Contacts of the helix formed by residues 698 - 708 (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 GLY 698 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B PHE* 3.9 20.2 - - - -
668B LEU* 5.3 1.3 - - - -
669B VAL* 3.0 22.3 + - - -
670B GLY* 4.3 4.3 - - - -
696B VAL 3.5 2.0 + - - -
697B ASP* 1.3 76.2 + - - +
699B ARG* 1.3 57.6 + - - +
701B LEU* 3.3 12.5 - - - +
702B ARG* 3.1 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 699 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B PRO* 3.5 22.4 - - - +
261B LEU* 3.0 32.7 + - - +
600B PHE* 4.0 3.6 - - - -
634B LEU* 3.6 41.6 - - + +
635B GLU 5.4 0.4 + - - -
636B ASP* 3.0 33.1 + - - +
642B VAL* 4.1 3.4 - - + +
643B PRO* 3.4 23.1 - - + +
697B ASP* 2.7 39.3 + - - +
698B GLY* 1.3 78.3 - - - +
700B TYR* 1.3 55.6 + - - +
702B ARG* 3.5 11.4 + - - +
703B TRP* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 700 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL* 4.7 3.2 - - + +
221B HIS 4.5 2.8 + - - -
223B GLY* 3.5 38.8 + - - -
603B LEU* 3.6 27.1 - - + -
606B VAL* 3.9 12.4 - - + +
622B LEU* 3.5 23.4 - - - +
642B VAL* 4.6 0.7 - - + -
643B PRO 3.5 16.5 + - - +
644B VAL* 3.8 41.3 - - + +
696B VAL* 4.0 7.9 - - + -
697B ASP 2.8 11.3 + - - +
699B ARG* 1.3 74.7 - - - +
701B LEU* 1.3 61.7 - - - +
703B TRP* 3.8 17.7 - + + -
704B ILE* 2.9 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 701 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B VAL* 4.2 18.6 - - + -
225B PHE* 3.5 48.9 - - + -
227B PHE* 4.7 6.3 - - + -
256B PHE* 4.7 14.6 - - + -
668B LEU* 5.5 2.5 - - + -
670B GLY 6.2 0.2 - - - -
671B LEU* 4.4 10.5 - - + -
696B VAL* 3.6 28.0 - - + +
697B ASP 3.2 18.6 + - - +
698B GLY* 3.3 13.7 - - - +
700B TYR* 1.3 79.6 - - - +
702B ARG* 1.3 65.3 + - + +
704B ILE* 3.3 2.1 + - - +
705B MET* 3.1 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 702 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B PHE* 3.7 32.1 - - + +
257B ALA 4.4 14.5 + - - -
634B LEU* 3.6 33.1 - - + +
698B GLY 3.1 18.0 + - - +
699B ARG* 3.7 10.0 - - - +
701B LEU* 1.3 81.4 - - - +
703B TRP* 1.3 57.1 + - - +
705B MET* 3.3 3.0 + - - +
706B GLN* 2.9 43.5 + - - +
715B LEU* 4.4 18.9 - - + +
720B VAL* 3.8 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 703 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B LEU* 3.7 27.8 - - + +
622B LEU* 4.0 10.8 - - + -
625B ALA* 3.9 18.8 - - + -
626B VAL* 3.8 22.9 - - + -
630B ARG 2.9 26.4 + - - -
631B TYR* 3.6 25.1 - - - +
632B GLY* 4.7 0.4 - - - -
634B LEU* 3.6 9.8 - - + +
642B VAL* 3.9 13.5 - - + -
699B ARG 2.9 19.2 + - - +
700B TYR* 3.7 22.9 - + - +
701B LEU 3.2 0.2 - - - -
702B ARG* 1.3 74.1 - - - +
704B ILE* 1.3 72.1 + - + +
706B GLN* 4.4 2.0 - - - -
707B GLU* 2.8 45.2 + - + +
708B VAL* 3.4 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 704 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B TYR* 3.7 17.3 - - - +
202B PRO* 4.4 4.9 - - + -
206B VAL* 3.7 24.5 - - + -
225B PHE* 3.9 15.0 - - + -
622B LEU* 4.1 6.1 - - + -
700B TYR* 2.9 57.2 + - + +
701B LEU 3.7 4.0 - - - +
703B TRP* 1.3 90.6 - - + +
705B MET* 1.3 58.8 + - - +
708B VAL* 3.0 25.8 + - + -
709B TYR* 3.0 32.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 705 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B TYR* 3.8 17.0 - - + +
225B PHE* 4.0 10.3 - - + -
227B PHE* 3.7 35.0 - - + -
256B PHE* 6.3 0.9 - - - -
701B LEU* 3.1 22.2 + - - +
702B ARG* 3.6 4.7 - - - +
703B TRP 3.2 0.2 - - - -
704B ILE* 1.3 75.6 - - - +
706B GLN* 1.3 57.6 + - - +
709B TYR 3.8 8.1 - - - -
710B PRO* 3.3 5.5 - - - +
711B ALA* 3.0 34.4 + - + +
712B PRO* 4.6 0.9 - - - +
714B LEU* 3.7 32.3 - - + -
715B LEU* 3.4 31.4 - - + +
718B MET* 4.1 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 706 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632B GLY* 3.1 25.2 + - - +
634B LEU* 3.6 23.1 - - - +
702B ARG* 2.9 33.6 + - - +
703B TRP 3.8 2.9 - - - +
705B MET* 1.3 79.7 - - - +
707B GLU* 1.3 81.8 + - + +
708B VAL 3.8 0.2 - - - -
710B PRO* 4.4 12.8 - - - +
715B LEU* 4.0 15.0 - - + +
720B VAL 4.6 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 707 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B ALA* 4.0 15.4 - - - +
625B ALA* 4.3 10.4 - - + +
630B ARG* 4.2 29.7 + - - +
632B GLY* 3.6 15.5 - - - -
703B TRP* 2.8 52.7 + - + +
706B GLN* 1.3 98.1 - - + +
708B VAL* 1.3 63.1 + - + +
710B PRO* 5.2 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 708 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL* 4.6 3.4 - - + -
619B PRO* 4.0 33.1 - - + +
621B ALA* 3.8 14.2 - - + +
622B LEU* 3.9 21.8 - - + +
703B TRP* 3.4 38.4 - - + -
704B ILE* 3.0 23.9 + - + +
706B GLN 3.8 0.2 - - - -
707B GLU* 1.3 86.2 - - - +
709B TYR* 1.3 68.8 + - + +
710B PRO* 3.6 7.3 - - - +
----------------------------------------------------------
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