Contacts of the helix formed by residues 586 - 597 (chain C) in PDB entry 5Y3R
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 GLN 586 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584C GLU* 3.0 25.9 + - + +
585C ILE* 1.3 78.3 - - - +
587C THR* 1.3 59.7 + - + +
588C VAL 3.7 0.2 - - - -
589C GLY 4.3 0.7 - - - -
590C GLU* 2.8 45.5 - - - +
1087C ARG* 2.8 48.7 + - - +
1088C GLU* 3.5 25.3 - - + +
1091C GLU* 6.6 0.2 - - - -
1137C ILE* 6.0 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 587 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585C ILE* 2.9 33.0 - - + +
586C GLN* 1.3 82.2 - - + +
588C VAL* 1.3 73.4 + - - +
590C GLU* 4.1 3.9 + - - +
591C GLN* 3.7 22.7 + - - +
1088C GLU* 4.0 19.5 - - + +
1089C PHE* 6.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 588 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580C ASP 5.6 0.2 - - - +
583C LEU* 3.8 30.1 - - + -
584C GLU* 3.7 8.1 - - - -
585C ILE* 3.3 34.8 - - + +
587C THR* 1.3 85.9 + - - +
589C GLY* 1.3 69.0 + - - +
591C GLN* 3.2 19.7 + - - +
592C GLU* 3.0 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 589 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580C ASP* 2.6 34.2 - - - +
584C GLU* 3.4 27.4 - - - +
587C THR 3.5 0.2 - - - -
588C VAL* 1.3 83.8 - - - +
590C GLU* 1.3 60.1 + - - +
593C ASN* 2.7 23.5 + - - +
1087C ARG* 3.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 590 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584C GLU* 3.8 1.0 + - - -
586C GLN* 2.8 36.9 + - - +
587C THR 4.2 4.5 - - - +
588C VAL 3.4 0.4 - - - -
589C GLY* 1.3 73.0 - - - +
591C GLN* 1.3 66.9 + - + +
593C ASN* 3.0 12.3 + - - +
594C GLY* 3.0 16.6 + - - -
1033C ILE* 5.0 1.9 - - - +
1081C ALA* 5.6 0.9 - - - +
1084C ASN* 2.6 31.5 - - - +
1085C ILE* 3.1 16.5 - - - +
1087C ARG* 2.9 9.7 - - - +
1088C GLU* 2.2 52.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 591 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587C THR 3.7 14.6 - - - +
588C VAL* 3.2 21.9 + - - +
590C GLU* 1.3 83.4 - - - +
592C GLU* 1.3 62.7 + - + +
593C ASN 2.8 3.8 + - - -
594C GLY* 2.8 7.6 + - - -
595C ASP* 2.8 29.0 - - - +
1033C ILE* 6.0 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 592 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579C LEU* 2.8 53.9 - - - +
580C ASP* 2.9 14.0 + - + +
583C LEU* 5.5 3.7 - - - +
588C VAL* 3.0 18.2 + - - +
591C GLN* 1.3 81.4 - - + +
593C ASN* 1.3 56.3 + - - +
595C ASP* 3.1 15.1 - - + +
596C GLU* 2.9 33.3 + - - +
601C TRP* 3.3 25.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 593 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580C ASP* 2.2 33.0 + - - +
581C LEU* 4.5 10.1 - - - +
584C GLU* 4.5 1.4 + - - +
589C GLY 2.7 21.2 + - - +
590C GLU* 3.1 7.0 - - - +
591C GLN 2.8 0.8 + - - -
592C GLU* 1.3 71.2 - - - +
594C GLY* 1.3 56.7 + - - +
595C ASP 2.8 3.4 - - - -
596C GLU* 2.7 29.1 + - - +
597C ALA* 3.1 12.0 + - - +
1080C LEU* 4.8 4.1 - - + +
1084C ASN* 4.5 16.4 - - + +
1087C ARG* 2.4 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 594 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590C GLU 3.0 4.0 + - - -
591C GLN 2.8 10.2 + - - -
593C ASN* 1.3 76.1 - - - +
595C ASP* 1.3 62.9 + - - +
597C ALA* 4.2 1.8 - - - +
598C PRO* 3.3 20.1 - - - +
1026C ARG* 4.1 13.5 - - - +
1080C LEU* 4.7 4.7 - - - -
1081C ALA* 3.6 30.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 595 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591C GLN* 2.8 36.5 + - - +
592C GLU* 3.1 20.8 + - + +
594C GLY* 1.3 81.8 - - - +
596C GLU* 1.3 63.5 + - - +
598C PRO* 3.6 8.4 - - - +
599C GLY 3.8 4.9 - - - +
600C VAL 4.8 1.0 - - - +
601C TRP* 3.7 18.2 - - + +
1026C ARG* 3.6 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 596 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576C VAL* 3.5 8.6 - - + +
577C GLU* 3.1 41.7 - - - +
580C ASP* 3.2 27.3 - - - +
581C LEU* 5.4 0.7 - - - +
592C GLU 2.9 18.1 + - - +
593C ASN* 2.7 17.0 + - - +
595C ASP* 1.3 71.7 - - - +
597C ALA* 1.3 61.6 + - - +
599C GLY 2.7 23.7 - - - +
600C VAL* 4.2 1.7 - - - -
601C TRP* 3.2 21.3 - - + +
721C TYR* 4.0 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 597 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593C ASN 3.1 7.9 + - - +
594C GLY 4.4 2.2 - - - +
596C GLU* 1.3 77.9 - - - +
598C PRO* 1.4 63.4 - - + +
721C TYR* 3.0 25.6 + - - -
1077C GLY* 4.6 9.0 - - - -
1080C LEU* 3.6 39.9 - - + -
1126C GLN* 4.5 18.5 + - - +
1127C CYS* 5.9 0.2 - - - -
----------------------------------------------------------
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