Contacts of the helix formed by residues 513 - 525 (chain A) in PDB entry 6X70
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 SER 513 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356A TYR* 5.2 2.5 - - - -
358A ILE* 4.0 8.0 - - - +
511A SER* 3.4 3.6 + - - -
512A ASP* 1.3 78.8 + - - +
514A LEU* 1.3 59.4 + - - +
515A VAL* 3.4 0.9 - - - +
516A LEU* 3.0 22.5 + - - +
517A ALA* 2.9 30.3 + - - +
534A LYS* 3.6 10.5 - - - -
601A GLY 2.8 29.0 + - - -
603A ASP* 3.4 18.8 - - - -
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Residues in contact with LEU 514 (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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358A ILE* 4.0 18.5 - - + +
360A HIS* 4.8 3.3 + - - +
470A VAL* 3.8 31.6 - - + -
513A SER* 1.3 71.6 - - - +
515A VAL* 1.3 62.4 + - - +
517A ALA* 3.2 5.1 + - - +
518A ARG* 3.0 23.9 + - - +
603A ASP* 2.8 26.2 + - - +
607A SER* 3.4 33.4 - - - +
608A LEU* 4.5 1.6 - - + -
610A ILE* 4.4 9.0 - - + -
611A LEU* 4.1 29.2 - - + -
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Residues in contact with VAL 515 (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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513A SER* 3.4 9.6 - - - +
514A LEU* 1.3 73.3 - - - +
516A LEU* 1.3 66.6 + - + +
518A ARG* 3.3 6.0 + - - +
519A LEU* 3.1 34.4 + - + +
550A LEU* 5.0 0.2 - - + -
551A PRO* 4.0 28.7 - - + -
598A ALA* 3.9 25.8 - - + +
601A GLY* 3.7 13.7 - - - +
602A GLN 3.7 20.0 - - - +
603A ASP* 2.8 23.7 + - - +
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Residues in contact with LEU 516 (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 SER* 3.1 28.0 - - - +
513A SER* 3.0 14.8 + - - +
515A VAL* 1.3 77.8 - - + +
517A ALA* 1.3 56.8 + - - +
519A LEU* 3.1 7.6 + - + +
520A ALA* 2.7 32.1 + - - +
532A THR 4.1 6.9 - - - +
534A LYS* 3.7 38.8 - - + +
537A LEU* 3.9 13.5 - - + -
541A PHE* 3.8 30.7 - - + -
542A TRP* 4.2 6.5 - - + -
598A ALA 5.2 0.2 - - - +
601A GLY* 3.6 23.3 - - - +
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Residues in contact with ALA 517 (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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358A ILE* 3.4 33.9 - - + +
360A HIS* 3.9 7.0 - - + +
509A GLY* 3.4 25.9 - - - +
511A SER* 3.6 9.8 - - - +
513A SER 2.9 19.1 + - - +
514A LEU 3.2 3.1 + - - +
516A LEU* 1.3 77.2 - - - +
518A ARG* 1.3 61.7 + - - +
520A ALA* 4.3 0.7 - - - -
521A LEU* 3.1 20.1 + - - +
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Residues in contact with ARG 518 (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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360A HIS* 4.0 25.7 + - + +
468A GLU* 5.5 0.4 - - - -
514A LEU 3.0 15.2 + - - +
515A VAL* 3.8 6.3 - - - +
516A LEU 3.2 0.2 - - - -
517A ALA* 1.3 75.2 - - - +
519A LEU* 1.3 67.2 + - - +
521A LEU* 3.2 9.6 + - + +
522A LYS* 3.1 48.6 + - + +
548A ASP 5.0 0.2 + - - -
549A ASP 3.0 23.3 + - - -
550A LEU 4.3 2.4 + - - -
551A PRO* 3.2 41.3 - - + +
11P A 4.4 1.8 + - - -
12P G 2.9 42.0 + - - -
801P MG 4.4 8.1 - - - -
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Residues in contact with LEU 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 VAL* 3.1 29.3 + - + +
516A LEU* 3.7 12.1 - - + +
518A ARG* 1.3 77.3 - - - +
520A ALA* 1.3 60.6 + - - +
522A LYS* 3.1 7.3 + - + -
523A MET 2.9 24.3 + - - -
541A PHE* 3.8 11.4 - - + -
542A TRP* 3.9 28.3 - - + -
545A PHE* 3.1 44.1 - - + -
549A ASP* 3.7 29.4 - - + +
550A LEU* 4.6 5.4 - - + +
571A LEU* 4.3 9.9 - - + -
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Residues in contact with ALA 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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509A GLY* 3.7 18.6 - - - -
510A CYS 4.0 8.1 - - - +
516A LEU 2.7 21.0 + - - +
517A ALA* 3.8 1.3 - - - +
519A LEU* 1.3 72.2 - - - +
521A LEU* 1.3 52.0 + - - +
523A MET* 3.2 5.8 + - - +
524A ALA* 2.7 35.2 + - - +
530A ASN* 3.3 32.3 - - - +
532A THR* 4.7 7.4 - - - +
541A PHE* 4.4 5.4 - - - -
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Residues in contact with LEU 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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360A HIS* 3.6 36.8 - - + +
362A ASP* 3.8 23.3 - - + -
468A GLU* 4.8 2.7 - - - +
507A SER* 3.3 42.6 - - - +
508A ILE 3.5 4.0 - - - +
509A GLY* 3.4 9.8 - - - +
517A ALA 3.1 15.6 + - - +
518A ARG* 3.4 12.3 - - + +
519A LEU 3.1 0.2 - - - -
520A ALA* 1.3 73.7 - - - +
522A LYS* 1.3 68.7 + - + +
524A ALA* 3.0 10.0 + - - +
525A LYS* 3.3 23.7 + - - +
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Residues in contact with LYS 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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518A ARG* 3.1 52.7 + - + +
519A LEU* 3.1 14.1 + - + +
521A LEU* 1.3 79.1 - - + +
523A MET* 1.3 62.7 + - - +
524A ALA 3.3 0.2 + - - -
525A LYS* 3.5 29.0 + - + +
545A PHE* 4.1 7.6 - - + -
548A ASP 5.4 1.0 + - - -
549A ASP* 3.5 44.8 + - + +
12P G 5.7 0.2 + - - -
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Residues in contact with MET 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 LEU 2.9 12.9 + - - +
520A ALA* 3.2 9.4 + - - +
522A LYS* 1.3 76.1 - - - +
524A ALA* 1.3 61.3 + - - +
525A LYS 3.4 6.6 + - - +
530A ASN* 3.1 31.9 - - - +
532A THR* 4.8 0.4 - - - -
540A GLU 4.8 0.2 - - - +
541A PHE* 3.7 32.3 - - + +
544A SER* 3.4 35.0 - - - +
545A PHE* 3.9 10.2 - - + -
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Residues in contact with ALA 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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507A SER* 4.1 1.8 - - - -
508A ILE 3.5 9.6 - - - +
520A ALA 2.7 18.8 + - - +
521A LEU 3.0 6.8 + - - +
523A MET* 1.3 73.4 - - - +
525A LYS* 1.3 63.9 + - - +
526A PRO 3.7 1.4 - - - +
528A GLY* 3.5 24.0 + - - +
529A TYR* 3.4 38.1 + - - +
530A ASN* 3.5 5.8 - - - +
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Residues in contact with LYS 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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362A ASP* 3.3 26.9 + - - -
363A PHE 5.3 2.1 + - - -
364A ASP* 4.1 8.1 - - - +
405A TYR* 3.6 19.7 - - + +
408A ARG* 5.5 3.6 - - - +
507A SER* 3.6 15.7 - - - +
521A LEU* 3.3 30.8 + - - +
522A LYS* 3.9 21.9 - - + +
523A MET 3.3 8.0 - - - +
524A ALA* 1.3 79.2 - - - +
526A PRO* 1.4 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
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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