Contacts of the helix formed by residues 652 - 660 (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 ASP 652 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603D HIS* 4.9 1.6 - - - -
650D ASN 4.1 0.4 + - - -
651D ALA* 1.3 78.1 - - - +
653D LEU* 1.3 64.2 + - - +
654D ASN* 3.2 12.7 + - - +
655D THR* 2.9 42.5 + - - -
656D ILE* 3.1 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 653 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603D HIS* 4.1 17.7 - - + +
639D LEU* 3.9 26.0 - - + -
651D ALA 3.8 0.8 + - - -
652D ASP* 1.3 72.8 - - - +
654D ASN* 1.3 65.7 + - - +
656D ILE* 3.1 9.5 + - + +
657D VAL* 3.0 22.1 + - + +
668D ALA* 3.7 26.0 - - + +
671D THR* 4.0 6.5 - - + -
672D LEU* 3.8 38.1 - - + +
675D ASN* 3.9 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 654 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652D ASP* 3.2 8.8 + - - +
653D LEU* 1.3 78.4 - - - +
655D THR* 1.3 58.2 + - - +
657D VAL* 3.4 5.0 + - - +
658D GLN* 3.0 30.0 + - - +
672D LEU* 3.6 29.4 - - - +
746D VAL* 3.5 19.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 655 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648D PHE* 4.9 4.7 - - + -
651D ALA* 4.3 13.0 - - + -
652D ASP* 2.9 37.6 + - - -
654D ASN* 1.3 73.3 - - - +
656D ILE* 1.3 67.0 + - - +
658D GLN* 3.3 9.7 + - - +
659D LYS* 3.0 44.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 656 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603D HIS* 4.0 17.0 - - + +
639D LEU* 4.3 6.7 - - + -
643D ILE* 4.2 10.5 - - + -
648D PHE* 3.8 26.5 - - + +
651D ALA* 3.7 30.1 - - + +
652D ASP 3.1 13.9 + - - +
653D LEU* 3.1 9.8 + - + +
655D THR* 1.3 77.6 - - - +
657D VAL* 1.3 57.6 + - - +
660D SER* 2.7 38.1 + - - +
664D ILE* 3.4 32.1 - - + -
668D ALA* 3.6 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 657 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653D LEU* 3.0 17.0 + - + +
654D ASN 3.7 7.0 - - - +
656D ILE* 1.3 77.5 - - - +
658D GLN* 1.3 57.9 + - - +
665D PHE* 3.1 23.8 - - + -
668D ALA* 3.4 35.4 - - + +
669D GLY* 3.9 3.6 - - - -
672D LEU* 3.9 18.8 - - + -
744D ASN* 3.7 31.2 - - + -
746D VAL* 4.2 10.3 - - + -
747D ARG* 2.8 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 658 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654D ASN 3.0 17.6 + - - +
655D THR* 3.7 10.3 + - - +
656D ILE 3.2 0.2 - - - -
657D VAL* 1.3 79.1 - - - +
659D LYS* 1.3 77.7 + - + +
746D VAL* 3.2 35.7 + - + +
747D ARG* 3.1 28.4 + - - +
749D GLY* 4.5 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 659 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647D GLU* 5.4 5.2 - - - +
648D PHE* 3.6 18.2 - - + -
655D THR* 3.0 31.6 + - + +
658D GLN* 1.3 100.9 + - + +
660D SER* 1.3 67.6 + - - +
661D GLU* 4.5 4.9 - - - +
747D ARG* 3.6 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 660 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648D PHE* 3.5 27.5 - - - -
656D ILE* 2.7 29.0 + - - +
659D LYS* 1.3 72.1 - - - +
661D GLU* 1.3 62.1 + - - +
664D ILE* 3.6 22.6 - - - +
665D PHE* 3.1 27.3 + - - +
747D ARG* 2.9 28.8 + - - +
----------------------------------------------------------
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