Contacts of the helix formed by residues 759 - 762 (chain D) in PDB entry 1UES
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 TRP 759 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519C PHE* 3.7 27.8 - + - -
520C GLY* 3.5 32.5 - - - -
560C GLU* 3.7 17.0 - - + -
571C ARG* 5.4 3.1 - - - -
635D TYR* 3.6 15.5 - - - -
670D GLN* 3.4 15.9 - - - -
721D SER* 3.5 21.1 - - - -
722D GLY 3.3 22.4 - - - +
723D TRP* 3.5 7.6 - - - +
741D ASN* 2.9 28.3 + - - -
757D ASP* 3.1 22.1 + - - +
758D VAL* 1.3 80.5 - - - +
760D GLU* 1.3 64.2 + - - +
761D HIS* 3.5 32.8 - + + +
762D ALA* 3.1 17.3 + - - +
763D TYR* 3.5 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 760 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C HIS* 3.5 15.8 - - - -
521C SER* 5.1 0.7 + - - -
559C TRP* 3.9 17.2 - - + -
560C GLU* 3.2 26.7 + - + -
561C HIS* 2.8 50.0 + - - +
720D GLY 6.1 0.9 - - - +
721D SER* 5.1 1.8 + - - -
758D VAL 3.4 2.6 + - - +
759D TRP* 1.3 71.7 - - - +
761D HIS* 1.3 57.8 + - - +
762D ALA 3.0 0.9 + - - -
763D TYR* 3.1 29.0 + - + +
764D TYR* 2.8 43.5 + - + +
771D ARG* 5.2 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 761 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560C GLU* 2.7 30.4 + - - +
564C TYR* 3.4 48.2 + - + +
623D THR* 4.1 12.3 + - - +
627D HIS* 3.3 19.5 + + - +
631D HIS* 3.4 23.3 - + + +
635D TYR* 3.9 9.4 - - - -
674D HIS* 4.0 0.6 + - - -
757D ASP* 4.2 0.2 - - - -
759D TRP* 3.5 29.1 - + + +
760D GLU* 1.3 75.2 - - - +
762D ALA* 1.3 66.1 + - - +
763D TYR 3.2 0.7 + - - -
764D TYR 4.3 2.6 + - - -
765D LEU* 5.3 0.9 + - - +
792D MN 2.3 35.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 762 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618D VAL 5.4 0.9 - - - +
619D ILE* 5.1 3.5 - - - +
623D THR* 3.7 16.5 - - - +
627D HIS* 3.6 28.9 + - + -
677D TYR* 4.0 8.4 + - - +
757D ASP* 3.6 28.9 - - + +
759D TRP 3.1 14.2 + - - +
760D GLU 3.0 1.0 - - - -
761D HIS* 1.3 81.7 - - - +
763D TYR* 1.3 62.9 + - + +
774D HIS* 4.0 11.5 - - - +
----------------------------------------------------------
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