Contacts of the helix formed by residues 89 - 98 (chain C) in PDB entry 2W3S
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 89 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ILE* 3.4 31.3 + - + +
87C ARG 3.9 1.0 + - - -
88C LEU* 1.3 73.3 - - - +
90C PRO* 1.4 97.6 - - + +
91C VAL* 3.0 23.5 + - + +
92C GLN* 2.8 28.7 + - - +
93C GLN* 3.0 10.4 + - - +
115C ALA* 4.1 10.0 + - + +
118C HIS* 3.8 30.4 + + + +
119C ASP 5.6 0.4 + - - -
155C ALA* 3.7 21.8 + - + +
157C TRP* 4.1 5.3 - + - -
158C LEU* 3.6 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LEU 4.1 4.0 - - - +
89C HIS* 1.4 104.2 - - + +
91C VAL* 1.3 50.5 + - - +
93C GLN* 3.8 7.7 - - + +
94C ALA* 2.8 34.7 + - - +
118C HIS* 4.1 10.1 - - + +
149C ALA* 4.0 11.4 - - + +
152C GLU* 3.6 39.3 - - + -
153C PRO 4.3 6.5 - - - +
155C ALA* 5.1 3.4 - - + +
157C TRP* 4.7 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C HIS* 3.0 22.9 + - + +
90C PRO* 1.3 74.0 - - - +
92C GLN* 1.3 61.1 + - + +
94C ALA* 3.1 4.0 + - - +
95C MET* 2.8 34.0 + - - +
111C ILE* 3.6 30.1 - - + +
114C MET* 3.5 51.6 - - + +
115C ALA* 4.2 1.3 - - + +
118C HIS* 4.4 5.2 - - + -
145C ALA 6.2 0.2 - - - -
146C ALA* 5.7 2.2 - - - -
149C ALA* 3.8 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ILE* 4.3 3.0 + - - +
81C ILE* 3.7 22.1 - - - +
82C ALA* 3.7 12.8 - - - +
88C LEU* 3.3 21.2 - - + +
89C HIS* 2.8 35.4 + - + +
91C VAL* 1.3 72.7 - - - +
93C GLN* 1.3 66.5 + - - +
95C MET 3.3 1.0 + - - -
96C ILE* 3.2 23.4 + - - +
111C ILE* 3.8 13.3 - - + +
16D VAL* 3.2 53.6 + - + +
17D THR* 4.0 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LEU* 3.9 24.8 - - + +
89C HIS 3.0 11.4 + - - +
90C PRO* 3.8 10.8 - - + +
92C GLN* 1.3 73.1 - - - +
94C ALA* 1.3 68.2 + - - +
96C ILE* 3.2 13.7 + - - +
97C ASP* 2.7 55.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C PRO 2.8 20.2 + - - +
91C VAL* 3.1 7.2 + - - +
93C GLN* 1.3 75.4 - - - +
95C MET* 1.3 57.1 + - - +
97C ASP* 2.9 23.6 + - - -
98C HIS* 2.9 21.8 + - - +
145C ALA* 3.4 33.2 - - + +
148C ALA* 4.8 4.9 - - + -
149C ALA* 4.1 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C VAL 2.8 19.5 + - - +
93C GLN 3.2 0.2 - - - -
94C ALA* 1.3 75.5 - - - +
96C ILE* 1.3 62.2 + - - +
99C HIS* 3.2 2.9 + - - -
100C GLY* 2.9 60.7 + - - +
101C SER* 4.5 4.3 + - - -
107C THR* 4.0 20.9 - - + -
110C PHE* 4.1 7.0 - - + -
111C ILE* 3.7 9.4 - - + -
114C MET* 3.3 31.2 - - + +
142C ILE* 4.1 14.1 - - + -
145C ALA* 3.6 22.4 - - + -
12D ALA* 5.8 0.3 - - - +
16D VAL* 3.7 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LEU* 4.3 12.1 - - + -
92C GLN 3.2 9.9 + - - +
93C GLN* 3.2 15.1 + - - +
95C MET* 1.3 79.0 - - - +
97C ASP* 1.3 67.5 + - - +
98C HIS 3.4 0.7 + - - -
99C HIS* 3.4 12.3 + - - -
8D PRO* 4.4 23.8 - - + +
12D ALA* 4.0 32.7 - - + +
13D ARG* 3.6 34.8 - - + +
16D VAL* 3.7 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C GLN* 2.7 46.8 + - - +
94C ALA* 2.9 9.8 + - - +
96C ILE* 1.3 79.5 - - - +
98C HIS* 1.3 73.3 + - + +
99C HIS* 3.5 13.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ALA* 2.9 19.4 + - - +
97C ASP* 1.3 87.6 - - + +
99C HIS* 1.3 77.4 + - - +
100C GLY 3.3 2.5 + - - +
141C PRO* 3.4 28.8 - - - +
144C ARG* 3.5 35.9 + - + +
145C ALA* 4.2 9.9 - - + +
148C ALA* 3.6 28.5 - - + +
----------------------------------------------------------
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