Contacts of the helix formed by residues 620 - 626 (chain C) in PDB entry 3JW0
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 ARG 620 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591C PRO* 5.4 0.8 - - - +
593C ASP* 2.8 53.9 + - - +
594C ILE* 4.0 8.1 - - - +
618C VAL* 4.5 0.8 - - - +
619C LYS* 1.3 80.8 - - + +
621C PRO* 1.3 56.3 - - - +
622C ASP* 2.5 48.5 + - - +
623C VAL* 2.8 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 621 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618C VAL* 4.3 6.5 - - + +
619C LYS 2.8 22.5 - - - +
620C ARG* 1.3 74.5 - - - +
622C ASP* 1.3 70.9 + - - +
623C VAL 3.4 0.2 - - - -
624C LEU* 3.0 33.0 - - + +
625C LYS* 4.8 0.2 - - - +
695C ARG* 4.2 14.8 - - - +
813C GLU* 4.0 44.1 - - + +
814C LEU* 4.5 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 622 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591C PRO* 4.0 21.2 - - + +
594C ILE* 3.9 7.0 - - + +
620C ARG* 2.5 37.5 + - - +
621C PRO* 1.3 84.0 - - - +
623C VAL* 1.3 51.4 + - - +
624C LEU 2.9 5.2 - - - -
625C LYS* 2.7 62.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 623 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594C ILE* 3.8 16.4 - - + +
595C PRO* 4.5 20.8 - - + +
598C PHE* 3.8 29.4 - - + -
618C VAL* 4.1 12.1 - - + -
620C ARG* 2.8 38.6 + - + +
622C ASP* 1.3 73.9 - - - +
624C LEU* 1.3 67.1 + - + +
625C LYS 2.9 0.2 - - - -
626C ALA* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 624 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598C PHE* 3.8 37.3 - - + +
615C ILE* 4.1 19.3 - - + -
618C VAL* 3.7 17.9 - - + -
621C PRO* 3.0 25.8 - - + +
622C ASP 2.9 0.2 + - - -
623C VAL* 1.3 77.2 - - + +
625C LYS* 1.3 57.7 + - - +
626C ALA 3.2 5.3 + - - +
628C LEU* 5.6 0.9 - - - +
695C ARG* 3.5 37.5 - - + +
699C LEU* 3.2 20.0 - - + +
703C HIS* 3.2 18.4 + - - -
814C LEU* 4.1 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 625 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589C LYS 4.2 5.9 + - - +
590C LYS* 2.9 27.1 + - + +
591C PRO* 3.4 30.4 - - + +
594C ILE* 4.0 3.4 - - + -
622C ASP* 2.7 42.5 + - - +
624C LEU* 1.3 77.0 - - - +
626C ALA* 1.3 64.1 + - - +
702C PHE* 3.2 33.8 - - + -
703C HIS* 3.6 12.5 - - - -
813C GLU 4.9 3.8 - - - -
814C LEU* 3.9 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 626 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590C LYS* 5.1 1.1 - - - -
594C ILE* 3.8 9.3 - - + +
595C PRO* 3.6 26.2 - - + +
596C ASN 4.7 0.9 - - - -
597C ARG* 3.6 22.0 - - - +
598C PHE* 3.8 4.2 - - - +
623C VAL 2.9 16.9 + - - +
624C LEU 3.7 3.3 - - - +
625C LYS* 1.3 81.0 - - - +
627C ARG* 1.3 66.5 + - - +
628C LEU* 3.6 1.7 + - - +
703C HIS* 3.2 17.9 + - - -
----------------------------------------------------------
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