Contacts of the helix formed by residues 82 - 88 (chain J) 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 J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J TYR* 3.5 20.0 - - - +
80J PHE* 3.4 17.3 - - - +
81J MET* 1.3 85.4 - - + +
83J PHE* 1.3 63.3 + - - +
84J ASN* 2.9 32.4 + - - +
85J PHE* 3.2 32.8 + - + +
117J PRO* 3.4 17.0 - - + -
128J HIS* 5.0 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80J PHE* 4.1 17.3 - + + -
82J THR* 1.3 68.7 - - - +
84J ASN* 1.3 59.3 + - - +
85J PHE 3.0 2.0 - - - -
86J SER* 2.6 45.5 + - - +
114J PHE* 4.0 20.0 - - + -
115J ARG* 3.9 2.2 - - - -
116J GLY* 3.3 28.5 - - - -
117J PRO 3.0 11.7 + - - +
118J ASN* 3.9 10.3 - - + +
132J PHE* 3.4 23.5 - - + -
136J TYR* 3.7 26.5 - + - -
168J VAL* 3.7 31.4 - - + -
169J VAL 3.2 25.8 - - - -
170J LEU* 3.7 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 84 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82J THR* 2.9 25.4 + - - +
83J PHE* 1.3 79.5 - - - +
85J PHE* 1.3 66.8 + - + +
86J SER 3.3 0.9 + - - -
87J MET* 3.4 25.6 + - - +
88J GLN 4.9 0.3 + - - -
118J ASN* 6.0 1.2 - - - +
119J GLY 5.1 2.4 + - - +
126J ALA 5.0 0.2 - - - +
127J GLN 3.4 24.6 - - - +
128J HIS* 3.1 26.1 + - - +
129J SER* 3.4 2.8 + - - +
130J GLN* 3.0 37.5 + - - +
132J PHE* 3.4 12.0 - - - -
137K ILE* 4.8 1.0 - - - +
91L ASP* 5.3 0.5 - - - +
95L ASN* 4.2 8.1 + - - +
99L LYS* 5.3 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 85 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J GLU* 5.4 1.6 - - - -
59J GLU* 3.5 40.9 - - + +
80J PHE* 4.5 2.9 - - + -
81J MET* 3.6 31.0 - - + +
82J THR* 3.2 36.3 + - + +
83J PHE 3.0 0.8 - - - -
84J ASN* 1.3 74.6 - - + +
86J SER* 1.3 64.1 + - - +
87J MET 3.1 1.5 + - - -
88J GLN* 3.7 14.3 + - - +
128J HIS* 3.7 32.3 - + - -
136K GLY 4.6 5.8 - - - -
137K ILE* 3.6 33.4 - - + -
138K VAL* 5.4 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 86 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80J PHE* 3.8 28.9 - - - -
82J THR 3.9 1.4 + - - -
83J PHE* 2.6 37.0 + - - -
85J PHE* 1.3 79.5 - - - +
87J MET* 1.3 64.4 + - - +
88J GLN 3.1 0.2 - - - -
89J ALA* 2.7 22.9 + - - +
90J ILE* 3.0 10.0 + - - -
132J PHE* 4.8 1.0 - - - -
136J TYR* 2.6 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 87 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84J ASN 3.4 6.5 + - - +
85J PHE 3.1 1.8 - - - -
86J SER* 1.3 81.9 + - - +
88J GLN* 1.3 62.7 + - - +
89J ALA 3.0 1.2 + - - -
90J ILE* 3.3 25.6 + - + +
130J GLN* 4.5 1.6 - - - +
132J PHE* 3.5 32.5 - - + -
135J TRP* 3.8 26.9 - - + -
87L MET 4.0 7.6 - - - +
88L GLN 4.9 0.5 - - - +
90L ILE* 4.0 14.4 - - + +
91L ASP* 3.6 24.7 + - + +
94L ILE* 4.0 21.8 - - + -
95L ASN* 3.0 40.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 88 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177I GLU* 5.5 1.0 + - - -
59J GLU* 3.2 36.0 + - + +
60J MET* 3.4 33.6 - - + +
84J ASN 4.9 0.4 + - - +
85J PHE* 3.7 13.5 + - - +
86J SER 3.1 0.2 - - - -
87J MET* 1.3 77.9 - - - +
89J ALA* 1.3 55.9 + - - +
90J ILE 3.6 0.4 + - - -
137K ILE* 4.1 17.4 - - + +
138K VAL 4.2 0.7 - - - +
172K GLN* 3.1 31.1 + - - +
174K GLN* 3.2 16.8 + - - -
60L MET* 3.7 25.7 - - + +
87L MET 5.2 0.7 - - - +
88L GLN 4.6 3.9 - - - +
91L ASP* 4.2 10.9 - - + +
----------------------------------------------------------
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