Contacts of the helix formed by residues 602 - 608 (chain D) in PDB entry 5X22
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 602 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540D LEU* 4.2 4.3 - - - -
543D LEU* 4.1 4.7 - - - -
580D ALA 3.6 6.7 - - - -
581D LEU 3.2 19.1 - - - -
582D LEU 3.6 2.9 - - - -
583D ASP* 3.6 4.9 - - - -
584D ASN* 3.0 28.7 + - - -
600D LEU 3.6 1.6 + - - -
601D ARG* 1.3 76.5 - - - +
603D LEU* 1.3 64.8 + - - +
604D THR* 3.9 0.2 - - - -
605D ASP* 2.8 32.1 + - - -
606D ILE* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 603 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1091C GLU* 4.5 11.6 - - + +
1094C ALA* 3.3 48.9 - - + +
1095C LEU* 3.7 29.4 - - + -
520D LEU* 4.5 8.1 - - + -
540D LEU* 3.7 34.1 - - + +
544D TYR* 4.9 4.3 - - - +
581D LEU* 3.5 12.7 + - + +
582D LEU* 3.9 10.1 - - + +
602D SER* 1.3 72.6 - - - +
604D THR* 1.3 61.2 + - - +
606D ILE* 3.1 11.9 + - + +
607D LEU* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 604 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095C LEU* 4.3 1.3 - - - +
103D TRP* 3.0 30.7 + - + -
582D LEU 2.8 20.0 + - - -
583D ASP* 3.4 33.3 - - - +
602D SER* 3.9 0.7 - - - -
603D LEU* 1.3 76.7 - - - +
605D ASP* 1.3 64.4 + - - +
607D LEU* 3.3 3.6 + - - +
608D SER* 3.0 35.5 + - - +
1444D THR* 3.6 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 605 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583D ASP* 4.2 8.7 - - - +
584D ASN* 4.2 11.1 - - - +
600D LEU 3.6 11.6 - - - +
601D ARG* 3.4 33.1 + - + +
602D SER* 2.8 34.6 + - - +
603D LEU 3.3 0.2 - - - -
604D THR* 1.3 78.5 - - - +
606D ILE* 1.3 58.4 + - - +
608D SER* 3.0 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 606 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016C ILE* 6.3 2.5 - - + -
1091C GLU* 3.3 37.7 - - + +
524D LEU 5.7 2.0 - - - +
538D SER* 5.6 1.1 - - - +
540D LEU* 3.7 31.9 - - + -
601D ARG* 3.9 26.1 + - + +
602D SER 3.1 14.2 + - - +
603D LEU* 3.1 14.9 + - + +
605D ASP* 1.3 78.0 - - - +
607D LEU* 1.3 53.5 + - + +
611D GLN 4.7 0.7 - - - +
612D GLY* 3.3 3.8 - - - -
613D ARG* 2.7 51.1 + - - +
318F GLU* 5.4 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 607 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088C LEU* 3.8 26.2 - - + +
1091C GLU* 4.0 29.4 - - + +
1092C LEU* 3.6 26.0 - - + -
1095C LEU* 3.5 26.5 - - + -
103D TRP* 4.4 4.0 - - + -
603D LEU 2.9 18.5 + - - +
604D THR* 3.9 4.5 - - - +
606D ILE* 1.3 77.5 - - + +
608D SER* 1.3 60.6 + - - +
612D GLY* 3.5 0.7 - - - -
613D ARG* 3.1 19.7 + - + +
614D PHE* 3.5 26.7 + - + +
1443D THR* 4.9 3.4 - - + -
1447D LEU* 4.1 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 608 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604D THR* 3.0 24.5 + - - +
605D ASP* 3.0 20.3 - - - +
607D LEU* 1.3 78.4 - - - +
609D GLY* 1.3 64.0 + - - +
612D GLY* 3.1 9.2 + - - -
614D PHE* 5.3 1.3 - - - -
1443D THR* 3.3 36.3 - - - -
1444D THR* 4.9 3.8 - - - +
12G G 5.6 4.5 - - - -
----------------------------------------------------------
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