Contacts of the helix formed by residues 513 - 532 (chain A) in PDB entry 4Y05
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 513 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498A ARG 3.4 22.2 - - - +
512A GLU* 1.3 77.4 + - - +
514A ALA* 1.3 60.4 + - - +
515A GLU 3.5 1.8 - - - -
516A ILE* 3.9 13.5 - - - +
517A ASN* 3.1 28.8 + - - +
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Residues in contact with ALA 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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512A GLU* 3.5 5.3 + - + +
513A GLY* 1.3 76.5 - - - +
515A GLU* 1.4 64.4 + - - +
517A ASN* 3.6 4.5 + - - +
518A LYS* 3.1 29.6 + - - +
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Residues in contact with GLU 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ASN* 3.5 30.8 - - - +
407A GLY* 4.1 10.0 - - - +
512A GLU* 3.3 20.0 + - + +
514A ALA* 1.4 75.7 - - - +
516A ILE* 1.4 65.9 + - + +
518A LYS* 3.1 20.5 + - - +
519A SER* 3.0 25.3 + - - -
704A SO4 3.0 34.5 + - - +
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Residues in contact with ILE 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A SER 4.8 0.7 - - - +
469A ARG* 3.7 47.3 - - + +
471A HIS* 4.9 4.0 - - + +
494A ALA* 3.8 21.3 - - + -
495A GLY 3.4 24.5 - - - +
496A ASN* 5.0 0.9 - - - -
498A ARG 5.5 4.0 - - - +
512A GLU* 3.7 13.8 + - - +
513A GLY* 3.8 13.9 + - - +
514A ALA 3.4 0.2 - - - -
515A GLU* 1.4 77.4 - - + +
517A ASN* 1.3 57.8 + - - +
519A SER* 3.1 9.3 - - - -
520A LEU* 2.9 43.5 + - + +
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Residues in contact with ASN 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A ASN 5.3 4.9 + - - -
498A ARG 4.2 12.2 + - - +
513A GLY 3.1 19.7 + - - +
514A ALA* 3.6 4.9 + - - +
516A ILE* 1.3 77.3 - - - +
518A LYS* 1.3 57.6 + - - +
520A LEU* 3.4 8.2 + - - +
521A LEU* 3.0 55.2 + - - +
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Residues in contact with LYS 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 ALA 3.1 18.6 + - - +
515A GLU* 3.1 28.1 + - - +
517A ASN* 1.3 73.0 + - - +
519A SER* 1.3 60.2 + - - +
521A LEU* 3.8 8.0 - - - +
522A ALA* 2.9 31.4 + - - +
541A GLU* 3.1 32.3 + - + +
542A SER* 4.8 1.3 - - - -
704A SO4 2.8 34.8 + - - +
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Residues in contact with SER 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A HIS* 2.8 33.4 + - - -
515A GLU 3.0 15.0 + - - -
516A ILE 3.1 10.8 - - - -
518A LYS* 1.3 77.9 - - - +
520A LEU* 1.3 57.3 + - - +
522A ALA* 3.3 3.8 + - - +
523A LEU* 2.9 27.9 + - - +
542A SER* 3.7 19.7 + - - -
544A LEU* 3.8 16.2 + - - +
545A THR* 4.6 0.3 - - - +
704A SO4 4.8 2.9 - - - -
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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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347A TYR* 3.9 29.2 - - + +
471A HIS* 4.4 9.2 - - + -
493A LEU* 4.0 29.2 - - + -
494A ALA 4.2 4.5 - - - +
496A ASN* 3.8 30.7 - - + -
516A ILE* 2.9 38.8 + - + +
517A ASN* 3.9 9.4 - - - +
519A SER* 1.3 72.6 - - - +
521A LEU* 1.3 67.3 + - + +
523A LEU* 3.3 5.0 + - + -
524A LYS 3.1 9.2 + - - -
544A LEU* 5.4 0.2 - - + -
581A TYR* 2.8 29.0 + - + +
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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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517A ASN* 3.0 46.9 + - - +
518A LYS* 3.8 8.1 - - - +
520A LEU* 1.3 81.0 - - + +
522A ALA* 1.3 60.7 + - - +
524A LYS* 3.4 16.6 + - - +
525A GLU* 3.2 27.0 + - + +
581A TYR* 4.9 11.0 - - + -
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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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518A LYS 2.9 19.1 + - - +
519A SER 3.5 5.4 - - - +
521A LEU* 1.3 75.5 - - - +
523A LEU* 1.3 62.2 + - - +
525A GLU* 3.2 8.0 + - - +
526A CYS* 3.0 25.8 + - - -
538A PRO* 4.6 5.1 - - - +
541A GLU* 4.0 22.9 - - + -
542A SER* 3.7 16.6 - - - +
545A THR* 3.7 11.2 - - - +
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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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345A PHE* 3.6 39.5 - - + -
493A LEU* 3.8 34.3 - - + -
519A SER 2.9 13.5 + - - +
520A LEU* 3.5 11.7 - - + +
522A ALA* 1.3 76.1 - - - +
524A LYS* 1.4 56.3 + - - +
526A CYS* 3.1 2.3 + - - -
527A ILE* 2.8 39.8 + - + +
544A LEU* 4.3 8.3 - - + -
545A THR* 3.5 12.7 - - + +
552A PHE* 3.7 17.5 - - + -
561A MET* 4.0 12.6 - - + -
581A TYR* 4.2 5.4 - - - +
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Residues in contact with LYS 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 LEU 3.1 8.2 + - - +
521A LEU* 3.6 19.8 + - - +
523A LEU* 1.4 74.3 - - - +
525A GLU* 1.4 65.1 + - - +
527A ILE* 3.3 6.9 + - - +
528A ARG* 2.8 52.0 + - + +
581A TYR* 3.6 54.9 + - + +
584A ARG* 3.6 48.8 - - + +
585A VAL* 3.9 14.1 - - + +
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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 LEU 3.2 11.7 + - - +
522A ALA* 3.2 7.6 + - - +
524A LYS* 1.4 92.7 + - - +
526A CYS* 1.3 57.4 + - - +
528A ARG* 3.5 26.8 + - - +
529A ALA* 2.9 29.3 + - - +
534A LYS* 5.9 1.4 + - - -
538A PRO* 3.6 29.5 - - + +
584A ARG* 5.2 3.8 + - - -
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Residues in contact with CYS 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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522A ALA 3.0 17.6 + - - +
523A LEU 3.1 6.7 + - - +
525A GLU* 1.3 72.2 - - - +
527A ILE* 1.3 65.4 + - - +
529A ALA* 3.3 2.3 + - - +
530A LEU* 3.0 22.9 + - - +
537A THR* 3.2 26.0 - - - +
538A PRO* 4.0 5.4 - - - -
539A PHE* 3.9 14.4 - - - -
545A THR* 3.6 23.6 - - + -
552A PHE* 3.6 36.0 - - + +
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Residues in contact with ILE 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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259A ILE* 3.9 20.8 - - + +
345A PHE* 4.3 8.7 - - + -
523A LEU* 2.8 39.6 + - + +
524A LYS* 3.7 5.6 - - - +
526A CYS* 1.3 71.3 - - - +
528A ARG* 1.3 67.3 + - - +
530A LEU* 3.2 9.8 + - - +
531A GLY* 3.0 19.2 + - - -
552A PHE* 4.3 11.4 - - + -
559A THR* 3.9 19.1 - - + +
561A MET* 3.7 31.9 - - + -
585A VAL* 3.5 30.9 - - + +
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Residues in contact with ARG 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 LYS* 2.8 37.6 + - + +
525A GLU* 3.7 26.5 + - - +
527A ILE* 1.3 72.2 - - - +
529A ALA* 1.3 57.1 + - - +
531A GLY* 3.2 4.7 + - - -
532A GLN* 3.2 32.1 + - + +
584A ARG* 2.7 55.4 + - - +
585A VAL 3.6 13.5 - - - +
587A GLU* 3.2 55.4 + - - +
588A LEU 5.2 4.2 + - - -
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Residues in contact with ALA 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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525A GLU 2.9 18.0 + - - +
526A CYS 3.7 1.1 - - - +
527A ILE 3.2 0.4 - - - -
528A ARG* 1.3 72.4 - - - +
530A LEU* 1.3 64.8 + - - +
532A GLN 3.1 2.9 + - - -
533A ASN 3.1 16.8 + - - -
534A LYS* 3.1 39.9 + - + +
536A HIS 4.3 1.1 - - - +
537A THR* 3.4 34.1 - - + -
538A PRO* 5.2 0.9 - - + -
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Residues in contact with LEU 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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258A ARG* 3.1 56.7 + - - +
259A ILE* 3.5 22.7 - - + -
526A CYS 3.0 12.2 + - - +
527A ILE* 3.4 7.2 - - - +
529A ALA* 1.3 73.7 - - - +
531A GLY* 1.3 58.8 - - - +
533A ASN* 2.9 17.8 + - - +
534A LYS 5.2 0.2 - - - +
551A SER 4.4 11.4 - - - +
552A PHE* 3.6 34.4 + - + +
553A ILE 4.6 0.2 - - - +
557A SER* 3.5 24.7 - - - +
558A ARG 4.4 0.2 - - - -
559A THR* 3.7 28.3 - - + +
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Residues in contact with GLY 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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258A ARG* 4.5 9.3 + - - -
259A ILE* 3.8 23.3 - - - -
527A ILE 3.0 11.0 + - - -
528A ARG* 3.5 6.5 - - - -
529A ALA 3.2 0.4 - - - -
530A LEU* 1.3 77.8 - - - +
532A GLN* 1.3 57.2 + - - +
533A ASN* 3.5 3.3 + - - +
587A GLU 6.1 1.3 - - - -
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Residues in contact with GLN 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 ARG* 3.2 15.2 + - + +
529A ALA 3.1 6.9 + - - +
531A GLY* 1.3 74.6 - - - +
533A ASN* 1.4 68.2 + - - +
534A LYS* 3.1 22.1 + - + +
587A GLU 4.8 2.5 - - - +
588A LEU* 3.4 26.5 - - - +
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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
------------------------------------------------------------
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