Contacts of the helix formed by residues 619 - 628 (chain B) in PDB entry 3WOO
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 PRO 619 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B PRO* 4.1 14.4 - - + -
205B SER* 3.3 19.7 - - - +
206B VAL* 3.6 27.6 - - + -
617B ASP 3.6 0.6 - - - -
618B SER* 1.3 90.1 - - - +
620B LYS* 1.3 65.8 + - - +
621B ALA* 4.2 5.2 - - + +
622B LEU* 2.9 17.5 + - + +
623B LEU* 3.2 10.6 + - - +
708B VAL* 4.0 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 620 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B SER 3.5 1.4 + - - +
619B PRO* 1.3 71.8 - - - +
621B ALA* 1.3 63.7 + - - +
622B LEU 3.1 0.3 + - - -
623B LEU* 3.2 27.7 + - + +
624B ASP* 2.7 65.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 621 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B PRO* 3.2 3.6 - - + +
620B LYS* 1.3 80.7 - - - +
622B LEU* 1.3 60.2 + - - +
624B ASP* 4.1 6.4 - - - +
625B ALA* 3.1 26.5 + - - +
630B ARG* 4.9 1.4 + - - -
707B GLU 4.0 13.1 - - - +
708B VAL* 3.8 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 622 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL* 4.4 11.0 - - + -
603B LEU* 6.1 0.2 - - + -
606B VAL* 4.0 13.5 - - + -
607B VAL* 3.8 23.1 - - + -
618B SER* 4.0 25.4 - - - +
619B PRO* 2.9 11.8 + - + +
621B ALA* 1.3 76.6 - - - +
623B LEU* 1.3 68.9 + - - +
625B ALA* 3.2 1.2 + - - +
626B VAL* 3.0 36.4 + - + +
700B TYR* 3.5 24.2 - - - +
703B TRP* 4.0 12.6 - - + -
704B ILE* 4.1 16.6 - - + -
708B VAL* 3.9 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 623 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B VAL* 3.9 29.3 - - + +
610B GLU* 3.7 47.1 - - + +
618B SER* 4.1 16.6 - - - +
619B PRO 3.2 9.5 + - - +
620B LYS* 3.8 31.0 - - + +
622B LEU* 1.3 79.5 - - - +
624B ASP* 1.3 61.6 + - - +
626B VAL* 4.0 1.6 - - - +
627B ALA* 3.1 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 624 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620B LYS* 2.7 55.6 + - - +
621B ALA* 4.1 5.6 - - - +
623B LEU* 1.3 77.8 - - - +
625B ALA* 1.3 58.9 + - - +
627B ALA* 3.4 5.5 + - - +
628B ALA* 3.0 24.4 + - - +
630B ARG* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 625 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B ALA 3.1 19.3 + - - +
622B LEU 3.2 1.1 + - - +
624B ASP* 1.3 78.5 - - - +
626B VAL* 1.3 60.9 + - - +
628B ALA 3.6 0.3 + - - -
629B LYS 3.4 2.6 + - - -
630B ARG* 2.9 61.3 + - + +
703B TRP* 3.9 22.9 - - + -
707B GLU* 4.3 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 626 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B LEU* 3.9 27.8 - - + +
604B GLU* 3.8 23.9 - - + +
607B VAL* 3.5 44.0 - - + -
622B LEU* 3.0 28.7 + - + +
623B LEU 4.0 0.2 - - - +
625B ALA* 1.3 75.2 - - - +
627B ALA* 1.3 65.7 + - - +
629B LYS* 3.1 19.7 + - - +
631B TYR* 5.5 0.7 - - - -
703B TRP* 3.8 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 627 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B VAL* 5.5 0.6 - - - +
623B LEU 3.1 18.1 + - - +
624B ASP* 3.8 6.3 - - - +
626B VAL* 1.3 76.8 - - - +
628B ALA* 1.3 58.3 + - - +
629B LYS* 3.4 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 628 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624B ASP 3.0 18.2 + - - +
625B ALA 4.0 0.4 - - - +
626B VAL 3.2 0.4 - - - -
627B ALA* 1.3 73.9 - - - +
629B LYS* 1.3 67.4 + - - +
630B ARG* 3.0 31.3 + - + +
----------------------------------------------------------
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