Contacts of the helix formed by residues 620 - 628 (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 SER 620 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612D VAL 4.4 0.2 - - - -
616D ALA* 4.3 12.1 - - - +
617D PRO* 4.0 6.8 + - - -
618D VAL 3.9 2.2 + - - -
619D ILE* 1.3 78.7 - - - +
621D LYS* 1.3 59.5 + - - +
622D GLU* 3.4 12.3 + - - +
623D THR* 3.0 28.4 + - - -
624D VAL* 2.8 28.9 + - - +
765D LEU* 5.4 0.2 - - - +
766D THR* 3.9 16.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 621 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612D VAL* 3.4 37.5 + - + +
613D ASP* 4.0 29.7 + - + +
616D ALA* 4.6 6.4 - - + +
620D SER* 1.3 74.4 - - - +
622D GLU* 1.3 63.5 + - - +
624D VAL* 3.2 2.3 + - - +
625D GLU* 2.9 51.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 622 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568C GLN* 5.3 3.3 + - - -
620D SER* 3.2 9.0 + - - +
621D LYS* 1.3 80.7 - - - +
623D THR* 1.3 60.1 + - - +
625D GLU* 3.5 14.0 + - - +
626D PHE* 3.1 49.7 + - + -
765D LEU* 3.7 31.0 - - + +
766D THR* 5.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 623 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619D ILE* 3.8 15.7 - - + -
620D SER* 3.0 25.1 + - - -
622D GLU* 1.3 74.8 - - - +
624D VAL* 1.3 57.0 + - - +
626D PHE* 4.4 4.3 - - + +
627D HIS* 2.6 46.9 + - + +
761D HIS 4.1 13.4 + - - +
762D ALA 3.7 23.1 - - - +
763D TYR* 5.6 1.6 - - - -
765D LEU* 3.7 27.4 + - + +
766D THR* 4.4 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 624 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608D LEU* 3.5 33.0 - - + -
610D TYR* 5.2 2.0 - - + -
612D VAL* 3.4 34.5 - - + +
615D LEU* 4.7 14.1 - - + -
619D ILE* 3.7 22.7 - - + +
620D SER 2.8 21.1 + - - +
621D LYS 3.2 2.0 + - - +
623D THR* 1.3 75.1 - - - +
625D GLU* 1.3 59.6 + - - +
627D HIS* 4.5 4.3 - - - -
628D HIS* 2.8 35.0 + - + +
629D GLY 3.5 0.3 + - - -
678D PHE* 5.3 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 625 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612D VAL* 4.7 16.1 - - + +
621D LYS* 2.9 48.7 + - + +
622D GLU* 3.5 14.9 - - - +
624D VAL* 1.3 77.4 - - - +
626D PHE* 1.3 60.6 + - + +
629D GLY* 3.0 29.6 + - - +
630D LYS* 3.6 6.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 626 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564C TYR* 3.7 17.3 - - + +
568C GLN* 3.5 40.4 - - + -
569C ASN* 3.7 22.7 - - - -
570C ARG* 6.2 1.1 - - - -
622D GLU* 3.1 47.6 + - + +
623D THR* 4.0 3.6 - - - +
625D GLU* 1.3 79.7 - - + +
627D HIS* 1.3 59.9 + - - +
630D LYS* 3.0 29.5 + - + +
631D HIS* 2.9 29.3 + - + -
765D LEU* 3.8 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 627 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564C TYR* 5.4 0.2 - - - -
619D ILE* 5.5 1.8 - - - +
623D THR* 2.6 33.2 + - + +
624D VAL* 4.1 0.9 - - - +
626D PHE* 1.3 74.6 - - - +
628D HIS* 1.3 57.7 + - - +
631D HIS* 3.3 9.3 - - + +
632D LEU* 3.1 26.0 + - - +
674D HIS* 3.2 11.8 + + - -
677D TYR* 3.6 25.5 + + - -
678D PHE* 3.6 12.4 - + + -
757D ASP* 3.0 15.9 - - - -
761D HIS* 3.3 14.8 + + + +
762D ALA* 3.6 24.7 + - + -
792D MN 2.3 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 628 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605D LEU* 3.6 34.4 - - + +
606D ILE* 2.7 31.4 + - + +
607D SER* 5.2 0.7 - - - -
608D LEU* 3.5 37.3 - - + +
624D VAL* 2.8 21.7 + - + +
627D HIS* 1.3 76.0 - - - +
629D GLY* 1.3 67.0 + - - +
630D LYS 3.6 0.2 + - - -
632D LEU* 3.4 36.8 - - + +
633D LYS 3.7 0.5 + - - -
678D PHE* 3.6 23.3 - + + -
----------------------------------------------------------
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