Contacts of the helix formed by residues 509 - 520 (chain A) in PDB entry 4I1R
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 GLY 509 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A ALA* 3.8 13.8 - - - +
365A ASP* 3.0 26.6 + - - -
462A ASP* 5.3 3.6 - - - -
493A CYS 5.6 1.8 - - - -
494A GLN* 5.6 3.6 - - - -
496A ALA* 3.9 6.5 - - - -
508A ASN* 1.3 74.0 - - - +
510A ILE* 1.4 60.4 + - - -
511A PHE 3.4 2.7 - - - -
512A MET 3.4 3.1 + - - -
513A LYS* 2.9 28.6 + - - +
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Residues in contact with ILE 510 (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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462A ASP* 5.8 0.2 + - - -
493A CYS* 4.0 29.1 + - + +
495A GLY 3.2 31.4 - - - +
496A ALA* 3.7 14.5 - - - +
508A ASN 5.2 0.4 - - - +
509A GLY* 1.4 71.0 - - - -
511A PHE* 1.3 61.6 + - - +
513A LYS* 3.3 17.2 - - + +
514A PHE* 3.0 45.8 - - + -
536A MET* 4.8 0.7 - - - -
539A CYS* 4.2 7.4 - - - -
541A LEU* 4.2 17.5 - - + -
542A THR* 3.6 24.0 - - + +
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Residues in contact with PHE 511 (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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411A TYR* 4.3 9.0 - + - -
460A LEU* 3.8 36.6 - - + -
461A LEU 5.1 2.9 - - - -
462A ASP* 3.4 35.5 + - + +
489A GLY 5.2 1.6 - - - -
491A ALA* 4.0 17.0 - - + -
493A CYS* 4.4 5.7 + - - -
509A GLY 3.4 0.6 - - - -
510A ILE* 1.3 77.2 - - - +
512A MET* 1.4 51.8 + - + +
514A PHE* 3.3 3.5 + - - +
515A LEU* 2.8 63.1 + - + +
529A LEU* 5.5 3.1 - - + -
532A VAL* 4.1 10.1 - - + +
536A MET* 3.4 26.5 - - + -
548A LEU* 3.7 31.2 - - + -
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Residues in contact with MET 512 (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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365A ASP* 3.3 42.4 - - - +
368A GLU* 5.0 3.8 - - + +
369A LEU* 3.8 34.1 - - + -
372A LEU* 6.2 0.2 - - - -
411A TYR* 3.6 32.3 - - + +
462A ASP* 4.4 1.6 + - - -
508A ASN* 4.1 7.4 - - - +
509A GLY 3.4 2.9 + - - +
511A PHE* 1.4 75.3 - - + +
513A LYS* 1.4 59.5 + - - +
514A PHE 3.0 0.3 + - - -
515A LEU* 3.8 31.6 - - + -
516A LYS* 2.8 50.7 + - + +
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Residues in contact with LYS 513 (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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508A ASN* 4.2 21.8 - - + +
509A GLY 2.9 14.7 + - - +
510A ILE* 3.3 21.7 - - + +
512A MET* 1.4 75.1 - - - +
514A PHE* 1.4 84.5 + - + +
516A LYS* 3.6 12.5 - - - +
517A ASP* 3.2 18.7 - - - +
539A CYS* 5.5 6.1 - - - +
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Residues in contact with PHE 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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510A ILE* 3.0 43.7 - - + -
511A PHE 3.3 3.8 + - - +
512A MET 3.1 0.4 - - - -
513A LYS* 1.4 97.2 - - + +
515A LEU* 1.3 68.9 + - - +
516A LYS 3.3 2.0 - - - -
517A ASP* 3.3 17.9 + - + +
518A ARG* 3.5 16.8 + - - +
532A VAL* 4.1 11.4 - - + -
535A ASP* 3.7 42.0 - - + +
536A MET* 3.6 21.5 - - + -
539A CYS* 3.5 25.8 - - + -
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Residues in contact with LEU 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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369A LEU* 4.7 2.7 - - + -
460A LEU* 3.7 19.7 - - + -
511A PHE* 2.8 54.9 + - + +
512A MET* 3.0 26.7 + - + +
514A PHE* 1.3 78.0 - - - +
516A LYS* 1.3 57.1 + - - +
518A ARG* 3.3 1.2 + - - +
519A LEU* 2.8 52.1 + - + +
525A ILE* 6.0 1.8 - - + -
528A LEU* 6.3 1.8 - - + -
529A LEU* 4.7 14.6 - - + -
532A VAL* 3.9 20.5 - - + +
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Residues in contact with LYS 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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368A GLU* 2.8 42.0 + - + +
372A LEU* 3.6 34.7 - - + +
508A ASN* 3.1 21.0 - - - +
512A MET* 2.8 32.3 + - + +
513A LYS* 3.6 12.3 - - - +
515A LEU* 1.3 72.5 - - - +
517A ASP* 1.3 68.9 + - - +
518A ARG 3.3 0.7 + - - -
519A LEU* 3.5 7.2 + - - +
520A LEU* 4.4 6.1 + - - +
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Residues in contact with ASP 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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513A LYS 3.2 19.6 - - - +
514A PHE* 3.3 15.0 + - - +
516A LYS* 1.3 83.5 - - - +
518A ARG* 1.3 64.9 + - + +
520A LEU* 4.5 4.9 + - - +
521A GLU* 4.8 4.9 + - - +
535A ASP* 5.5 2.2 - - - +
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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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514A PHE 3.5 13.2 + - - +
515A LEU 3.3 1.2 + - - -
516A LYS 3.3 0.2 - - - -
517A ASP* 1.3 77.7 - - + +
519A LEU* 1.3 66.1 + - - +
520A LEU 3.0 4.9 + - - -
521A GLU* 2.8 60.8 + - - +
523A LYS* 5.7 0.8 - - - +
528A LEU* 3.4 19.3 - - + +
531A GLU* 3.1 41.8 + - - +
532A VAL* 3.8 19.7 - - + -
535A ASP* 2.7 38.9 + - - +
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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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369A LEU* 3.8 25.8 - - + -
372A LEU* 3.7 38.1 - - + -
373A LEU* 4.0 13.2 - - + -
376A LEU* 3.7 18.7 - - + +
409A LEU* 5.7 0.7 - - + -
460A LEU* 5.6 2.7 - - + -
512A MET* 5.9 0.4 - - - -
515A LEU* 2.8 45.3 + - + +
516A LYS 3.5 8.6 + - - +
518A ARG* 1.3 75.7 - - - +
520A LEU* 1.3 59.7 + - + +
521A GLU 3.7 2.1 + - - +
525A ILE* 5.9 1.3 - - + -
528A LEU* 4.5 9.2 - - - +
560A LEU* 4.3 24.2 - - + +
561A THR* 4.3 3.8 - - - +
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Residues in contact with LEU 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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372A LEU* 3.9 38.6 - - + +
375A GLN* 3.7 27.8 - - + +
376A LEU* 3.8 31.1 - - + +
516A LYS 4.4 4.8 + - - +
517A ASP 4.5 4.1 + - - +
518A ARG 3.0 1.6 + - - -
519A LEU* 1.3 76.3 - - + +
521A GLU* 1.3 62.5 + - - +
522A ASP 3.9 0.5 + - - -
561A THR* 3.6 12.5 - - - +
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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