Contacts of the helix formed by residues 508 - 519 (chain A) in PDB entry 1RQG
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 LEU 508 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ASP* 3.1 54.1 - - + +
368A ARG* 3.9 1.8 - - + -
369A TYR* 3.6 23.1 - - + +
396A LEU* 4.0 28.9 - - + -
400A LEU* 5.4 0.4 - - + -
456A LEU* 5.8 1.3 - - + -
504A LEU* 2.9 22.6 + - + +
505A GLU 3.7 2.5 - - - -
507A PHE* 1.3 94.6 - - + +
509A PRO* 1.3 68.4 - - - +
510A ASP 3.2 2.0 + - - -
511A ALA* 3.9 15.4 - - + +
512A SER* 3.1 20.4 + - - -
545A PHE* 5.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ARG* 3.3 41.7 - - - +
86A LYS* 4.3 18.8 - - + -
365A ASP* 4.3 2.0 - - - +
368A ARG* 3.5 24.7 - - - +
505A GLU* 3.4 23.2 - - - +
507A PHE 3.5 0.7 - - - +
508A LEU* 1.3 87.6 - - - +
510A ASP* 1.3 58.7 + - - +
512A SER* 3.0 17.5 - - - -
513A GLU* 3.0 14.2 + - - +
525A LYS* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LYS* 2.7 42.4 + - - +
364A ALA* 4.2 10.7 + - - +
365A ASP* 3.4 21.4 + - - +
508A LEU 3.3 1.2 - - - -
509A PRO* 1.3 72.9 - - - +
511A ALA* 1.3 58.0 + - - +
512A SER 2.9 4.9 - - - -
513A GLU* 3.3 6.5 + - - +
514A LYS* 2.9 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ASP* 3.3 9.2 + - - +
504A LEU* 4.5 7.9 - - + -
508A LEU* 3.4 19.8 + - + +
510A ASP* 1.3 78.1 - - - +
512A SER* 1.3 60.7 + - - +
514A LYS* 3.8 13.5 - - - +
515A ILE* 3.3 31.5 + - - +
544A LEU* 4.5 1.0 - - + +
545A PHE* 3.4 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A GLY* 2.9 23.4 + - - +
504A LEU* 4.6 3.8 - - - -
505A GLU* 3.4 27.9 + - - +
508A LEU 3.1 13.8 + - - -
509A PRO* 3.0 16.6 - - - -
510A ASP 2.9 0.2 - - - -
511A ALA* 1.3 78.5 - - - +
513A GLU* 1.3 57.1 + - - +
515A ILE* 3.4 6.0 + - - +
516A TRP 3.1 20.8 + - - -
525A LYS* 3.0 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A PRO 3.0 14.8 + - - +
510A ASP* 3.3 6.5 + - - +
512A SER* 1.3 72.6 - - - +
514A LYS* 1.3 66.9 + - - +
516A TRP* 4.1 11.4 - - - +
517A HIS* 3.0 70.3 + - + +
525A LYS* 3.8 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ASP* 3.9 20.0 + - - -
510A ASP* 2.9 20.2 + - - +
511A ALA* 3.8 11.8 - - - +
513A GLU* 1.3 79.8 - - - +
515A ILE* 1.3 61.7 + - - +
517A HIS* 3.3 7.2 + - - +
518A LEU* 3.1 31.4 + - + +
542A GLU* 6.2 3.4 - - + -
543A ILE 4.1 10.1 - - - +
544A LEU* 3.4 46.7 + - + +
545A PHE* 4.1 5.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A LEU* 5.2 0.7 - - + -
404A VAL* 4.0 27.1 - - + -
497A VAL* 3.6 32.3 - - + +
500A LEU* 4.5 4.0 - - + +
501A GLY* 3.8 19.5 - - - +
504A LEU* 4.1 20.4 - - + -
511A ALA 3.3 18.5 + - - +
512A SER 3.4 3.6 + - - +
513A GLU 3.3 0.2 - - - -
514A LYS* 1.3 80.7 - - - +
516A TRP* 1.3 57.4 + - - +
518A LEU* 3.3 8.2 + - - +
519A LEU* 2.9 35.7 + - + +
544A LEU* 3.8 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A LYS* 3.4 33.4 - - + -
501A GLY* 4.2 9.4 - - - -
502A ILE* 3.5 31.2 - - + -
512A SER 3.1 6.0 + - - +
513A GLU* 3.2 19.0 + - - +
515A ILE* 1.3 77.3 - - - +
517A HIS* 1.3 60.2 + + + +
519A LEU* 3.6 5.9 + - + -
520A ASN 3.0 5.4 + - - -
521A LEU* 2.9 82.7 + - + +
522A ASP 5.0 0.9 - - - -
523A GLU* 2.9 37.5 + - + -
524A VAL 5.1 0.2 - - - -
525A LYS* 3.4 47.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A GLU* 3.0 62.2 + - + +
514A LYS* 3.7 6.5 - - - +
516A TRP* 1.3 78.7 - + + +
518A LEU* 1.3 59.6 + - + +
520A ASN* 2.6 19.8 + - - +
521A LEU 4.8 3.4 - - - +
539A ARG* 2.9 47.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A VAL* 4.3 11.9 - - + -
408A LEU* 3.6 34.4 - - + +
514A LYS* 3.1 23.1 + - + +
515A ILE* 3.3 14.8 + - + +
517A HIS* 1.3 76.1 - - + +
519A LEU* 1.3 61.0 + - + +
520A ASN 3.3 0.2 + - - -
538A VAL* 3.7 6.2 - - - +
539A ARG* 2.9 36.1 + - + +
540A LYS 3.8 15.7 - - - +
542A GLU* 3.5 34.5 - - + +
543A ILE 5.4 0.7 - - - +
544A LEU* 4.4 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A LEU* 4.3 11.4 - - + -
494A LEU* 5.1 5.2 - - + +
497A VAL* 3.7 21.5 - - + -
498A LYS* 3.2 42.4 - - + +
515A ILE* 2.9 27.0 + - + +
516A TRP* 3.9 2.2 - - + +
518A LEU* 1.3 76.5 - - + +
520A ASN* 1.3 67.4 + - - +
521A LEU* 3.7 20.6 - - + +
532A LEU* 4.0 19.3 - - + -
536A HIS* 2.9 25.5 + - - -
538A VAL* 3.9 17.4 - - + +
----------------------------------------------------------
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