Contacts of the helix formed by residues 658 - 668 (chain C) in PDB entry 1U0O
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 658 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624C SER 3.3 8.6 + - - -
625C GLN* 3.2 31.7 + - - -
656C HIS 3.5 3.0 + - - -
657C ALA* 1.3 67.6 - - - +
659C LEU* 1.3 55.5 + - - +
660C LYS* 3.8 8.3 + - - +
661C GLN* 2.9 52.1 + - - +
662C ILE* 2.8 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 659 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657C ALA 2.8 8.7 + - - +
658C SER* 1.3 72.1 - - - +
660C LYS* 1.3 73.3 + - + +
662C ILE* 3.4 7.8 + - + +
663C ARG* 2.6 68.2 + - + +
676C LEU* 3.3 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 660 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TYR* 3.9 39.6 - - + +
625C GLN* 3.9 16.1 + - - +
657C ALA 5.1 0.4 + - - -
658C SER* 4.0 6.4 - - - +
659C LEU* 1.3 99.0 - - + +
661C GLN* 1.3 59.6 + - - +
663C ARG* 3.3 11.7 + - - +
664C LEU* 3.1 25.1 + - - +
667C LYS* 5.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 661 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TYR* 3.2 27.9 + - + -
594C THR* 4.6 4.7 + - - +
625C GLN* 3.8 6.8 - - - +
626C GLU* 2.7 50.3 + - - +
628C PRO* 4.7 2.2 - - - +
631C ALA* 3.6 16.9 - - + +
634C LEU* 3.5 23.1 - - + +
658C SER* 2.9 31.9 + - - +
660C LYS* 1.3 74.8 - - - +
662C ILE* 1.3 63.8 + - - +
664C LEU* 3.3 11.4 - - - +
665C ILE* 3.3 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 662 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622C THR* 4.8 12.6 - - + -
650C PRO* 3.7 24.0 - - + +
652C GLY* 4.2 9.6 - - - +
657C ALA* 3.9 21.1 - - + +
658C SER 2.8 31.8 + - - +
659C LEU* 3.6 11.2 - - - +
661C GLN* 1.3 73.5 - - + +
663C ARG* 1.3 70.9 + - + +
665C ILE* 3.3 14.2 + - + +
666C GLU* 3.2 21.4 + - + +
674C ALA* 4.0 17.9 - - + -
676C LEU* 4.0 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 663 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659C LEU* 2.6 47.2 + - + +
660C LYS* 3.4 11.2 - - - +
661C GLN 3.3 0.2 - - - -
662C ILE* 1.3 77.2 - - - +
664C LEU* 1.3 64.7 + - - +
666C GLU* 3.2 36.5 + - - +
667C LYS* 3.1 49.5 + - - +
674C ALA* 4.4 6.9 - - - +
676C LEU* 3.3 32.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 664 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 3.2 31.2 - - + +
291B TYR* 4.0 29.8 - - + -
292B LEU* 4.9 9.6 - - + +
631C ALA 4.1 8.7 - - - +
634C LEU* 3.9 27.4 - - + -
635C VAL* 3.3 26.9 - - + -
638C VAL* 5.5 0.9 - - - -
660C LYS 3.1 13.6 + - - +
661C GLN 3.3 11.2 - - - +
662C ILE 3.2 0.2 - - - -
663C ARG* 1.3 79.1 - - - +
665C ILE* 1.3 59.6 - - - +
666C GLU 3.4 0.2 + - - -
667C LYS* 3.8 9.9 + - + +
668C GLN* 2.8 27.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 665 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594C THR* 4.9 4.5 - - + +
598C LEU* 4.6 2.0 - - + -
620C LEU* 3.7 27.4 - - + -
622C THR* 6.1 1.1 - - + -
634C LEU* 4.0 21.5 - - + -
638C VAL* 3.6 31.8 - - + +
648C VAL* 3.6 24.2 - - + -
650C PRO* 3.3 28.3 - - + -
661C GLN* 3.3 18.2 - - + +
662C ILE* 3.3 9.1 + - + +
664C LEU* 1.3 75.7 - - - +
666C GLU* 1.3 59.2 + - - +
668C GLN* 3.6 1.0 - - - +
672C ASN* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 666 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650C PRO* 4.9 2.2 - - + -
662C ILE 3.2 14.0 + - - +
663C ARG* 3.3 40.2 + - - +
665C ILE* 1.3 75.1 - - - +
667C LYS* 1.3 57.6 + - + +
668C GLN 2.5 18.4 + - - -
669C ALA 2.9 24.2 + - - +
672C ASN* 3.4 21.1 - - - +
673C LYS* 3.8 4.9 - - - +
674C ALA* 3.0 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 667 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 3.2 58.2 - - + +
49A LYS* 5.7 0.3 + - - -
288B ASP 3.4 24.5 + - - -
289B ASP* 3.7 24.1 + - - +
291B TYR* 5.5 4.6 - - - +
660C LYS 5.7 0.4 + - - -
663C ARG* 3.2 35.5 - - - +
664C LEU* 4.0 9.1 - - - +
666C GLU* 1.3 78.7 - - + +
668C GLN* 1.3 61.1 + - - +
669C ALA* 3.2 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 668 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 3.9 19.8 - - - -
49A LYS* 3.3 24.2 + - - +
635C VAL* 3.7 33.1 - - - +
638C VAL* 3.4 39.2 - - + +
639C GLN* 3.4 19.6 - - - +
642C LYS* 3.2 24.6 + - + +
664C LEU 2.8 25.5 + - - -
665C ILE 3.6 5.6 - - - +
666C GLU 2.5 7.1 + - - -
667C LYS* 1.3 74.2 - - - +
669C ALA* 1.3 60.2 + - + +
672C ASN* 3.9 2.0 - - - +
----------------------------------------------------------
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