Contacts of the strand formed by residues 524 - 529 (chain D) in PDB entry 3G2G
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 THR 524 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B THR* 4.1 14.4 - - + +
525B MET 3.4 2.7 - - - -
526B ARG* 4.0 11.8 - - - +
412D THR* 4.1 5.1 - - - +
437D TYR* 4.5 2.1 + - - -
511D VAL 3.7 0.2 - - - +
512D LEU* 3.6 8.1 - - - +
513D THR* 3.6 41.8 + - + +
514D GLY 5.5 0.4 - - - +
522D THR* 3.2 19.0 + - - -
523D ASN* 1.3 75.4 + - - +
525D MET* 1.3 62.3 + - - +
526D ARG* 3.9 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 525 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B THR* 4.2 16.6 - - + +
415B GLY* 5.0 1.1 - - - -
524B THR* 3.5 1.6 - - - -
525B MET* 2.7 70.4 + - + +
412D THR* 4.1 8.0 - - + +
415D GLY 4.0 6.1 - - - +
416D ALA* 3.6 30.5 - - - -
419D ALA* 4.3 8.5 - - + -
510D ILE* 3.5 22.0 - - + -
511D VAL 3.4 2.9 - - - -
512D LEU* 3.5 14.6 - - + -
524D THR* 1.3 73.5 - - - +
526D ARG* 1.3 63.1 + - - +
527D VAL* 3.8 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 526 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B ASN 3.4 8.3 - - - +
524B THR* 4.0 14.6 - - + +
509D VAL 4.0 0.3 - - - +
510D ILE* 3.4 6.2 - - - +
511D VAL* 2.8 45.4 + - + +
513D THR* 5.0 7.9 - - + -
524D THR* 3.9 18.8 - - + -
525D MET* 1.3 76.5 - - - +
527D VAL* 1.3 63.7 + - - +
528D VAL* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 527 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B PRO* 3.6 35.6 - - + +
411B ALA* 4.6 5.2 - - + -
412B THR* 3.1 31.0 - - - +
523B ASN* 3.1 26.7 + - + +
423D CYS* 5.2 2.5 - - - -
508D VAL* 5.1 10.1 - - + -
509D VAL 3.7 5.4 - - - +
510D ILE* 3.7 25.4 - - + -
525D MET* 3.8 14.4 - - + -
526D ARG* 1.3 73.6 - - - +
528D VAL* 1.3 64.9 + - - +
529D PRO* 4.4 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 528 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B PRO* 6.5 0.2 - - - -
490D VAL* 6.1 1.1 - - + -
494D MET* 4.1 12.6 - - + -
508D VAL* 3.4 3.9 - - - -
509D VAL* 2.8 48.5 + - + +
511D VAL* 4.0 15.7 - - + -
526D ARG* 3.8 23.1 - - + -
527D VAL* 1.3 81.7 - - - +
529D PRO* 1.3 86.6 - - + +
531D PRO* 5.6 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 529 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B PRO* 5.9 7.6 - - + -
494D MET* 4.3 1.0 - - - +
506D GLY* 5.0 8.1 - - - +
507D ASP 3.1 10.1 - - - +
508D VAL* 4.4 2.0 - - + -
527D VAL 4.4 3.1 - - - +
528D VAL* 1.3 105.5 - - + +
530D VAL* 1.3 66.3 + - - +
531D PRO* 3.4 7.6 - - - +
----------------------------------------------------------
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