Contacts of the helix formed by residues 86 - 95 (chain B) in PDB entry 3A9L
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 GLU 86 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG* 5.9 0.2 + - - -
91A CYS* 5.4 0.7 - - - -
10B ILE* 3.7 28.1 - - + +
14B GLU* 3.9 4.8 - - - +
25B ILE* 3.6 26.6 - - + +
64B TYR* 2.5 36.0 + - - +
66B PHE* 4.5 2.0 - - + -
84B PHE* 3.7 16.3 + - + -
85B ASP* 1.3 75.0 + - - +
87B PRO* 1.4 80.2 - - + +
88B MET* 2.9 26.3 + - - +
89B ALA* 2.9 24.8 + - - +
90B VAL* 3.0 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A CYS* 4.0 24.0 - - - -
95A LYS* 4.7 7.4 - - - +
10B ILE* 5.3 2.9 - - + -
11B GLU* 4.8 9.9 - - + +
14B GLU* 5.3 5.4 - - - +
85B ASP 3.5 9.0 - - - +
86B GLU* 1.4 94.6 - - + +
88B MET* 1.3 56.6 + - - +
90B VAL* 3.6 7.4 - - + +
91B CYS* 2.8 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 4.0 15.9 - - + -
29A ARG* 4.8 3.1 - - + -
88A MET* 4.3 26.6 - - + +
91A CYS* 4.5 16.6 - - + -
92A MET* 3.8 34.1 - - - +
25B ILE* 3.6 36.8 - - + -
27B VAL* 3.9 13.0 - - + -
64B TYR* 4.2 4.5 - - + -
86B GLU* 2.9 17.2 + - - +
87B PRO* 1.3 72.9 - - - +
89B ALA* 1.3 55.2 + - - +
91B CYS* 3.1 8.0 + - - +
92B MET* 2.7 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 5.8 0.4 - - + -
64B TYR* 3.2 45.8 - - + +
84B PHE* 3.9 14.4 - - + -
86B GLU* 2.9 15.2 + - - +
88B MET* 1.3 76.0 - - - +
90B VAL* 1.3 56.1 + - - +
92B MET* 3.7 2.6 - - - +
93B LEU* 3.0 43.2 + - + +
152B ILE* 4.8 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ASP* 3.7 28.9 - - + +
86B GLU 3.0 18.2 + - - +
87B PRO* 3.6 9.9 - - + +
89B ALA* 1.3 74.2 - - - +
91B CYS* 1.3 65.9 + - - +
93B LEU* 3.6 3.2 + - - +
94B SER* 3.3 22.7 + - - -
152B ILE* 4.5 11.9 - - + -
155B ARG* 3.7 35.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLU* 5.5 0.2 - - - -
87A PRO* 4.0 30.3 - - - -
88A MET* 4.2 16.2 - - + -
87B PRO 2.8 14.7 + - - +
88B MET* 3.3 12.3 - - - +
90B VAL* 1.3 73.6 - - - +
92B MET* 1.3 66.5 + - - +
94B SER* 2.8 26.8 + - - -
95B LYS* 3.5 19.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A MET* 4.0 11.9 - - - +
27B VAL* 3.5 26.0 - - + -
29B ARG* 3.6 46.7 - - + +
35B ILE* 3.5 24.7 - - + -
62B SER* 4.0 6.3 - - - -
63B LEU 3.4 25.4 - - - +
64B TYR* 4.7 4.0 - - + -
88B MET 2.7 23.3 + - - +
89B ALA* 3.7 7.4 - - - +
91B CYS* 1.3 72.2 - - - +
93B LEU* 1.3 57.9 - - - +
95B LYS* 3.2 9.4 + - - +
96B HIS* 2.6 30.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 4.1 13.5 - - + -
37B PHE* 3.8 32.8 - - + -
64B TYR* 5.7 0.7 - - + -
89B ALA* 3.0 34.8 + - + +
90B VAL* 4.0 4.9 - - - +
92B MET* 1.3 76.6 - - - +
94B SER* 1.3 63.7 + - - +
95B LYS 3.1 1.2 + - - -
96B HIS* 3.1 14.8 + - - +
99B ALA* 3.4 33.4 - - + -
152B ILE* 3.7 28.5 - - + +
153B VAL 4.3 0.4 - - - +
155B ARG* 3.5 16.2 - - + +
156B CYS* 3.2 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B VAL* 3.3 11.7 + - - -
91B CYS* 2.8 19.7 + - - -
93B LEU* 1.3 77.9 - - - +
95B LYS* 1.3 70.9 + - - +
155B ARG 3.9 7.4 + - - -
156B CYS 4.9 0.2 - - - -
157B ALA* 3.5 22.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
14A GLU* 3.7 15.7 + - - +
87A PRO* 4.1 24.4 - - - +
29B ARG* 3.5 47.4 + - - +
32B PRO* 3.7 12.6 - - - +
91B CYS* 3.9 16.5 - - - +
92B MET* 3.2 7.8 + - - +
93B LEU 3.1 1.2 - - - -
94B SER* 1.3 91.8 + - - +
96B HIS* 1.3 61.2 + - - +
157B ALA* 5.2 1.1 - - - -
----------------------------------------------------------
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