Contacts of the helix formed by residues 412 - 419 (chain A) in PDB entry 2GPV
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 ARG 412 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A ASP* 3.0 12.8 + - - +
411A PRO* 1.3 99.3 - - + +
413A ARG* 1.3 63.9 + - - +
414A ALA 3.4 2.5 - - - -
415A GLY 4.2 1.8 - - - +
416A LYS* 3.1 30.7 + - - +
393D ASP* 3.5 23.7 + - - +
396D HIS* 3.4 21.7 - - + +
397D GLU* 3.7 60.3 + - - +
400D GLN* 4.7 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A MET* 2.8 38.9 + - + +
360A LYS* 3.3 10.9 + - - +
362A GLU* 4.3 0.2 + - - -
365A GLU* 2.9 35.7 + - - -
403A GLU* 3.0 25.0 + - + +
407A HIS* 3.4 38.8 + - + -
409A GLU* 5.3 1.4 + - - -
410A ASP* 3.3 35.5 + - - +
411A PRO 3.6 0.4 - - - -
412A ARG* 1.3 76.2 - - - +
414A ALA* 1.3 59.5 + - - +
416A LYS* 3.3 8.3 + - + +
417A MET* 3.0 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A HIS* 5.7 1.3 - - - +
399A LEU* 4.1 14.2 - - + +
400A GLN* 3.1 38.1 - - + +
403A GLU* 4.1 22.4 - - + +
411A PRO 5.4 0.6 + - - -
412A ARG 3.4 0.6 - - - -
413A ARG* 1.3 76.3 - - - +
415A GLY* 1.3 58.8 + - - +
417A MET* 2.9 10.1 + - - +
418A LEU* 2.8 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A GLN* 4.8 1.2 + - - -
412A ARG* 3.7 3.6 + - - +
413A ARG 3.4 0.2 - - - -
414A ALA* 1.3 75.8 - - - +
416A LYS* 1.3 58.9 + - - +
418A LEU* 3.3 9.0 + - - +
419A MET* 2.8 34.7 + - - +
396D HIS* 3.5 24.7 - - - -
400D GLN* 5.6 2.9 - - - +
415D GLY* 5.9 0.7 - - - -
418D LEU* 3.8 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A MET* 4.2 20.4 - - + +
410A ASP* 2.7 43.6 + - - +
412A ARG* 3.1 17.2 + - - +
413A ARG* 3.4 10.3 - - + +
414A ALA 3.3 0.2 - - - -
415A GLY* 1.3 75.8 - - - +
417A MET* 1.3 63.9 + - - +
419A MET* 3.3 20.2 + - + +
420A THR* 3.4 14.0 - - - +
393D ASP* 3.3 35.2 + - - +
396D HIS* 3.6 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A TYR* 4.3 4.3 - - - -
359A MET* 2.9 31.6 - - + -
361A LEU* 3.3 27.1 - - + -
365A GLU* 3.1 35.7 - - - +
369A LEU* 3.8 24.7 - - + +
399A LEU* 4.3 11.9 - - + -
403A GLU* 4.1 11.4 - - - +
413A ARG* 3.0 29.5 + - - +
414A ALA* 2.9 11.8 + - - +
416A LYS* 1.3 77.8 - - - +
418A LEU* 1.3 60.2 + - - +
420A THR* 2.7 29.2 + - - -
421A LEU 4.1 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LEU* 4.9 2.2 - - + -
372A ILE* 4.6 11.2 - - + -
396A HIS* 3.8 16.8 - - + +
399A LEU* 4.1 17.7 - - + -
414A ALA* 2.8 18.2 + - + +
415A GLY* 3.7 13.2 - - - +
417A MET* 1.3 77.0 - - - +
419A MET* 1.3 55.6 + - - +
420A THR 3.1 0.4 - - - -
421A LEU* 3.1 40.8 + - + +
422A PRO* 3.9 2.8 - - - +
415D GLY* 3.7 37.5 - - - +
418D LEU* 4.6 16.3 - - + +
419D MET* 3.7 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A LYS* 3.9 4.9 + - - -
415A GLY 2.8 20.5 + - - +
416A LYS* 3.5 12.6 - - + +
417A MET 3.2 1.0 - - - -
418A LEU* 1.3 73.0 - - - +
420A THR* 1.3 59.3 + - - +
421A LEU 3.4 0.7 - - - -
422A PRO* 3.6 6.5 - - - +
372D ILE* 4.9 9.9 - - + -
376D ASN* 2.8 49.3 + - + +
378D ASP* 4.9 0.7 - - - +
392D GLN* 3.4 47.1 - - + +
396D HIS* 3.8 32.8 - - + +
418D LEU* 4.1 25.4 - - + -
421D LEU* 5.1 2.7 - - + -
----------------------------------------------------------
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