Contacts of the helix formed by residues 89 - 98 (chain B) in PDB entry 3GJ9
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 89 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLY* 4.2 1.8 - - - -
37B ILE* 3.6 23.8 - - + -
38B ASP* 3.2 25.4 - - + +
55B ILE* 4.9 0.2 - - - -
88B VAL* 1.3 78.3 - - - +
90B HIS* 1.3 66.1 + - - +
91B ASP* 3.6 6.4 + - - +
92B GLN* 2.7 49.1 + - - +
93B ALA* 3.1 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 3.3 36.0 - - + +
34B GLY* 3.8 10.5 - - - -
35B GLY 3.1 28.8 + - - +
36B GLY* 4.7 0.2 - - - -
38B ASP* 2.7 18.7 + - - +
39B GLN* 4.2 4.0 - - + +
55B ILE* 4.7 3.8 - - - +
89B THR* 1.3 72.8 - - - +
91B ASP* 1.3 64.2 + - - +
93B ALA* 3.2 3.3 + - - +
94B ARG* 3.0 22.0 + - + +
441D ARG* 3.2 53.3 + - + +
442D GLU 4.0 4.6 + - - -
443D SER* 2.8 30.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASP* 4.8 1.3 + - - +
89B THR* 3.3 7.4 + - - +
90B HIS* 1.3 80.3 - - - +
92B GLN* 1.3 57.5 + - + +
94B ARG* 3.0 36.4 + - - +
95B LYS* 2.9 38.9 + - + +
441D ARG* 2.5 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 4.9 0.5 - - - +
87B MET 4.3 1.6 - - - +
88B VAL* 3.1 23.3 - - + +
89B THR* 2.7 51.6 + - + +
91B ASP* 1.3 77.2 - - + +
93B ALA* 1.3 64.5 + - - +
95B LYS* 3.0 10.5 + - - +
96B ARG* 2.9 49.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 4.0 9.0 - - + -
55B ILE* 3.6 30.5 - - + -
85B MET* 3.4 30.7 - - + +
88B VAL* 4.0 3.7 - - + +
89B THR 3.1 4.6 + - - +
90B HIS 3.6 7.6 - - - +
92B GLN* 1.3 78.3 - - - +
94B ARG* 1.3 61.6 + - - +
96B ARG 3.4 0.5 + - - -
97B LEU* 3.2 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 4.2 7.4 - - + +
90B HIS 3.0 13.7 + - - +
91B ASP* 3.0 51.4 + - - +
93B ALA* 1.3 79.0 - - - +
95B LYS* 1.3 87.3 + - - +
97B LEU* 3.5 3.1 + - - +
98B THR* 2.6 50.0 + - - +
441D ARG* 5.5 1.6 - - - +
443D SER* 3.6 32.7 + - - +
445D ILE* 4.7 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASP* 2.9 27.1 + - + +
92B GLN* 3.0 7.8 + - + +
94B ARG* 1.3 109.8 - - - +
96B ARG* 1.3 61.7 + - + +
97B LEU 3.1 3.3 + - - -
98B THR* 3.3 15.0 + - - +
99B LYS* 3.4 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 3.5 21.3 - - + +
83B TRP* 3.5 50.7 - - + +
84B ASP* 2.8 30.9 + - - +
85B MET* 4.0 20.2 - - + -
88B VAL* 3.6 18.8 - - - +
92B GLN* 2.9 37.6 + - - +
93B ALA 3.4 4.9 + - - +
95B LYS* 1.3 77.2 - - + +
97B LEU* 1.3 58.7 + - - +
98B THR 3.5 0.2 - - - -
99B LYS* 4.5 22.2 + - - +
102B GLU* 4.4 11.6 - - - +
105B VAL* 4.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LYS* 3.5 15.0 + - - -
29B LEU* 3.4 30.0 - - + +
31B PHE* 4.1 14.6 - - + -
33B ILE* 4.2 14.6 - - + -
77B ILE* 4.5 3.6 - - + -
80B VAL* 3.5 34.1 - - + -
85B MET* 4.0 11.4 - - + -
93B ALA 3.2 21.9 + - - +
94B ARG* 4.1 3.8 - - - +
95B LYS 3.1 0.4 - - - -
96B ARG* 1.3 79.2 - - - +
98B THR* 1.3 63.7 + - + +
99B LYS 3.6 1.6 - - - -
105B VAL* 4.1 4.7 - - + +
107B LEU* 4.1 12.3 - - + -
445D ILE* 3.5 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LYS* 4.0 3.8 - - - +
27B LEU 5.7 5.4 - - - +
29B LEU* 5.7 0.2 - - + -
94B ARG* 2.6 33.6 + - - +
95B LYS* 3.3 11.6 + - - +
97B LEU* 1.3 81.9 - - - +
99B LYS* 1.3 57.9 + - - +
100B ARG* 3.0 11.3 + - - +
445D ILE* 3.5 30.5 - - + +
----------------------------------------------------------
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