Contacts of the strand formed by residues 152 - 160 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10Q VAL* 3.5 2.8 - - - -
11Q PHE* 2.7 48.5 + - - +
40Q TYR 3.5 10.1 - - - -
150Q PHE* 3.4 7.7 - - - -
151Q VAL* 1.3 76.6 - - - +
153Q GLU* 1.3 62.0 + - - -
115R VAL* 3.6 15.9 - - - -
116R LYS 4.8 2.5 - - - -
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Residues in contact with GLU 153 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Q VAL* 3.4 19.2 - - + +
9Q PHE 3.3 6.1 - - - +
10Q VAL* 4.2 15.3 - - + -
39Q ALA* 3.2 5.2 - - - -
40Q TYR* 2.8 39.5 + - - +
150Q PHE* 3.4 2.6 - - - -
152Q GLY* 1.3 78.9 - - - +
154Q ILE* 1.3 65.2 + - - +
200Q PRO 4.9 0.7 - - - +
203Q TRP* 2.8 45.7 + - + +
114R LEU 4.1 1.9 - - - +
115R VAL* 3.8 6.4 - - - -
116R LYS* 3.0 48.8 + - - +
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Residues in contact with ILE 154 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Q VAL* 3.4 4.3 - - - -
9Q PHE* 2.9 32.1 + - + +
11Q PHE* 4.1 16.8 - - + -
37Q PHE* 4.4 9.6 - - + -
38Q ARG 3.2 11.7 - - - +
39Q ALA* 4.4 5.2 - - + -
49Q LEU* 4.1 22.9 - - + +
133Q LEU* 4.1 17.5 - - + -
134Q GLY 5.1 0.4 - - - +
150Q PHE* 3.4 40.8 - - + -
153Q GLU* 1.3 73.8 - - - +
155Q GLY* 1.3 65.4 + - - +
157Q LEU* 4.3 23.3 - - + -
185Q TRP* 3.7 7.4 - - + -
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Residues in contact with GLY 155 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Q LYS 4.0 1.1 - - - -
8Q VAL* 3.8 16.0 - - - +
37Q PHE* 3.7 3.5 - - - +
38Q ARG* 2.8 35.8 + - - +
154Q ILE* 1.3 75.2 - - - +
156Q ASP* 1.3 67.5 + - - -
157Q LEU 3.3 3.4 + - - -
185Q TRP* 3.5 15.5 - - - -
201Q LEU* 6.0 0.9 - - - -
203Q TRP* 4.9 0.4 - - - -
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Residues in contact with ASP 156 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Q SER* 5.8 0.2 - - - -
6Q GLY* 5.1 5.9 + - - -
7Q LYS 5.2 1.0 + - - +
36Q CYS* 3.3 2.8 - - - +
37Q PHE* 3.3 14.4 - - - -
38Q ARG* 2.6 45.5 + - + +
93Q HIS* 5.2 3.4 + - + +
155Q GLY* 1.3 73.4 - - - +
157Q LEU* 1.3 58.5 + - - +
158Q TYR* 3.3 28.4 + - + -
172Q ALA 5.9 0.2 - - - +
175Q GLY* 5.8 1.5 - - - -
185Q TRP* 3.4 28.6 + - - +
201Q LEU* 4.2 14.9 - - - +
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Residues in contact with LEU 157 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22Q LEU* 4.3 9.2 - - + -
35Q LEU* 3.6 22.4 - - + -
36Q CYS 3.3 4.9 - - - -
37Q PHE* 3.8 26.2 - - + -
49Q LEU 5.6 1.1 - - - +
50Q PHE* 4.1 19.7 - - + -
133Q LEU* 4.2 19.1 - - + -
154Q ILE* 4.3 6.5 - - + -
155Q GLY 4.5 1.3 - - - +
156Q ASP* 1.3 75.1 - - - +
158Q TYR* 1.3 66.2 + - - +
183Q LEU* 4.2 22.8 - - + +
184Q ASP* 4.0 2.9 + - - -
185Q TRP* 3.1 50.4 + - + +
188Q LEU* 4.8 2.4 - - + +
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Residues in contact with TYR 158 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Q LEU* 3.4 5.0 - - - +
36Q CYS* 2.8 37.0 + - + +
156Q ASP* 3.3 36.7 + - + -
157Q LEU* 1.3 77.2 - - - +
159Q MET* 1.3 59.8 + - - +
160Q TRP* 3.4 27.9 - + + -
172Q ALA* 5.8 1.6 - - + -
177Q PRO* 3.6 33.1 - - + +
178Q LEU 4.9 2.7 - - - -
179Q PRO* 6.4 0.7 - - + -
180Q ALA* 4.0 11.0 - - + -
183Q LEU 3.4 4.7 - - - -
184Q ASP* 3.2 30.1 - - - -
185Q TRP* 3.6 18.3 - - + +
186Q GLN* 3.1 30.4 + - - +
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Residues in contact with MET 159 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Q LEU* 4.1 12.3 - - + -
33Q PHE* 3.8 23.8 - - + -
34Q THR 3.2 12.3 - - - +
35Q LEU* 3.9 12.6 - - + -
50Q PHE* 3.9 26.7 - - + -
52Q TYR* 4.9 3.8 - - + -
61Q LEU* 3.7 30.3 - - + -
131Q ILE* 5.3 3.1 - - - -
158Q TYR* 1.3 74.9 - - - +
160Q TRP* 1.3 62.7 + - - +
180Q ALA* 3.4 7.0 - - - +
182Q ILE* 3.0 48.8 + - + -
183Q LEU* 2.9 29.5 + - + +
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Residues in contact with TRP 160 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Q PHE* 3.1 8.8 - - - +
34Q THR* 2.8 51.4 + - - +
36Q CYS* 3.7 25.1 - - + -
158Q TYR* 3.4 34.8 - + + -
159Q MET* 1.3 77.1 - - - +
161Q ASP* 1.3 60.0 + - - +
162Q SER* 3.1 19.5 - - - +
164Q LEU* 3.6 42.8 - - + -
172Q ALA* 4.4 9.9 - - + -
177Q PRO* 4.3 3.8 - - + -
178Q LEU* 3.1 38.2 + - + +
179Q PRO 3.0 28.7 + - - -
180Q ALA* 3.6 7.6 - - + -
181Q ASN* 3.6 7.4 - - - +
182Q ILE* 3.5 5.5 - - - +
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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