Contacts of the helix formed by residues 611 - 622 (chain C) in PDB entry 3KSA
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 LEU 611 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523C TYR* 3.5 18.1 + - + +
527C ARG* 4.2 31.0 - - + +
531C GLU* 6.2 2.9 - - + -
608C ILE* 4.0 14.1 - - + -
610C ASP* 1.3 77.4 - - - +
612C ALA* 1.3 63.6 + - - +
613C ARG 3.3 1.6 - - - -
614C ALA* 3.1 5.7 + - - +
615C GLU* 2.9 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 612 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610C ASP* 3.7 10.5 - - - +
611C LEU* 1.3 81.5 - - - +
613C ARG* 1.3 55.4 + - - +
615C GLU* 3.7 6.4 - - - +
616C ARG* 2.9 49.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 613 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU* 5.1 11.9 - - + -
608C ILE* 5.6 0.2 - - + -
609C GLU* 5.6 1.8 + - - +
610C ASP* 3.2 39.7 + - + +
611C LEU 3.3 0.4 - - - -
612C ALA* 1.3 73.6 - - - +
614C ALA* 1.3 61.3 - - - +
616C ARG* 3.2 19.4 + - - +
617C ARG* 2.8 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 614 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 4.2 15.5 - - + -
10A GLU* 5.0 7.1 - - - +
523C TYR* 3.7 19.7 - - + -
608C ILE* 3.4 29.9 - - + +
611C LEU 3.1 7.6 + - - +
613C ARG* 1.3 78.4 - - - +
615C GLU* 1.3 64.8 + - - +
617C ARG* 3.1 4.9 + - - +
618C VAL* 2.8 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 615 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523C TYR* 2.9 35.9 + - - +
524C ARG* 4.8 8.5 + - - -
527C ARG* 4.6 4.2 + - - -
611C LEU* 2.9 15.1 + - + +
612C ALA* 3.7 7.6 - - - +
614C ALA* 1.3 74.3 - - - +
616C ARG* 1.3 64.3 + - - +
618C VAL* 4.8 0.4 - - - -
619C ASN* 3.0 59.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 616 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610C ASP* 5.3 0.2 + - - -
612C ALA* 2.9 44.3 + - - +
613C ARG* 3.3 21.6 - - - +
615C GLU* 1.3 78.9 - - - +
617C ARG* 1.3 55.0 + - - +
619C ASN* 3.6 4.2 + - - +
620C VAL* 2.8 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 617 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU* 3.4 43.1 + - + +
11A ASP* 4.5 4.0 - - - +
13A MET* 4.8 4.9 - - + -
14A GLY* 4.2 8.1 - - - +
613C ARG 2.8 20.2 + - - +
614C ALA* 3.7 4.5 - - - +
616C ARG* 1.3 72.2 - - - +
618C VAL* 1.3 70.1 + - + +
620C VAL* 3.0 17.3 + - - +
621C LEU* 3.2 37.1 + - + +
632C TRP* 3.3 43.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 618 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 4.1 21.8 - - + -
13A MET* 3.9 23.6 - - + -
463C ALA* 5.0 3.1 - - + -
520C THR* 4.0 16.2 - - + -
523C TYR* 4.4 13.5 - - + -
524C ARG* 4.7 14.6 - - - -
614C ALA* 2.8 26.1 + - - +
615C GLU* 4.1 2.9 - - - +
617C ARG* 1.3 72.9 - - + +
619C ASN* 1.3 67.0 + - - +
622C MET* 2.8 53.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 619 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C ALA* 5.4 2.8 - - - +
524C ARG* 4.3 13.5 + - - -
615C GLU* 3.0 52.8 + - - +
616C ARG* 4.0 4.8 - - - +
618C VAL* 1.3 86.5 - - - +
620C VAL* 1.3 56.3 + - - +
623C GLY* 2.8 29.0 - - - +
624C ASP 4.4 0.2 + - - -
625C LYS* 5.5 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 620 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616C ARG* 2.8 26.2 - - + +
617C ARG* 3.3 10.3 - - - +
619C ASN* 1.3 76.1 - - - +
621C LEU* 1.3 76.5 + - + +
623C GLY* 3.6 2.9 + - - -
625C LYS 5.9 0.2 + - - -
626C VAL 5.5 0.5 + - - -
628C PRO* 3.5 36.5 - - + +
629C ARG* 3.6 29.7 + - - +
632C TRP* 4.7 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 621 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A MET* 3.6 36.1 - - + +
14A GLY* 4.6 2.2 - - - +
17A PHE* 3.8 30.6 - - + -
617C ARG* 3.2 36.5 + - + +
618C VAL 4.1 0.9 - - - +
620C VAL* 1.3 79.9 - - + +
622C MET* 1.3 66.6 + - + +
623C GLY 3.2 0.2 - - - -
629C ARG* 3.0 37.7 + - + -
632C TRP* 3.8 45.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 622 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A MET* 3.6 11.0 - - + -
17A PHE* 4.1 12.6 - - + -
461C ASN* 3.0 35.4 + - - +
463C ALA* 4.2 9.8 - - + +
513C HIS* 5.0 2.9 - - - +
516C THR* 3.0 37.0 - - + -
517C LEU* 3.7 25.8 - - + -
520C THR* 3.2 31.2 - - + +
618C VAL* 2.8 23.2 + - + +
621C LEU* 1.3 78.1 - - - +
623C GLY* 1.3 67.8 + - - +
629C ARG* 4.4 1.3 - - - +
----------------------------------------------------------
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