Contacts of the strand formed by residues 152 - 160 (chain R) in PDB entry 2A3W
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 GLY 152 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10R VAL* 3.6 2.1 - - - -
11R PHE* 2.8 40.1 + - - -
40R TYR 3.2 11.4 - - - -
150R PHE* 3.5 7.5 - - - -
151R VAL* 1.3 75.9 - - - +
153R GLU* 1.3 63.6 + - - -
115S VAL* 3.5 16.2 - - - -
116S LYS 4.8 2.0 - - - -
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Residues in contact with GLU 153 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8R VAL* 3.3 19.5 - - + +
9R PHE 3.2 7.6 - - - +
10R VAL* 3.9 16.8 - - + -
39R ALA* 3.3 4.3 - - - -
40R TYR* 2.8 42.1 + - - +
150R PHE* 3.6 1.7 - - - -
152R GLY* 1.3 79.7 - - - +
154R ILE* 1.3 63.4 + - - +
200R PRO 4.9 0.5 - - - +
203R TRP* 2.8 46.3 + - + +
114S LEU 4.3 1.7 - - - +
115S VAL* 4.0 5.7 - - - -
116S LYS* 3.2 48.8 + - + +
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Residues in contact with ILE 154 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8R VAL* 3.4 4.5 - - - -
9R PHE* 2.8 37.5 + - + -
11R PHE* 4.3 13.9 - - + -
37R PHE* 4.5 15.3 - - + -
38R ARG 3.3 11.4 - - - +
39R ALA* 4.3 6.5 - - + -
49R LEU* 4.1 25.1 - - + +
133R LEU* 4.3 18.8 - - + -
134R GLY 5.2 0.7 - - - +
150R PHE* 3.5 41.0 - - + -
153R GLU* 1.3 75.0 - - - +
155R GLY* 1.3 67.0 + - - +
157R LEU* 4.6 14.4 - - + -
185R TRP* 3.7 7.1 - - + -
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Residues in contact with GLY 155 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7R LYS 4.1 1.3 - - - -
8R VAL* 3.9 15.6 - - - +
37R PHE* 3.7 2.8 - - - +
38R ARG* 2.8 38.4 + - - +
153R GLU 4.5 0.2 + - - -
154R ILE* 1.3 75.0 - - - +
156R ASP* 1.3 66.9 + - - -
157R LEU* 3.3 4.0 + - - -
185R TRP* 3.5 13.9 - - - -
201R LEU* 6.0 1.6 - - - -
203R TRP* 4.8 0.6 - - - -
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Residues in contact with ASP 156 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5R SER* 5.5 0.5 - - - -
6R GLY 4.9 6.9 + - - -
7R LYS 4.6 0.9 + - - +
36R CYS* 3.4 2.4 - - - +
37R PHE* 3.3 13.9 - - - -
38R ARG* 2.8 42.8 + - + +
93R HIS* 5.4 3.7 + - + -
155R GLY* 1.3 71.2 - - - +
157R LEU* 1.3 59.3 + - - +
158R TYR* 3.3 27.3 + - + -
172R ALA 6.0 0.7 - - - +
185R TRP* 3.3 29.1 + - - +
201R LEU* 3.9 18.3 - - - +
204R VAL* 5.9 0.2 - - - +
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Residues in contact with LEU 157 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22R LEU* 4.5 10.3 - - + -
35R LEU* 3.7 20.6 - - + -
36R CYS 3.3 4.7 - - - -
37R PHE* 3.5 37.5 - - + -
49R LEU 5.8 0.7 - - - +
50R PHE* 4.1 14.1 - - + -
133R LEU* 4.6 9.0 - - + -
154R ILE* 4.6 9.9 - - + -
155R GLY 3.3 2.0 + - - +
156R ASP* 1.3 73.7 - - - +
158R TYR* 1.3 67.0 + - - +
183R LEU* 3.9 29.2 - - + -
184R ASP* 3.9 2.1 + - - -
185R TRP* 3.1 51.8 + - + +
188R LEU* 4.8 1.9 - - + +
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Residues in contact with TYR 158 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35R LEU* 3.4 5.5 - - - +
36R CYS* 2.7 40.2 + - + +
156R ASP* 3.3 37.0 + - + -
157R LEU* 1.3 74.5 - - - +
159R MET* 1.3 60.9 + - - +
160R TRP* 3.4 27.9 - + + -
172R ALA* 5.9 0.9 - - + -
177R PRO* 3.6 32.8 - - + +
178R LEU 4.6 5.6 - - - -
180R ALA* 4.1 5.4 - - + -
183R LEU 3.4 6.1 - - - +
184R ASP* 3.5 33.4 - - - -
185R TRP* 3.6 25.7 - - + +
186R GLN* 3.1 26.1 + - - +
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Residues in contact with MET 159 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30R LEU* 3.7 29.4 - - + -
33R PHE* 4.1 11.7 - - + -
34R THR 3.2 13.5 - - - +
35R LEU* 3.9 12.8 - - + -
50R PHE* 3.8 26.9 - - + -
52R TYR* 4.5 5.8 - - + -
61R LEU* 3.8 22.7 - - + -
131R ILE* 5.1 2.2 - - - -
158R TYR* 1.3 74.2 - - - +
160R TRP* 1.3 62.4 + - - +
180R ALA* 3.4 6.5 - - - +
182R ILE* 3.0 46.8 + - + -
183R LEU* 2.9 31.1 + - + +
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Residues in contact with TRP 160 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33R PHE* 3.2 9.2 - - - +
34R THR* 2.8 51.0 + - - +
36R CYS* 3.7 31.2 - - + -
158R TYR* 3.4 34.5 - + + -
159R MET* 1.3 75.9 - - - +
161R ASP* 1.3 59.8 + - - +
162R SER* 3.2 13.7 - - - +
164R LEU* 3.5 45.0 - - + +
168R ASN 5.9 0.2 - - - -
172R ALA* 4.4 9.0 - - + -
177R PRO* 4.4 3.6 - - + -
178R LEU* 3.4 38.8 + - + +
179R PRO 3.3 25.8 + - - -
180R ALA* 3.6 9.6 - - + +
181R ASN* 3.4 8.5 - - - +
182R ILE* 3.5 6.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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