------------------
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