Contacts of the helix formed by residues 78 - 92 (chain A) in PDB entry 2WH6
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 HIS 78 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A THR* 3.3 1.8 - - - -
77A GLU* 1.3 94.0 - - + +
79A VAL* 1.3 67.8 + - - +
80A ASP* 3.3 6.1 + - - +
81A LEU* 3.3 31.3 + - + +
82A ASP* 2.9 47.5 + - - -
1159A BR 3.9 5.2 - - - -
51B ASP* 6.0 2.7 - - - -
52B MET* 4.8 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 4.1 2.5 - - + -
73A ILE* 4.1 14.1 - - + -
76A THR* 3.4 27.6 - - + -
78A HIS* 1.3 73.0 - - - +
80A ASP* 1.3 66.7 + - - +
82A ASP* 3.3 10.1 + - - +
83A PHE* 3.3 21.2 + - + -
125A VAL* 5.0 11.2 - - + +
128A LEU* 4.0 11.4 - - + +
129A SER* 3.2 40.6 - - - +
1159A BR 3.4 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A HIS* 4.2 6.9 - - - +
79A VAL* 1.3 78.7 + - - +
81A LEU* 1.3 81.1 + - - +
83A PHE* 3.3 15.9 + - - +
84A ASN* 3.9 3.6 + - - +
128A LEU* 3.5 49.3 + - + +
131A ARG* 5.0 3.9 - - + +
132A GLY* 3.9 18.1 - - - +
135A GLU* 5.1 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A HIS* 3.3 36.7 + - + +
80A ASP* 1.3 95.8 + - - +
82A ASP* 1.3 65.1 + - - +
84A ASN* 3.1 23.8 + - - +
85A SER* 3.6 6.5 + - - -
52B MET* 5.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 3.7 15.2 - - + -
76A THR* 2.4 39.6 + - - +
77A GLU 3.9 0.2 + - - -
78A HIS* 2.9 39.5 + - - +
79A VAL 3.8 0.4 - - - +
80A ASP 3.2 0.6 - - - -
81A LEU* 1.3 82.0 - - - +
83A PHE* 1.3 62.3 + - - +
85A SER* 3.2 16.9 + - - -
86A VAL* 3.4 16.6 + - - +
52B MET* 3.4 15.7 - - - +
55B GLU* 3.7 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TRP* 3.5 24.2 - + - -
72A PHE* 3.7 18.6 - + - -
79A VAL* 3.3 23.3 + - + -
80A ASP 3.3 8.6 + - - +
81A LEU 3.2 0.4 - - - -
82A ASP* 1.3 77.0 - - - +
84A ASN* 1.3 62.8 + - - +
86A VAL* 3.4 6.0 + - - +
87A PHE* 3.1 23.2 + - - +
104A TRP* 3.7 18.4 - + - -
107A TRP* 3.8 22.2 - + - -
108A CYS* 4.4 3.4 - - - -
111A ALA* 5.0 0.4 - - + -
129A SER* 3.6 35.7 - - - -
132A GLY* 3.6 17.0 - - - +
133A MET* 3.7 39.5 - - + -
136A ALA* 4.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASP 3.9 3.7 + - - +
81A LEU* 3.1 19.0 + - - +
83A PHE* 1.3 80.0 - - - +
85A SER* 1.3 54.2 + - - +
87A PHE* 3.4 3.6 + - - +
88A LEU* 3.0 49.1 + - - +
135A GLU* 4.9 1.7 - - - +
136A ALA* 3.7 26.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU 3.7 9.0 + - - -
82A ASP 3.2 8.6 + - - -
84A ASN* 1.3 74.8 - - - +
86A VAL* 1.3 65.3 + - - +
88A LEU* 3.5 6.9 + - - +
89A GLU* 3.2 29.8 + - - +
52B MET* 3.3 32.5 - - - +
55B GLU* 4.5 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 3.9 18.4 - - + -
82A ASP 3.4 12.8 + - - +
83A PHE* 3.4 8.0 + - - +
85A SER* 1.3 76.4 - - - +
87A PHE* 1.4 65.4 + - - +
89A GLU* 3.3 2.8 + - - +
90A ILE* 3.2 36.9 + - + +
104A TRP* 3.7 19.5 - - + -
107A TRP* 4.6 4.9 - - + -
55B GLU* 3.7 31.4 - - + +
58B ILE* 3.9 25.1 - - + -
59B ALA* 3.9 5.3 - - - +
62B LEU* 4.6 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE 3.1 12.6 + - - +
84A ASN* 3.6 9.2 - - - +
86A VAL* 1.4 77.2 - - - +
88A LEU* 1.3 80.9 + - + +
90A ILE* 3.1 11.9 + - - +
91A PHE* 3.1 57.9 + + + +
92A HIS* 5.1 4.7 - + - -
104A TRP* 3.6 38.5 - + + -
136A ALA* 3.6 25.6 - - + -
137A SER* 4.2 1.8 - - - -
139A GLY* 3.5 38.8 - - - -
140A LEU* 3.7 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASN* 3.0 36.2 + - - +
85A SER* 4.2 5.6 - - - +
86A VAL 3.4 0.2 - - - -
87A PHE* 1.3 88.9 - - + +
89A GLU* 1.3 60.3 + - + +
91A PHE 4.6 0.2 - - - +
92A HIS* 2.9 61.2 + - + +
93A ARG* 4.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A SER* 3.2 17.7 + - - +
86A VAL* 4.8 0.2 - - - -
87A PHE 3.3 0.2 - - - -
88A LEU* 1.3 78.8 - - + +
90A ILE* 1.3 58.9 + - - +
93A ARG* 2.9 52.3 + - - +
55B GLU* 5.1 1.6 - - + +
56B ILE* 5.2 21.2 - - + +
59B ALA* 3.4 22.0 - - + -
63B ARG* 2.7 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 3.2 17.5 - - + +
87A PHE* 3.1 5.7 + - - +
89A GLU* 1.3 78.9 - - - +
91A PHE* 1.3 87.3 + - + +
92A HIS 3.7 0.6 + - - -
93A ARG 4.0 2.1 + - - -
100A ARG* 3.3 45.4 + - + +
104A TRP* 3.5 36.1 - - + -
59B ALA* 3.9 19.5 - - + +
62B LEU* 3.6 26.5 - - + -
63B ARG* 3.8 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE* 3.1 63.2 + + + +
90A ILE* 1.3 89.5 - - + +
92A HIS* 1.3 73.5 + - + +
93A ARG 3.4 4.5 - - - -
94A GLY 3.2 14.1 - - - +
96A PRO* 3.9 41.2 - - + +
100A ARG* 3.5 30.1 - - + -
101A ALA* 3.6 26.5 - - + -
104A TRP* 3.7 15.7 - + + -
140A LEU* 3.7 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE* 5.1 5.7 - + - -
88A LEU* 2.9 39.7 + - + +
91A PHE* 1.3 92.6 + - + +
93A ARG* 1.3 66.1 + - - +
94A GLY 3.5 5.9 + - - -
139A GLY 5.7 2.8 + - - -
----------------------------------------------------------
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