Contacts of the strand formed by residues 152 - 160 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115F VAL* 3.6 16.6 - - - -
116F LYS 4.8 1.3 - - - -
10J VAL* 3.6 1.9 - - - -
11J PHE* 2.8 42.5 + - - +
40J TYR 3.3 11.0 - - - -
150J PHE* 3.4 12.0 - - - -
151J VAL* 1.3 74.7 - - - +
153J GLU* 1.3 62.7 + - - -
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Residues in contact with GLU 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F LEU 4.2 1.6 - - - +
115F VAL* 3.9 6.1 - - - -
116F LYS* 3.0 50.0 + - + +
8J VAL* 3.5 17.8 - - + +
9J PHE 3.3 5.8 - - - +
10J VAL* 3.9 17.7 - - + -
39J ALA* 3.2 5.4 - - - -
40J TYR* 2.8 36.5 + - - +
150J PHE* 3.6 2.2 - - - -
152J GLY* 1.3 79.1 - - - +
154J ILE* 1.3 63.9 + - - +
200J PRO 4.9 0.3 - - - +
203J TRP* 2.7 46.1 + - + +
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Residues in contact with ILE 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J VAL* 3.4 4.6 - - - -
9J PHE* 2.8 33.9 + - + +
11J PHE* 4.0 16.6 - - + -
37J PHE* 4.5 15.9 - - + -
38J ARG 3.3 10.5 - - - +
39J ALA* 4.3 6.1 - - + -
49J LEU* 4.1 16.2 - - + +
133J LEU* 4.1 31.0 - - + -
134J GLY 5.1 1.1 - - - +
150J PHE* 3.5 40.4 - - + -
153J GLU* 1.3 74.5 - - - +
155J GLY* 1.3 67.6 + - - +
157J LEU* 4.6 9.2 - - + -
185J TRP* 3.7 6.2 - - + -
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Residues in contact with GLY 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J LYS 4.1 1.1 - - - -
8J VAL* 3.9 15.5 - - - +
37J PHE* 3.7 3.8 - - - +
38J ARG* 2.9 31.9 + - - +
153J GLU 4.4 0.2 - - - -
154J ILE* 1.3 75.9 - - - +
156J ASP* 1.3 71.8 + - - -
157J LEU 3.2 3.2 + - - -
185J TRP* 3.5 14.1 - - - -
201J LEU* 5.8 1.3 - - - -
203J TRP* 4.9 0.4 - - - -
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Residues in contact with ASP 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J SER* 5.6 0.3 - - - -
6J GLY 5.0 5.9 + - - -
7J LYS 4.6 1.2 + - - +
36J CYS* 3.4 1.9 - - - +
37J PHE* 3.2 15.5 + - - -
38J ARG* 2.7 41.4 + - + +
93J HIS* 5.1 4.1 + - + +
155J GLY* 1.3 72.1 - - - +
157J LEU* 1.3 60.0 + - - +
158J TYR* 3.3 27.5 + - + -
175J GLY* 5.7 2.1 - - - -
185J TRP* 3.3 29.5 + - - +
201J LEU* 4.2 15.9 - - - +
204J VAL* 5.1 0.2 - - - +
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Residues in contact with LEU 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J LEU* 4.2 9.6 - - + -
35J LEU* 3.7 16.8 - - + -
36J CYS 3.2 5.2 - - - -
37J PHE* 3.8 32.5 - - + -
50J PHE* 4.1 18.8 - - + -
133J LEU* 4.2 17.3 - - + -
154J ILE* 4.6 5.2 - - + -
155J GLY 3.2 1.5 + - - +
156J ASP* 1.3 74.3 - - - +
158J TYR* 1.3 63.3 + - - +
183J LEU* 3.9 31.2 - - + +
184J ASP 4.0 1.6 - - - -
185J TRP* 3.1 51.7 + - + +
188J LEU* 4.8 2.8 - - + +
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Residues in contact with TYR 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J SER* 5.3 0.3 + - - -
35J LEU* 3.4 4.7 - - - +
36J CYS* 2.8 37.8 + - + +
156J ASP* 3.3 36.9 + - + -
157J LEU* 1.3 74.8 - - - +
159J MET* 1.3 61.7 + - - +
160J TRP* 3.4 25.6 - + + -
172J ALA* 5.9 1.6 - - + -
177J PRO* 3.5 33.3 - - + +
178J LEU 4.8 2.7 - - - -
180J ALA* 4.0 7.2 - - + -
183J LEU 3.3 5.4 - - - +
184J ASP* 3.3 37.5 - - - -
185J TRP* 3.7 18.7 - - + +
186J GLN* 2.8 31.7 + - - +
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Residues in contact with MET 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J LEU* 4.0 13.0 - - + -
33J PHE* 3.8 24.5 - - + -
34J THR 3.2 13.2 - - - +
35J LEU* 4.0 11.7 - - + -
50J PHE* 4.0 25.4 - - + -
52J TYR* 4.9 3.6 - - + -
61J LEU* 3.7 30.3 - - + -
131J ILE* 5.3 3.1 - - - -
158J TYR* 1.3 75.7 - - - +
160J TRP* 1.3 64.5 + - - +
180J ALA* 3.4 6.6 - - - +
182J ILE* 3.0 45.7 + - + -
183J LEU* 2.9 31.7 + - + +
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Residues in contact with TRP 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J PHE* 3.2 8.5 - - - +
34J THR* 2.8 53.7 + - - +
36J CYS* 3.5 31.9 - - + -
158J TYR* 3.4 33.2 - + + -
159J MET* 1.3 75.1 - - - +
161J ASP* 1.3 59.8 + - - +
162J SER* 3.2 11.0 - - - +
164J LEU* 3.6 45.7 - - + +
172J ALA* 4.4 9.2 - - + -
177J PRO* 4.2 8.3 - - + -
178J LEU* 3.1 28.1 + - + +
179J PRO 3.0 28.3 + - - -
180J ALA* 3.4 12.0 - - + +
181J ASN* 3.5 9.6 - - - +
182J ILE* 3.6 6.2 - - - +
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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