Contacts of the helix formed by residues 82 - 88 (chain R) in PDB entry 3EXG
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 THR 82 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R TYR* 3.3 21.1 - - - +
80R PHE* 3.6 13.3 - - - +
81R MET* 1.3 88.2 - - + +
83R PHE* 1.3 66.1 + - - +
84R ASN* 3.1 27.0 + - - +
85R PHE* 3.0 36.8 + - + +
117R PRO* 3.4 19.5 - - + -
118R ASN* 5.9 0.4 - - - -
128R HIS* 5.1 7.7 - - + +
173R GLU* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80R PHE* 3.6 26.5 - + - -
82R THR* 1.3 68.9 - - - +
84R ASN* 1.3 61.8 + - - +
85R PHE 3.1 0.2 - - - -
86R SER* 2.7 46.6 + - - +
87R MET 3.9 0.3 + - - -
114R PHE* 4.1 4.3 - - + -
115R ARG* 3.9 9.4 - - - -
116R GLY* 3.3 35.9 - - - -
117R PRO 2.9 13.7 + - - +
118R ASN* 4.1 8.9 - - + +
132R PHE* 3.3 27.8 - - + -
136R TYR* 3.8 17.3 - + - -
168R VAL* 3.7 28.3 - - + -
169R VAL 3.5 15.3 - - - -
170R LEU* 3.8 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 84 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82R THR* 3.1 21.7 + - - +
83R PHE* 1.3 76.4 - - - +
85R PHE* 1.3 68.3 + - + +
87R MET* 3.4 27.5 + - - +
88R GLN* 4.9 1.0 + - - +
118R ASN* 6.2 1.2 - - - +
119R GLY 5.0 1.8 + - - +
127R GLN 3.4 23.4 - - - +
128R HIS* 2.9 29.4 + - - +
129R SER 3.4 2.0 + - - +
130R GLN* 3.1 39.1 + - - +
132R PHE* 3.6 11.0 - - - -
137S ILE* 4.8 2.1 - - - +
91T ASP* 5.0 0.7 - - - +
95T ASN* 4.5 6.5 + - - +
99T LYS* 5.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 85 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28R GLU* 5.2 1.1 - - - -
59R GLU* 3.6 41.0 - - + +
80R PHE* 4.6 1.8 - - + -
81R MET* 3.5 40.6 - - + +
82R THR* 3.0 30.0 + - + +
84R ASN* 1.3 76.4 - - + +
86R SER* 1.3 63.4 + - - +
87R MET 3.1 2.5 + - - -
88R GLN* 3.6 16.0 + - - +
128R HIS* 3.6 31.4 - + - -
136S GLY 4.0 7.4 - - - -
137S ILE* 3.9 33.9 - - + -
138S VAL* 5.2 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 86 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80R PHE* 3.5 37.9 - - - -
82R THR 3.7 1.6 + - - -
83R PHE* 2.7 31.3 + - - -
85R PHE* 1.3 77.7 - - - +
87R MET* 1.3 55.4 + - - +
88R GLN 3.1 0.2 - - - -
89R ALA 2.6 24.4 + - - -
90R ILE* 2.8 13.5 + - - +
132R PHE* 4.9 2.4 - - - -
136R TYR* 2.6 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 87 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84R ASN* 3.4 16.4 + - + +
85R PHE 3.1 2.2 - - - -
86R SER* 1.3 78.7 + - - +
88R GLN* 1.3 63.4 + - - +
89R ALA 3.2 0.7 + - - -
90R ILE* 3.4 23.4 + - + +
130R GLN* 4.4 3.4 - - - +
132R PHE* 3.7 30.5 - - + -
135R TRP* 3.9 21.8 - - + -
87T MET 3.8 3.5 - - - +
88T GLN 5.2 0.3 - - - +
90T ILE* 3.7 11.2 - - + +
91T ASP* 4.0 24.1 + - + +
94T ILE* 4.0 28.7 - - + -
95T ASN* 2.9 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 88 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177Q GLU* 5.5 0.4 + - - -
59R GLU* 3.1 36.8 + - + +
60R MET* 3.4 33.4 - - + +
84R ASN 5.5 0.4 - - - +
85R PHE* 3.8 16.2 - - - +
86R SER 3.1 0.2 - - - -
87R MET* 1.3 76.8 - - + +
89R ALA* 1.3 58.6 + - - +
90R ILE 3.8 0.2 + - - -
91R ASP 4.8 0.9 + - - -
137S ILE* 3.8 13.4 - - + +
138S VAL 4.8 0.8 + - - -
172S GLN* 3.4 20.2 + - - +
174S GLN* 3.5 23.4 + - - -
60T MET* 3.6 23.4 - - + +
87T MET 5.0 1.0 - - - +
88T GLN 4.9 3.2 - - - +
91T ASP* 3.6 19.3 - - + +
----------------------------------------------------------
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