Contacts of the helix formed by residues 86 - 94 (chain B) in PDB entry 3L2O
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 ASN 86 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1143A ASN 3.7 13.5 - - - +
1144A ASP* 3.6 5.7 - - - +
1145A PHE* 3.2 41.8 + - + +
1149A GLU* 4.8 5.4 + - - +
1153A VAL* 3.4 35.2 - - - +
83B GLY 3.0 10.7 + - - -
84B SER 3.1 1.7 - - - +
85B THR* 1.3 79.2 + - - +
87B HIS* 1.3 100.5 + - - +
89B TRP* 3.1 7.6 + - - -
90B ASN* 3.1 9.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141A ILE* 4.7 4.7 - - + +
1142A LYS* 2.9 34.5 + - + -
1144A ASP* 2.8 30.1 - - - +
60B THR* 5.5 2.8 + - + -
85B THR* 2.4 36.3 + - - -
86B ASN* 1.3 100.1 + - - +
88B TYR* 1.3 78.7 + - + +
89B TRP* 3.3 28.4 - + - -
90B ASN* 3.2 4.4 + - - +
91B GLU* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B THR* 4.3 23.9 + - + -
62B LEU 4.7 1.2 + - - -
64B ILE* 3.5 13.4 + - + +
67B GLN* 2.4 46.8 + - - -
87B HIS* 1.3 85.4 - - + +
89B TRP* 1.3 67.5 + + - +
91B GLU* 2.9 10.6 + - - +
92B THR* 2.6 64.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141A ILE* 3.8 15.6 - - + +
59B LEU* 3.6 31.4 - - + -
60B THR* 3.5 17.2 + - - -
67B GLN* 3.4 42.0 - - + -
71B LEU* 4.0 18.6 - - + -
82B LEU* 3.4 44.6 - - + +
83B GLY* 4.0 2.5 - - - -
85B THR* 3.1 24.5 - - - +
86B ASN 3.1 2.9 + - - +
87B HIS* 3.3 25.3 - + - -
88B TYR* 1.3 83.3 - + - +
90B ASN* 1.3 68.1 + - - +
92B THR* 3.2 25.1 - - - -
93B VAL* 2.7 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1153A VAL* 3.4 33.1 - - - +
1156A GLU* 6.0 2.2 - - - +
1157A ASN* 3.4 21.4 + - - +
83B GLY* 3.3 23.0 + - - +
86B ASN* 3.1 16.5 + - - +
87B HIS 3.5 8.7 - - - +
89B TRP* 1.3 77.4 - - - +
91B GLU* 1.3 67.7 - - + +
93B VAL* 3.5 3.8 + - - +
94B ARG* 3.0 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B HIS 3.1 16.7 + - - +
88B TYR* 2.9 10.1 + - - +
90B ASN* 1.3 82.8 - - + +
92B THR* 1.3 61.5 + - + +
94B ARG* 3.1 26.0 + - - +
95B ASP* 3.9 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 4.3 15.7 - - + -
67B GLN* 6.4 0.2 - - - -
68B LEU* 4.4 7.1 - - - +
71B LEU* 4.4 4.7 - - - +
88B TYR* 2.6 61.3 + - + +
89B TRP* 3.2 27.4 - - - -
91B GLU* 1.3 69.6 - - + +
93B VAL* 1.3 68.3 + - - +
94B ARG 2.9 2.5 - - - -
95B ASP* 2.8 28.7 + - - +
98B LEU* 5.1 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1157A ASN* 6.0 1.6 - - - +
71B LEU* 4.2 8.5 - - + -
79B LEU* 3.2 53.1 - - + +
80B CYS* 5.1 2.9 - - - -
82B LEU* 3.4 32.5 - - + -
83B GLY* 4.0 6.3 - - - +
89B TRP* 2.7 24.4 + - + +
90B ASN* 4.0 4.3 - - - +
92B THR* 1.3 73.6 + - - +
94B ARG* 1.3 64.7 + - + +
95B ASP 3.3 1.3 + - - -
98B LEU* 4.1 10.2 - - - +
99B TRP* 3.5 17.4 + - + +
140B MET* 6.4 0.9 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
1156A GLU* 3.2 47.7 + - - +
1157A ASN* 4.2 13.5 + - - +
80B CYS* 5.5 6.1 - - - -
90B ASN* 3.0 31.0 + - - +
91B GLU* 3.3 10.8 - - - +
92B THR 2.9 1.2 - - - -
93B VAL* 1.3 83.3 - - + +
95B ASP* 1.3 65.3 + - - +
96B PRO* 3.1 9.2 - - - +
99B TRP* 3.9 13.0 - - - +
140B MET* 3.9 41.6 - - + +
----------------------------------------------------------
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