Contacts of the helix formed by residues 82 - 87 (chain B) in PDB entry 3VHT
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 ASP 82 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B GLU* 5.4 3.1 - - + +
74B TYR* 3.4 38.0 - - + +
79B LYS* 3.6 14.0 + - + +
80B GLN 3.5 3.6 - - - -
81B HIS* 1.3 73.6 - - - +
83B PHE* 1.3 62.2 + - - +
84B PHE* 3.2 18.0 + - - +
85B LYS* 2.6 49.7 + - + +
86B SER* 3.5 19.4 + - - -
194B LEU* 3.7 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TYR* 4.8 0.2 + - - -
81B HIS 3.2 5.8 + - - +
82B ASP* 1.3 73.0 - - - +
84B PHE* 1.3 75.0 + + + +
86B SER* 2.8 17.5 + - - -
87B ALA* 3.3 8.8 + - + -
92B TYR* 4.4 18.6 - + + -
152B ILE* 6.2 0.2 - - + -
160B GLY* 3.9 17.0 - - - -
161B ILE* 3.6 39.7 - - + -
185B ASN* 3.7 32.3 - - + -
187B PRO* 3.9 28.5 - - + -
193B VAL* 4.1 22.2 - - + -
194B LEU 3.4 26.0 - - - +
195B LEU* 5.5 1.1 - - + -
196B PRO* 4.5 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLN* 3.1 48.0 - - + -
70B CYS* 3.4 25.4 - - + -
74B TYR* 3.6 22.4 - + - -
82B ASP* 3.2 11.3 + - - +
83B PHE* 1.3 86.0 - + + +
85B LYS* 1.3 61.4 + - - +
87B ALA 3.5 4.5 + - - -
88B MET* 3.4 15.2 - - - +
92B TYR* 3.5 38.5 - + + -
152B ILE* 3.8 18.2 - - + -
161B ILE* 3.5 28.5 - - + -
163B VAL* 5.1 0.2 - - + -
183B GLN* 4.9 0.2 - - - -
185B ASN* 4.2 10.5 - - - -
201B LEU* 4.2 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLY* 3.0 19.0 - - - -
5B GLU* 3.9 26.9 - - + +
8B PHE* 3.6 28.5 - - + -
37B ALA* 3.5 22.2 - - - -
69B GLN 5.0 0.2 + - - -
70B CYS 3.1 28.5 + - - +
72B ALA 2.9 23.6 + - - +
74B TYR* 3.8 9.7 - - - +
79B LYS* 6.1 3.1 - - - +
82B ASP* 2.6 35.2 + - - +
84B PHE* 1.3 72.7 - - - +
86B SER* 1.3 66.0 + - - +
88B MET* 3.0 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B SER* 3.4 30.4 - - - -
3B LYS* 3.8 17.1 + - - +
5B GLU 4.7 0.2 - - - +
82B ASP 3.5 13.3 + - - -
83B PHE 2.8 17.8 + - - -
85B LYS* 1.3 79.2 - - - +
87B ALA* 1.3 57.2 + - - +
88B MET 3.2 7.4 + - - +
192B PRO 3.8 6.2 - - - +
193B VAL* 3.4 8.9 - - - +
194B LEU* 3.0 30.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE* 3.3 13.4 + - + +
84B PHE 3.5 5.6 + - - +
85B LYS 3.2 1.0 - - - -
86B SER* 1.3 78.3 + - - +
88B MET* 1.3 61.3 + - - +
90B GLU* 3.4 7.3 + - - +
91B GLY 2.8 42.9 + - - +
92B TYR* 4.2 9.6 - - + -
187B PRO* 4.3 10.0 - - + +
189B GLY 5.7 0.2 + - - -
193B VAL* 3.7 20.0 - - + -
----------------------------------------------------------
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