Contacts of the helix formed by residues 530 - 542 (chain C) in PDB entry 3G4G
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 530 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C GLN* 4.5 4.7 + - - +
193C VAL* 5.3 0.6 - - - +
523C MET* 4.2 10.0 - - - +
528C ASN* 4.4 5.4 + - - -
529C ALA* 1.3 73.3 + - - +
531C VAL* 1.3 60.5 + - - +
532C GLU* 3.3 6.5 - - - -
533C LYS* 3.8 32.7 + - - +
534C SER* 3.0 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 531 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499C THR* 3.9 27.1 - - + -
503C MET* 3.7 34.1 - - + -
507C PHE* 5.0 3.8 - - + -
523C MET* 6.0 0.4 - - - -
529C ALA* 3.7 12.5 + - + +
530C SER* 1.3 70.2 - - - +
532C GLU* 1.3 79.5 + - - +
534C SER* 2.9 22.7 + - - +
535C GLN* 3.0 10.7 + - + +
572C TYR* 4.4 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 532 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530C SER* 4.3 4.2 - - - -
531C VAL* 1.3 91.9 + - - +
533C LYS* 1.3 63.5 + - - +
535C GLN* 3.3 12.3 + - - +
536C VAL* 3.4 16.1 + - - +
572C TYR* 3.9 16.2 - - + +
575C THR* 2.8 42.1 - - + +
576C ILE* 3.9 18.2 - - - -
577C PRO* 3.7 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 533 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C VAL* 4.3 9.6 - - + +
530C SER* 3.5 30.2 + - - +
531C VAL 3.3 0.2 - - - -
532C GLU* 1.3 81.1 - - - +
534C SER* 1.3 64.1 + - - +
536C VAL* 2.9 15.7 + - - +
537C GLY* 3.1 10.4 + - - -
576C ILE* 4.3 33.7 - - + -
577C PRO* 6.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 534 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C VAL* 3.4 14.8 - - - +
503C MET* 5.0 1.6 - - - -
523C MET* 3.5 22.6 - - - -
530C SER 3.0 12.5 + - - -
531C VAL* 2.9 19.2 + - - +
533C LYS* 1.3 79.9 - - - +
535C GLN* 1.3 61.0 + - - +
537C GLY 3.5 0.5 + - - -
538C PHE* 3.0 26.7 + - - +
903C D71 3.1 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 535 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C TYR* 2.4 30.7 + - - +
499C THR* 4.1 11.0 - - + +
503C MET* 5.4 0.6 - - - -
531C VAL* 3.0 15.7 + - - +
532C GLU 3.7 5.8 - - - +
533C LYS 3.1 0.4 - - - -
534C SER* 1.3 94.9 + - - +
536C VAL* 1.3 58.3 + - - +
538C PHE* 3.6 10.7 - - - +
539C ILE* 3.2 35.2 + - - +
572C TYR* 3.7 31.4 - - + -
903C D71 3.1 52.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 536 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532C GLU 3.4 11.2 + - - +
533C LYS* 2.9 10.3 + - - +
535C GLN* 1.3 76.2 - - - +
537C GLY* 1.3 59.4 + - - +
539C ILE* 4.1 0.6 - - - +
540C ASP* 2.9 39.5 + - - +
569C ARG* 3.3 44.0 - - + +
572C TYR* 3.9 7.2 - - + +
573C GLN* 3.6 43.3 - - + +
576C ILE* 4.4 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 537 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C VAL* 4.2 12.1 - - - -
197C ILE* 4.0 6.5 - - - +
533C LYS 3.1 11.5 + - - -
534C SER 3.9 2.0 - - - -
536C VAL* 1.3 75.8 - - - +
538C PHE* 1.3 57.9 + - - +
540C ASP* 4.7 0.2 - - - -
541C TYR* 2.9 56.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 538 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C ILE* 4.5 3.4 - - - -
201C PHE* 3.9 18.6 - + - -
485C LEU* 3.7 11.2 - - + -
488C PRO* 3.6 17.9 - - + -
534C SER 3.0 14.8 + - - +
535C GLN* 3.6 22.9 - - - +
537C GLY* 1.3 74.8 - - - +
539C ILE* 1.3 58.0 + - + +
542C ILE* 3.0 27.1 + - + +
543C VAL* 3.0 47.6 + - + -
903C D71 3.2 80.3 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 539 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488C PRO* 4.1 24.0 - - + -
495C TYR* 3.7 20.4 - - + +
535C GLN* 3.2 21.5 + - + +
536C VAL 4.1 0.7 - - - +
537C GLY 3.3 0.2 - - - -
538C PHE* 1.3 76.8 - - + +
540C ASP* 1.3 64.8 + - - +
543C VAL* 3.5 6.9 + - + -
544C HIS* 2.7 45.6 + - + +
545C PRO* 3.5 0.7 - - - +
565C LEU* 3.8 24.7 - - + +
568C ASN* 4.5 0.7 - - + +
569C ARG* 3.8 48.5 - - + +
572C TYR* 5.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 540 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C VAL* 2.9 24.9 + - - +
537C GLY* 4.7 0.7 - - - -
539C ILE* 1.3 77.1 - - - +
541C TYR* 1.3 80.0 + - + +
544C HIS* 4.6 4.2 + - - +
545C PRO* 3.3 18.5 - - - +
569C ARG* 2.7 48.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 541 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C VAL* 5.3 3.8 - - + -
197C ILE* 4.2 20.9 - - + -
442C HIS* 4.7 1.0 + - - -
443C MET* 4.5 11.3 - - - +
537C GLY* 2.9 39.7 + - - +
540C ASP* 1.3 93.4 - - + +
542C ILE* 1.3 64.0 + - + +
545C PRO* 3.8 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 542 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C ILE* 3.4 36.1 - - + -
201C PHE* 2.8 51.8 - - + -
442C HIS* 3.6 29.6 + - + +
443C MET* 4.8 2.2 - - + -
485C LEU* 4.0 14.4 - - + -
538C PHE* 3.0 29.7 + - + +
540C ASP 3.6 0.8 - - - -
541C TYR* 1.3 82.6 - - - +
543C VAL* 1.3 67.5 + - - +
544C HIS 3.5 0.9 - - - -
545C PRO* 3.6 2.3 - - - +
546C LEU* 3.3 24.4 + - - +
----------------------------------------------------------
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