Contacts of the helix formed by residues 490 - 497 (chain D) in PDB entry 2GL7
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 GLY 490 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448D VAL* 3.9 19.7 - - - -
485D VAL* 2.9 22.2 + - - -
486D ARG 4.2 0.4 + - - -
488D HIS 3.3 1.2 - - - -
489D TYR* 1.3 78.4 - - - +
491D LEU* 1.3 66.9 + - - +
492D PRO 3.4 1.1 - - - -
493D VAL* 3.2 11.2 + - - +
494D VAL* 3.1 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 491 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485D VAL* 4.0 8.2 + - + -
486D ARG* 3.6 26.2 - - + +
489D TYR* 4.6 0.2 - - - +
490D GLY* 1.3 76.4 - - - +
492D PRO* 1.3 71.1 - - + +
494D VAL* 4.4 2.7 - - - -
495D VAL* 3.0 28.7 + - - +
517D LEU* 3.7 31.0 - - + -
523D ASN* 3.6 28.7 - - - +
526D PRO* 3.8 24.9 - - + -
527D LEU* 3.9 25.4 - - + +
530D GLN* 4.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 492 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489D TYR* 3.8 20.9 - - + +
490D GLY 3.5 3.8 - - - -
491D LEU* 1.3 94.8 - - + +
493D VAL* 1.3 56.6 + - - +
495D VAL* 4.0 1.9 - - - +
496D LYS* 3.0 27.8 + - - +
530D GLN* 3.8 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 493 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448D VAL* 5.3 2.0 - - + +
451D VAL* 3.8 34.3 - - + +
452D LEU* 3.6 37.0 - - + -
455D GLY 6.2 0.2 - - - +
489D TYR 4.9 0.6 + - - -
490D GLY* 3.2 20.6 + - - +
492D PRO* 1.3 77.3 - - - +
494D VAL* 1.3 67.6 + - + +
496D LYS* 3.3 14.3 + - + +
497D LEU* 3.1 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 494 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448D VAL* 6.5 0.4 - - + -
451D VAL* 5.7 0.2 - - + -
465D ILE* 4.2 10.1 - - + -
468D LEU* 5.6 2.9 - - + -
485D VAL* 4.8 9.4 - - + -
490D GLY* 3.1 20.2 + - - +
491D LEU* 3.3 8.3 + - + +
493D VAL* 1.3 80.4 - - + +
495D VAL* 1.3 64.0 + - + +
497D LEU* 3.2 15.0 + - - +
510D THR* 3.2 29.5 - - + +
513D LEU* 3.7 31.6 - - + -
514D ILE* 3.5 28.9 - - + -
517D LEU* 4.4 6.7 - - + -
527D LEU* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 495 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491D LEU 3.0 16.7 + - - +
492D PRO 4.0 1.6 - - - +
494D VAL* 1.3 76.3 - - + +
496D LYS* 1.3 63.1 + - - +
498D LEU* 3.2 17.5 + - + +
499D HIS* 3.2 17.7 - - - +
514D ILE* 4.4 11.4 - - + -
527D LEU* 3.9 26.0 - - + -
530D GLN* 3.4 45.3 - - + +
531D GLY 4.3 1.6 - - - -
532D ALA* 4.1 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 496 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492D PRO 3.0 19.6 + - - +
493D VAL* 3.5 17.0 - - + +
494D VAL 3.2 0.4 - - - -
495D VAL* 1.3 76.8 - - - +
497D LEU* 1.3 60.2 + - + +
498D LEU 3.1 0.2 - - - -
499D HIS* 3.0 34.6 + - + +
500D PRO 5.3 0.3 - - - +
501D PRO* 6.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 497 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451D VAL* 3.8 25.6 - - + +
455D GLY 4.3 17.3 - - - +
456D ASP* 5.7 2.0 - - - -
461D THR* 4.3 6.1 - - + -
465D ILE* 3.9 25.4 - - + -
493D VAL* 3.1 27.1 + - + +
494D VAL* 3.2 8.9 + - - +
496D LYS* 1.3 75.2 - - + +
498D LEU* 1.3 61.1 + - - +
499D HIS 3.2 0.7 - - - -
502D SER* 2.8 32.5 + - - +
506D LEU* 4.1 27.6 - - + +
507D ILE* 4.0 4.2 - - - +
510D THR* 4.0 11.6 + - - +
----------------------------------------------------------
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