Contacts of the helix formed by residues 82 - 88 (chain B) in PDB entry 3DV0
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 PHE 82 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 4.6 3.6 - - + -
37B PHE* 3.5 38.4 - + - -
80B ILE* 3.0 9.6 + - - +
81B GLN* 1.3 107.1 - - + +
83B PHE* 1.3 58.9 + - - +
84B GLY 3.0 5.2 - - - +
85B PHE* 2.9 50.1 + + + -
116B SER* 3.3 3.8 - - - -
117B PRO* 3.8 10.3 - - + -
124B THR* 5.1 2.5 - - + -
128B HIS* 3.4 52.0 - + + +
173B LEU* 4.3 11.7 - - + -
502B PYR 3.3 19.3 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
80B ILE* 4.5 4.3 - - + -
82B PHE* 1.3 71.6 - - - +
84B GLY* 1.3 55.6 + - - +
85B PHE 2.9 1.3 - - - -
86B VAL* 2.9 61.7 + - + +
93B ILE* 5.2 5.2 - - + -
114B ILE* 5.7 4.5 - - + -
116B SER* 2.9 23.8 + - - +
117B PRO 3.1 14.4 + - - +
118B PHE* 4.4 13.0 - + + -
128B HIS 4.7 0.8 + - - -
130B ASP 4.8 2.7 - - - +
132B LEU* 3.7 49.4 - - + +
135B LEU* 6.2 0.2 - - + -
136B VAL* 4.2 22.7 - - + -
168B ILE* 4.4 8.3 - - + -
170B LEU* 3.7 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PHE* 2.9 3.6 + - - +
83B PHE* 1.3 77.8 - - - +
85B PHE* 1.3 63.4 + - - +
86B VAL 3.2 3.5 + - - -
87B TYR* 3.5 22.5 - - - -
88B GLU* 4.9 0.2 - - - +
127B LEU* 3.4 38.3 + - - +
128B HIS 4.8 3.4 + - - -
130B ASP* 5.0 5.6 + - - -
132B LEU* 4.1 9.9 - - - -
143C ILE* 4.4 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLU* 3.8 31.3 - - + +
80B ILE* 4.2 3.7 - - + +
81B GLN* 4.2 6.7 - - + -
82B PHE* 2.9 50.5 + + + +
84B GLY* 1.3 78.6 - - - +
86B VAL* 1.3 62.5 + - - +
87B TYR 3.1 3.4 + - - -
88B GLU* 3.5 20.0 + - - +
126B GLU 5.3 0.2 - - - -
127B LEU* 3.9 13.2 - - + -
128B HIS* 4.2 7.6 - + - -
502B PYR 3.8 9.4 - - - -
142C ILE* 4.8 0.9 - - + -
143C ILE* 3.4 30.5 - - + -
1370C TPW 3.3 57.4 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 4.7 3.4 - - + -
82B PHE 4.3 0.2 + - - -
83B PHE* 2.9 56.3 + - + +
84B GLY 3.2 0.4 - - - -
85B PHE* 1.3 77.9 - - - +
87B TYR* 1.3 81.1 + - + +
88B GLU 3.2 0.2 - - - -
89B VAL* 3.0 11.0 + - + +
90B MET* 3.0 37.7 + - - +
93B ILE* 3.9 23.1 - - + -
132B LEU* 4.1 11.7 - - + -
135B LEU* 4.7 4.9 - - + -
136B VAL* 5.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLY 3.5 21.1 - - - -
85B PHE 3.1 0.6 - - - -
86B VAL* 1.3 84.1 - - + +
88B GLU* 1.3 64.5 + - - +
89B VAL 3.5 0.3 + - - -
90B MET* 3.7 9.8 + - + -
127B LEU* 4.1 5.6 - - + -
132B LEU* 3.8 21.9 - - + +
135B LEU* 3.7 24.0 - - + +
87D TYR 3.8 14.9 - - - +
88D GLU 5.2 2.3 - - - +
90D MET* 3.9 24.6 + - + +
91D ASP* 3.5 43.4 + - + +
94D CYS* 3.8 15.4 - - + +
95D GLY* 3.9 16.6 - - - -
99D ARG* 3.2 24.7 + - - -
139D GLN* 3.5 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLU* 3.9 28.0 - - + +
60B SER* 3.3 23.3 + - - +
84B GLY 4.9 0.2 - - - +
85B PHE* 3.6 19.0 - - - +
86B VAL 3.2 0.8 - - - -
87B TYR* 1.3 79.6 - - - +
89B VAL* 1.3 58.5 + - - +
90B MET 3.6 0.6 + - - -
91B ASP 5.4 0.3 + - - -
1326B MG 3.5 22.0 - - - -
143C ILE* 3.7 21.1 - - - +
144C ILE 5.7 0.7 - - - +
178C GLN* 4.4 11.7 - - - +
180C ASP* 4.2 11.7 - - - +
1370C TPW 4.0 5.9 - - + +
87D TYR 5.5 1.1 - - - +
91D ASP* 3.0 36.7 - - - +
----------------------------------------------------------
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