Contacts of the helix formed by residues 480 - 496 (chain A) in PDB entry 5YD6
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 480 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A VAL* 2.9 26.8 + - - -
478A GLY 3.3 2.4 - - - -
479A PHE* 1.3 74.8 - - - +
481A GLU* 1.3 58.8 + - - -
482A TRP 2.9 12.0 + - - -
483A ILE* 3.3 23.3 + - - +
572A ARG* 3.6 17.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A GLY* 1.3 69.1 - - - -
482A TRP* 1.3 63.0 + - - +
483A ILE 3.5 0.2 - - - -
484A ASP* 3.3 28.3 + - + +
485A SER* 3.4 15.0 + - - +
571A GLN* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A PHE* 3.7 28.5 - + - -
410A LEU* 4.6 2.7 - - + -
444A LEU* 3.8 25.6 - - + -
447A PHE* 4.0 18.2 - + - -
448A VAL* 3.4 21.9 - - + +
479A PHE* 3.3 34.5 + + - +
480A GLY 2.9 2.6 + - - -
481A GLU* 1.3 78.3 - - - +
483A ILE* 1.3 54.9 + - - -
485A SER* 3.0 11.2 + - - -
486A ILE* 2.9 39.7 + - + +
565A LEU* 2.8 23.0 + - - +
568A GLN* 3.4 33.0 - - + +
569A GLY* 3.4 31.2 - - - -
572A ARG* 4.6 4.7 - - + -
573A ILE* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A LEU* 5.4 1.1 - - + -
462A LEU* 4.1 23.6 - - + -
464A PHE* 5.6 0.4 - - + -
472A ARG* 3.7 15.7 - - + +
475A CYS* 3.7 28.5 - - + +
476A VAL* 3.5 30.1 - - + -
479A PHE* 3.6 33.1 - - + +
480A GLY 3.3 18.5 + - - +
482A TRP* 1.3 75.1 - - - +
484A ASP* 1.3 71.4 + - - +
486A ILE* 3.6 10.0 - - + +
487A VAL* 2.7 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ARG* 2.9 38.1 + - - +
476A VAL* 5.5 2.1 - - - +
481A GLU* 3.3 23.5 + - + +
482A TRP 3.2 0.4 - - - -
483A ILE* 1.3 87.4 - - - +
485A SER* 1.3 55.6 + - - +
487A VAL* 3.6 4.6 + - - +
488A GLU* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A GLU* 3.4 12.7 + - - +
482A TRP* 3.0 11.7 + - - -
484A ASP* 1.3 74.9 - - - +
486A ILE* 1.3 59.7 + - - +
488A GLU* 3.5 10.9 + - - +
489A PHE* 2.9 30.1 + - - +
565A LEU* 3.6 11.1 - - - +
568A GLN* 3.5 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A PHE* 4.7 1.3 - - + -
448A VAL* 4.0 25.4 - - + +
451A LEU* 3.7 35.4 - - + -
452A ALA* 4.6 6.1 - - + +
462A LEU* 4.0 12.3 - - + -
479A PHE* 4.5 7.2 - - + -
482A TRP* 2.9 62.3 + - + +
483A ILE* 3.6 11.4 - - + +
485A SER* 1.3 76.1 - - - +
487A VAL* 1.3 51.8 + - - +
489A PHE* 3.2 5.0 + - - +
490A SER* 2.7 34.2 + - - -
565A LEU* 4.3 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A PRO* 3.8 27.4 - - + +
460A GLY* 5.3 5.8 - - - -
461A LYS 5.9 0.2 - - - +
462A LEU* 3.9 34.8 - - + -
472A ARG* 4.0 25.8 - - + -
483A ILE 2.7 22.4 + - - +
484A ASP* 4.1 3.1 - - - +
486A ILE* 1.3 69.5 - - - +
488A GLU* 1.3 61.4 + - - +
490A SER* 3.3 9.3 + - - -
491A SER* 2.9 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ASP 3.0 19.6 + - - +
485A SER* 3.7 9.3 - - - +
487A VAL* 1.3 77.9 - - - +
489A PHE* 1.3 62.7 + - - +
491A SER* 3.2 17.4 + - - -
492A ASN* 3.2 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A VAL* 4.2 5.6 - - + -
449A LEU* 4.3 13.7 - - + -
452A ALA* 3.6 24.5 - - + -
485A SER 2.9 19.5 + - - +
486A ILE* 3.5 4.0 - - - +
488A GLU* 1.3 73.4 + - - +
490A SER* 1.3 56.5 + - - +
492A ASN* 3.1 10.1 + - + +
493A LEU* 2.8 42.8 + - + +
558A LYS* 3.7 38.1 - - + -
561A GLU* 3.8 22.7 - - + -
562A LEU* 3.9 29.2 - - + -
565A LEU* 3.4 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A ALA* 2.6 41.3 + - - -
455A SER* 4.2 8.1 - - - -
457A PRO* 3.4 21.3 - - - +
462A LEU* 6.1 0.9 - - - -
486A ILE* 2.7 20.3 + - - -
487A VAL* 3.4 10.3 - - - -
489A PHE* 1.3 72.4 - - - +
491A SER* 1.3 56.4 + - - +
493A LEU* 3.8 0.8 - - - +
494A GLN* 3.0 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A PRO* 3.7 23.3 - - - +
458A VAL* 5.0 1.9 + - - +
487A VAL* 2.9 12.6 + - - +
488A GLU* 3.2 14.8 + - - -
490A SER* 1.3 75.8 - - - +
492A ASN* 1.3 58.6 + - - +
494A GLN* 3.9 1.0 - - - +
495A ASN* 3.0 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A GLU* 3.2 22.7 + - - +
489A PHE* 3.1 12.2 + - + +
491A SER* 1.3 77.6 - - - +
493A LEU* 1.3 68.0 - - - +
495A ASN* 3.3 18.3 + - - +
496A MET* 3.4 18.2 + - - +
558A LYS* 4.5 18.6 + - - +
561A GLU* 5.0 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A LEU* 4.1 26.2 - - + +
452A ALA* 3.8 12.6 - - + +
453A TYR* 3.7 47.9 - - + +
489A PHE* 2.8 25.6 + - + +
490A SER* 3.8 3.8 - - - +
492A ASN* 1.3 73.0 - - - +
494A GLN* 1.3 62.2 + - + +
496A MET* 3.4 17.3 + - - +
497A ASN 3.9 1.7 + - - -
498A ILE* 3.6 32.0 + - + +
503A PHE* 4.3 3.4 - - + -
506A ILE* 6.3 0.7 - - + -
558A LYS* 3.7 27.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A ALA 3.0 22.4 - - - +
453A TYR* 3.4 22.6 - - + +
455A SER 3.0 22.9 + - - +
456A ASN* 4.9 1.8 + - - +
457A PRO* 3.4 25.0 - - + +
458A VAL* 6.2 1.0 - - - +
490A SER* 3.0 17.6 + - - +
491A SER 4.2 2.5 - - - +
493A LEU* 1.3 74.1 - - + +
495A ASN* 1.3 63.8 + - - +
496A MET 3.1 1.8 - - - -
497A ASN* 3.1 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A SER* 3.0 28.9 + - - +
492A ASN* 3.3 11.9 + - - +
494A GLN* 1.3 79.2 - - - +
496A MET* 1.3 59.9 + - + +
497A ASN* 3.3 7.1 + - - +
360C PRO* 3.9 19.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ASN 3.4 12.0 + - - +
493A LEU 3.4 8.7 + - - +
494A GLN 3.1 0.8 - - - -
495A ASN* 1.3 76.3 - - + +
497A ASN* 1.3 60.4 + - - +
498A ILE* 3.9 11.4 - - + -
551A TYR* 2.7 43.0 + - + -
554A LYS* 3.6 40.8 - - + +
555A LEU* 3.9 20.2 - - + +
558A LYS* 3.6 37.9 - - - +
360C PRO* 4.6 11.2 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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