Contacts of the strand formed by residues 152 - 160 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10F VAL* 3.5 1.5 - - - -
11F PHE* 2.7 46.3 + - - +
40F TYR 3.4 9.9 - - - -
150F PHE* 3.4 6.8 - - - -
151F VAL* 1.3 75.1 - - - +
153F GLU* 1.3 63.7 + - - -
115G VAL* 3.5 17.3 - - - -
116G LYS 4.7 1.6 - - - -
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Residues in contact with GLU 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F VAL* 3.4 18.0 - - + +
9F PHE 3.3 5.8 - - - +
10F VAL* 4.0 13.9 - - + -
39F ALA* 3.3 5.4 - - - -
40F TYR* 2.9 36.2 + - - +
150F PHE* 3.5 2.0 - - - -
152F GLY* 1.3 81.1 - - - +
154F ILE* 1.3 65.4 + - - +
200F PRO 4.9 0.7 - - - +
202F VAL* 5.7 0.2 - - - +
203F TRP* 2.7 47.9 + - + +
114G LEU 4.2 1.9 - - - +
115G VAL* 3.9 5.6 - - + -
116G LYS* 3.0 50.0 + - - +
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Residues in contact with ILE 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F VAL* 3.3 4.9 - - - -
9F PHE* 2.8 39.8 + - + +
11F PHE* 4.1 10.3 - - + -
37F PHE* 4.6 13.9 - - + -
38F ARG 3.3 11.4 - - - +
39F ALA* 4.4 6.1 - - + -
49F LEU* 4.1 16.8 - - + +
133F LEU* 4.0 37.5 - - + -
134F GLY 5.0 0.9 - - - +
150F PHE* 3.5 35.4 - - + -
153F GLU* 1.3 78.3 - - - +
155F GLY* 1.3 68.2 + - - +
157F LEU* 4.8 8.1 - - + -
185F TRP* 3.7 6.1 - - + -
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Residues in contact with GLY 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F LYS 4.1 0.9 - - - -
8F VAL* 3.9 15.0 - - - +
37F PHE* 3.6 3.3 - - - +
38F ARG* 2.8 38.2 + - - +
154F ILE* 1.3 76.1 - - - +
156F ASP* 1.3 64.9 + - - -
157F LEU* 3.1 4.5 + - - -
185F TRP* 3.5 15.0 - - - -
201F LEU* 5.9 0.9 - - - -
203F TRP* 4.9 0.2 - - - -
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Residues in contact with ASP 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F SER* 5.6 0.3 - - - -
6F GLY 5.1 6.2 + - - -
7F LYS 5.2 0.9 - - - +
36F CYS* 3.3 9.2 - - - +
37F PHE* 3.4 6.8 - - - -
38F ARG* 2.8 42.9 + - + +
93F HIS* 5.2 3.7 + - + +
155F GLY* 1.3 73.0 - - - +
157F LEU* 1.3 57.6 + - - +
158F TYR* 3.2 28.6 + - + -
172F ALA 6.0 0.9 - - - +
175F GLY* 5.8 1.4 - - - -
185F TRP* 3.4 29.7 + - - +
201F LEU* 4.2 15.1 - - - +
204F VAL* 5.9 0.3 - - - +
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Residues in contact with LEU 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F LEU* 4.3 9.0 - - + -
35F LEU* 3.9 17.3 - - + -
36F CYS 3.2 5.8 - - - -
37F PHE* 3.8 24.2 - - + -
49F LEU 6.0 0.2 - - - +
50F PHE* 3.9 25.4 - - + -
133F LEU* 4.4 15.0 - - + -
154F ILE* 4.8 4.5 - - + -
155F GLY 3.1 1.7 + - - +
156F ASP* 1.3 74.1 - - - +
158F TYR* 1.3 67.6 + - - +
183F LEU* 4.0 29.6 - - + -
184F ASP 3.9 1.4 - - - -
185F TRP* 3.1 50.9 + - + +
188F LEU* 5.1 2.2 - - + +
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Residues in contact with TYR 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F LEU* 3.4 4.9 - - - +
36F CYS* 2.7 40.7 + - + +
156F ASP* 3.2 44.5 + - + -
157F LEU* 1.3 75.2 - - - +
159F MET* 1.3 61.6 + - - +
160F TRP* 3.3 27.9 - + + -
172F ALA* 5.9 0.9 - - + -
177F PRO* 3.6 31.7 - - + +
178F LEU 4.7 4.7 - - - -
179F PRO* 6.0 0.2 - - + -
180F ALA* 4.0 6.1 - - + -
183F LEU 3.4 3.6 - - - -
184F ASP* 3.6 25.8 - - - -
185F TRP* 3.5 35.7 - - + +
186F GLN* 3.1 28.5 + - - +
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Residues in contact with MET 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F LEU* 3.9 21.3 - - + -
33F PHE* 4.1 13.7 - - + -
34F THR 3.2 12.8 - - - +
35F LEU* 4.1 12.6 - - + -
50F PHE* 4.0 23.6 - - + -
52F TYR* 4.5 6.7 - - + -
61F LEU* 3.7 30.1 - - + -
131F ILE* 5.2 3.4 - - - -
158F TYR* 1.3 74.8 - - - +
160F TRP* 1.3 62.3 + - - +
180F ALA* 3.3 6.7 - - - +
182F ILE* 3.1 47.2 + - + -
183F LEU* 2.9 28.6 + - + +
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Residues in contact with TRP 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F PHE* 3.2 8.1 - - - +
34F THR* 2.8 39.6 + - - +
36F CYS* 3.6 33.2 - - + -
158F TYR* 3.3 33.4 - + + -
159F MET* 1.3 74.8 - - - +
161F ASP* 1.3 60.1 + - - +
162F SER* 3.2 18.2 - - - +
164F LEU* 3.5 39.7 - - + +
168F ASN 5.8 0.2 - - - -
172F ALA* 4.4 9.4 - - + -
177F PRO* 4.2 8.3 - - + -
178F LEU* 3.1 40.2 + - + +
179F PRO 3.2 18.6 + - - -
180F ALA* 3.4 14.0 - - + +
181F ASN* 3.5 9.0 - - - +
182F ILE* 3.5 5.7 - - - +
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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