Contacts of the helix formed by residues 169 - 177 (chain B) in PDB entry 3VBB
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 169 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LYS 4.2 0.6 + - - -
168B TYR* 1.3 74.6 - - - +
170B HIS* 1.3 63.5 + - - +
171B VAL* 2.9 28.4 + - - +
172B ASP* 3.5 15.2 + - - -
173B LEU* 3.1 29.4 + - - +
385B GLY* 4.3 6.3 - - - -
386B SER* 4.4 9.9 + - - -
442B GLU* 3.5 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B SER* 1.3 73.2 + - - +
171B VAL* 1.3 84.8 + - + +
173B LEU* 3.7 9.0 - - + -
174B VAL* 3.1 29.8 + - + +
314B GLY* 5.1 1.8 - - - -
315B ILE* 4.8 7.2 + - + -
316B PHE* 3.3 35.2 + + + +
383B PHE* 4.6 4.8 - + - -
386B SER* 3.9 8.5 + - - -
390B ARG* 6.4 0.9 - - - -
438B CYS* 3.2 47.0 - - + +
441B LEU* 5.0 2.0 - - + -
442B GLU* 2.8 33.0 + - + +
602B PO4 5.6 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B SER* 2.9 14.3 + - - +
170B HIS* 1.3 98.8 - - + +
172B ASP* 1.3 66.9 + - - +
174B VAL* 3.2 21.7 - - + +
175B VAL* 3.9 8.1 + - - +
180B PHE* 5.8 0.8 - - + -
312B THR* 5.9 0.7 - - - +
313B ARG 3.6 24.9 - - - +
314B GLY* 4.7 6.7 - - - -
475B PRO* 6.2 0.2 - - - -
602B PO4 6.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B TYR* 4.4 13.6 - - + -
169B SER* 3.5 20.4 + - - +
171B VAL* 1.3 81.9 - - - +
173B LEU* 1.3 66.7 + - - +
175B VAL* 3.0 14.8 + - - +
176B MET* 3.0 19.0 + - - +
474B ALA* 3.8 16.4 - - + +
475B PRO* 3.4 41.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B TYR* 3.6 36.1 - - + +
169B SER 3.1 21.3 + - - +
170B HIS* 3.4 3.3 + - - +
171B VAL 3.4 0.4 - - - -
172B ASP* 1.3 76.0 - - - +
174B VAL* 1.3 63.0 + - - +
176B MET* 4.3 6.3 - - - -
177B VAL* 3.2 30.1 + - - +
441B LEU* 3.5 49.1 - - + +
442B GLU* 3.8 6.7 - - - +
445B GLN* 4.0 10.3 - - + +
450B ILE* 4.1 8.7 - - + -
470B PHE* 4.1 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B HIS* 3.1 17.3 + - + +
171B VAL* 3.2 21.3 - - - +
173B LEU* 1.3 75.8 - - - +
175B VAL* 1.3 58.7 + - - +
177B VAL* 4.1 1.4 - - - +
178B ASP 3.6 0.9 + - - -
179B GLY* 3.1 27.0 + - - -
180B PHE* 3.5 39.8 - - + +
200B LEU* 4.1 17.3 - - + -
314B GLY* 5.5 1.3 - - - -
315B ILE* 4.2 29.6 - - + +
438B CYS* 5.2 0.9 - - - -
441B LEU* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B VAL 4.1 11.2 - - - +
172B ASP 3.0 8.6 + - - +
174B VAL* 1.3 75.3 - - - +
176B MET* 1.3 58.4 + - - +
177B VAL 3.2 1.8 - - - -
178B ASP* 2.6 31.7 + - - +
180B PHE* 4.3 24.0 - - + +
472B LYS* 4.1 20.0 - - + +
473B PRO 4.0 9.9 - - - +
475B PRO* 4.0 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B TYR* 4.0 31.6 - - + +
172B ASP 3.0 17.8 + - - +
173B LEU* 3.3 10.1 + - - +
175B VAL* 1.3 75.6 - - - +
177B VAL* 1.3 58.7 + - - +
178B ASP 3.2 0.2 - - - -
470B PHE* 3.2 47.7 - - + -
471B VAL 2.9 23.4 + - - -
472B LYS 3.3 20.1 + - - +
473B PRO* 5.8 0.2 - - + -
474B ALA* 3.3 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LEU 3.2 18.3 + - - +
174B VAL 4.1 2.7 - - - +
175B VAL 3.2 0.6 - - - -
176B MET* 1.3 77.4 - - - +
178B ASP* 1.3 69.6 + - - +
179B GLY 3.9 7.0 - - - +
199B VAL* 3.8 25.0 - - + +
200B LEU* 4.2 17.3 - - + -
441B LEU* 5.3 4.7 - - + -
450B ILE* 3.9 24.7 - - + -
468B ILE* 3.8 27.1 - - + +
469B PRO 3.9 14.2 - - - +
470B PHE* 4.1 7.2 - - + -
471B VAL* 4.5 8.4 - - - +
----------------------------------------------------------
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