Contacts of the helix formed by residues 398 - 409 (chain I) in PDB entry 6PST
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 398 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153I PRO* 3.6 14.7 - - - +
179I TYR* 3.0 36.5 - - - +
396I ASP* 3.5 11.0 + - - -
397I LEU* 1.3 75.1 - - - +
399I ALA* 1.3 59.3 + - - +
400I VAL* 3.2 9.1 - - - +
401I GLY* 3.4 3.6 - - - +
402I ARG* 2.7 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 399 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398I SER* 1.3 74.9 - - - +
400I VAL* 1.3 59.9 + - + +
402I ARG* 3.9 4.1 - - - +
403I MET* 2.9 30.0 + - - +
414I ILE 4.8 0.7 - - - +
584I TYR* 4.2 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 400 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152I SER* 4.2 8.7 - - - -
153I PRO* 4.5 6.5 - - + -
398I SER* 3.2 5.5 - - - +
399I ALA* 1.3 76.6 - - + +
401I GLY* 1.3 63.7 + - - +
403I MET* 3.3 3.6 + - + +
404I LYS* 2.9 24.5 + - + +
452I ARG* 3.9 21.1 - - - +
584I TYR* 3.6 37.0 - - + +
586I PHE* 3.3 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 401 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153I PRO* 3.6 36.0 - - - +
154I GLY* 4.2 3.9 - - - -
397I LEU* 4.2 8.5 - - - +
398I SER 2.9 12.5 + - - -
400I VAL* 1.3 80.4 - - - +
402I ARG* 1.3 57.3 + - - +
404I LYS* 3.5 1.6 + - - +
405I PHE* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 402 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397I LEU* 3.7 23.7 - - + +
398I SER 2.7 19.6 + - - +
399I ALA* 4.1 3.8 - - - +
401I GLY* 1.3 70.7 - - - +
403I MET* 1.3 65.5 + - - +
405I PHE* 3.1 25.9 - - - -
406I ASN* 2.9 44.6 + - - +
411I ARG* 4.5 1.2 - - - +
414I ILE 4.3 1.3 - - - +
415I GLU* 4.3 2.0 - - - -
416I GLY* 3.6 27.6 - - - +
417I SER* 3.5 32.7 + - - +
419I ILE 3.0 27.5 + - - -
420I LEU* 4.4 0.6 - - - +
424I ASP* 3.0 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 403 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399I ALA 2.9 19.4 + - - +
400I VAL* 3.6 4.9 - - + +
402I ARG* 1.3 76.3 - - - +
404I LYS* 1.3 67.5 + - - +
406I ASN* 4.0 1.0 - - - +
407I ARG* 2.9 46.8 + - - +
414I ILE* 3.3 38.7 + - + +
582I ASN* 5.9 0.7 - - - +
584I TYR* 3.3 39.0 - - + -
586I PHE* 3.4 34.1 - - + -
609I ILE* 4.6 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 404 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152I SER* 3.0 26.9 - - - +
153I PRO 3.7 13.1 + - - +
154I GLY* 4.5 2.0 - - - -
155I VAL* 4.2 12.2 + - - +
156I PHE* 3.2 28.7 - - - -
400I VAL 2.9 16.5 + - - +
403I MET* 1.3 86.8 - - - +
405I PHE* 1.3 57.4 + - - +
407I ARG* 4.5 3.4 - - + +
408I SER* 2.9 37.0 + - - -
443I ASP* 5.1 2.0 + - - -
449I GLY 3.0 27.4 - - - +
450I ASN* 3.7 11.4 + - - +
586I PHE* 3.8 14.1 - - + -
609I ILE* 5.1 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 405 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154I GLY* 4.7 3.3 - - - -
155I VAL* 3.6 26.0 - - + -
176I ILE* 4.1 22.0 - - + -
397I LEU* 4.2 13.2 - - + -
401I GLY 2.9 19.4 + - - +
402I ARG* 3.1 22.7 - - - +
403I MET 3.3 0.2 - - - -
404I LYS* 1.3 74.1 - - - +
406I ASN* 1.3 65.9 + - - +
408I SER* 4.2 0.5 - - - -
409I LEU* 3.0 51.1 + - + +
411I ARG* 3.8 3.1 - - - -
420I LEU* 4.7 4.7 - - + -
424I ASP* 3.0 55.9 - - + -
428I VAL* 3.5 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 406 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402I ARG* 2.9 44.0 + - - +
403I MET 4.1 1.6 - - - +
405I PHE* 1.3 77.9 - - - +
407I ARG* 1.3 60.5 + - - +
409I LEU 3.5 1.6 + - - -
410I LEU 3.2 3.8 + - - -
411I ARG* 2.8 67.1 + - + +
413I GLU* 2.8 41.6 + - - +
414I ILE* 4.8 1.1 - - - -
415I GLU 4.4 3.6 + - - -
416I GLY* 4.8 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 407 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403I MET* 2.9 32.5 + - - +
404I LYS* 4.3 3.8 - - + +
406I ASN* 1.3 77.8 - - - +
408I SER* 1.3 58.7 + - - +
410I LEU* 3.0 25.0 + - - +
411I ARG 4.2 13.8 + - - -
412I GLU* 5.7 6.1 + - - +
414I ILE* 4.3 35.6 - - - +
609I ILE* 4.9 21.9 - - + +
610I GLU* 4.5 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 408 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155I VAL* 3.7 31.3 + - - +
157I PHE* 3.8 11.1 - - - -
404I LYS* 2.9 27.3 + - - -
407I ARG* 1.3 79.1 - - - +
409I LEU* 1.3 60.3 + - - +
410I LEU* 3.3 5.5 + - - +
431I LYS* 3.4 20.8 + - - -
443I ASP* 4.7 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 409 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155I VAL* 4.4 4.9 - - + -
157I PHE* 4.1 24.7 - - + -
405I PHE* 3.0 62.7 + - + +
406I ASN 4.0 3.4 - - - +
408I SER* 1.3 78.4 - - - +
410I LEU* 1.3 71.1 + - - +
411I ARG* 4.1 21.2 - - - +
427I ASP* 4.0 24.1 - - + +
428I VAL* 4.2 6.7 - - + -
431I LYS* 4.4 17.6 - - + +
----------------------------------------------------------
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