Contacts of the helix formed by residues 406 - 412 (chain A) in PDB entry 1GPM
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 PRO 406 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ASN* 5.1 1.3 - - - -
264A LEU* 3.5 13.0 - - - +
308A ARG* 4.3 22.4 - - + +
311A ILE* 3.5 37.0 - - + -
404A PRO* 3.7 5.2 - - + -
405A GLY* 1.3 88.3 - - - +
407A GLY* 1.3 55.6 + - - +
408A LEU 3.4 0.3 + - - -
409A GLY* 2.9 23.7 + - - -
410A VAL* 3.5 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ASN* 5.5 0.4 - - - +
264A LEU* 3.6 5.8 - - - -
265A LEU* 5.6 1.1 - - - -
403A PHE* 3.5 23.6 - - - -
404A PRO* 2.9 27.9 + - - +
405A GLY 3.0 3.4 + - - -
406A PRO* 1.3 76.6 - - - +
408A LEU* 1.3 58.2 + - - -
409A GLY 3.0 5.4 + - - -
410A VAL* 3.3 20.4 - - - +
411A ARG* 3.7 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 2.9 30.9 + - + +
265A LEU 3.9 7.2 - - - +
266A ARG* 4.7 8.5 - - + -
403A PHE* 4.0 19.3 - - + -
407A GLY* 1.3 66.6 - - - -
409A GLY* 1.3 59.1 + - - +
410A VAL 3.0 3.1 - - - -
411A ARG* 2.9 38.3 + - + +
412A VAL* 3.1 20.4 + - + +
416A VAL* 5.1 0.2 - - - +
421A CYS* 3.9 15.9 - - - +
424A LEU* 4.1 21.1 - - + -
425A ARG* 3.8 36.1 - - + +
428A ASP* 5.3 7.2 - - + +
449A THR 5.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 4.1 20.2 - - - +
307A LYS* 2.9 32.7 + - - +
311A ILE* 4.2 9.4 - - - -
406A PRO 2.9 16.2 + - - -
408A LEU* 1.3 79.0 - - - +
410A VAL* 1.3 61.0 + - - +
412A VAL 3.8 0.8 - - - +
416A VAL* 3.8 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PRO 5.4 1.8 - - - +
307A LYS* 5.5 3.1 - - + -
308A ARG* 3.6 39.9 - - + +
311A ILE* 5.4 1.6 - - + -
404A PRO* 4.1 17.0 - - + -
406A PRO* 3.5 30.9 + - + -
407A GLY 3.3 15.5 - - - +
409A GLY* 1.3 77.6 - - - +
411A ARG* 1.3 60.6 + - + +
412A VAL 3.4 1.6 - - - -
413A LEU* 5.0 2.6 - - - +
450A VAL* 5.6 1.0 - - - +
523A GLU* 4.4 14.0 - - - +
524A TRP* 4.9 2.9 + - - +
525A GLU* 3.5 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ARG* 6.1 0.2 - - - +
402A PRO 4.5 1.0 + - - -
403A PHE* 4.1 18.2 - - - -
404A PRO* 3.0 23.9 - - - +
407A GLY 3.7 14.8 - - - +
408A LEU* 2.9 19.3 + - + +
410A VAL* 1.3 78.6 - - + +
412A VAL* 1.3 59.9 + - - +
413A LEU* 3.9 0.4 - - - -
424A LEU* 3.7 16.8 - - + +
428A ASP* 5.4 3.8 + - - -
446A GLN* 3.3 17.2 - - - +
448A PHE* 3.3 46.5 - - - +
449A THR 3.9 7.6 + - - +
450A VAL* 3.3 15.7 - - - +
451A PHE 2.9 24.9 + - - -
523A GLU* 2.7 40.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LYS* 2.8 27.2 + - - -
408A LEU* 3.1 15.9 + - + +
411A ARG* 1.3 76.6 - - - +
413A LEU* 1.3 63.8 + - - +
415A GLU 3.7 21.8 - - - +
416A VAL* 4.1 13.7 - - + -
420A TYR* 4.1 26.7 - - + +
421A CYS* 4.4 19.1 - - - -
424A LEU* 3.6 21.5 - - + -
451A PHE* 4.1 16.2 - - + -
525A GLU* 3.3 2.4 - - - +
----------------------------------------------------------
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