Contacts of the helix formed by residues 87 - 94 (chain B) in PDB entry 2WA2
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 SER 87 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B VAL* 3.5 19.7 - - - +
57B SER* 3.2 20.4 - - - -
59B GLY* 3.0 2.1 - - - -
60B THR* 2.7 53.0 + - - -
86B GLY* 1.3 77.3 - - - +
88B TRP* 1.3 56.3 + - - +
90B TYR* 3.6 3.8 + - - +
91B TYR* 3.1 21.0 + - - +
1267B SAM 2.2 29.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLY* 3.1 29.7 + - - -
62B LYS* 4.7 3.8 - - + +
63B LEU* 3.6 36.4 - - + +
66B ILE* 5.1 2.5 - - + -
80B ASP* 3.6 18.1 + - - +
86B GLY 3.3 0.8 - - - -
87B SER* 1.3 77.4 + - - +
89B SER* 1.3 61.2 + - - +
91B TYR* 3.3 2.9 + - - +
92B ALA* 2.9 30.4 + - - +
145B LEU* 3.8 20.2 - - + -
146B CYS 3.9 8.7 - - - -
147B ASP* 3.5 35.1 + - + -
182B CYS* 3.6 36.6 - - - -
222B TYR* 3.6 31.0 - + - -
1267B SAM 3.2 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASP* 2.6 33.1 + - - +
83B CYS* 4.1 0.7 - - - +
86B GLY 3.0 9.1 + - - -
88B TRP* 1.3 80.1 - - - +
90B TYR* 1.3 58.7 + - - +
92B ALA* 3.3 2.7 + - - +
93B ALA* 2.8 31.2 + - - +
101B VAL* 3.6 19.3 - - - +
103B ALA* 3.3 12.6 - - - +
125B ILE* 3.7 19.4 - - - +
127B PHE* 4.2 6.5 - - - -
145B LEU* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B VAL* 4.0 22.7 - - + +
60B THR* 5.1 0.2 - - - +
85B ARG 4.0 3.6 - - - -
86B GLY 2.9 28.1 + - - +
87B SER* 4.0 4.9 - - - +
89B SER* 1.3 74.9 - - - +
91B TYR* 1.3 66.8 + - - +
93B ALA* 3.4 2.8 + - - +
94B SER* 3.3 15.8 + - - -
115B ARG 2.5 30.1 + - - -
116B LEU* 3.3 5.2 - - - +
117B VAL* 3.0 36.2 + - + -
119B THR* 3.3 22.4 + - - +
120B PHE 4.4 2.5 - - - +
122B TRP* 3.9 12.3 - - + -
125B ILE* 3.4 20.4 - - + -
127B PHE* 3.6 25.1 - + - -
260B PHE* 3.3 19.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B THR* 3.9 25.4 - - + -
63B LEU* 3.7 25.6 - - + -
64B ALA* 3.6 29.9 + - + +
67B ASP* 2.6 41.3 + - + +
68B GLU* 4.6 6.2 + - - +
74B LEU* 3.5 15.9 - - + -
87B SER 3.1 15.5 + - - +
88B TRP* 3.6 7.2 - - - +
89B SER 3.3 0.4 - - - -
90B TYR* 1.3 74.6 - - - +
92B ALA* 1.3 64.1 + - - +
94B SER* 2.7 21.9 + - - -
95B GLN* 3.2 33.0 + - + +
258B TYR* 3.7 19.5 - + - -
260B PHE* 3.7 7.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 5.1 0.7 - - + -
74B LEU* 4.6 7.2 - - + -
78B VAL* 4.3 19.5 - - + -
88B TRP 2.9 16.8 + - - +
89B SER* 3.8 5.2 - - - +
91B TYR* 1.3 79.3 - - - +
93B ALA* 1.3 62.6 - - - +
95B GLN* 3.0 18.8 + - - +
98B VAL* 3.2 28.1 - - + +
101B VAL* 4.1 11.9 - - + -
145B LEU* 4.4 7.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
89B SER 2.8 18.4 + - - +
90B TYR* 3.8 5.4 - - - +
91B TYR 3.3 0.2 - - - -
92B ALA* 1.3 76.6 - - - +
94B SER* 1.3 56.4 + - - +
95B GLN 3.3 0.2 - - - -
98B VAL* 4.4 3.1 - - - -
101B VAL* 3.8 11.6 - - + +
120B PHE 3.9 1.3 - - - -
121B GLY* 3.3 27.3 - - - +
122B TRP 4.5 0.2 - - - +
124B LEU* 3.9 6.2 - - + +
125B ILE* 3.6 20.0 - - + -
265B ARG* 2.8 29.4 + - - -
----------------------------------------------------------
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 TYR 3.3 8.4 + - - -
91B TYR* 2.7 19.8 + - - -
93B ALA* 1.3 76.4 - - - +
95B GLN* 1.3 75.2 + - - +
96B PRO* 3.8 4.3 - - - +
120B PHE* 3.2 44.6 + - - -
258B TYR* 4.4 3.3 + - - -
260B PHE* 3.7 20.8 - - - -
265B ARG* 3.9 2.7 + - - -
----------------------------------------------------------
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