Contacts of the strand formed by residues 152 - 160 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A VAL* 3.6 1.4 - - - -
11A PHE* 2.8 41.7 + - - +
40A TYR 3.4 10.5 - - - -
150A PHE* 3.4 7.5 - - - -
151A VAL* 1.3 75.3 - - - +
153A GLU* 1.3 62.9 + - - -
115B VAL* 3.6 16.8 - - - -
116B LYS 4.6 2.0 - - - -
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Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 3.4 18.4 - - + +
9A PHE 3.2 7.2 - - - +
10A VAL* 4.0 15.7 - - + -
39A ALA* 3.2 4.9 - - - -
40A TYR* 2.8 42.0 + - - +
150A PHE* 3.6 2.2 - - - -
152A GLY* 1.3 80.9 - - - +
154A ILE* 1.3 63.2 + - - +
200A PRO 5.0 0.2 - - - +
203A TRP* 2.8 44.5 + - + +
114B LEU 4.2 2.1 - - - +
115B VAL* 3.9 5.9 - - - -
116B LYS* 3.0 50.1 + - + +
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Residues in contact with ILE 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 3.3 5.4 - - - -
9A PHE* 2.8 33.0 + - + -
11A PHE* 4.3 15.7 - - + -
37A PHE* 4.7 14.1 - - + -
38A ARG 3.3 8.5 - - - +
39A ALA* 4.2 9.4 - - + -
49A LEU* 4.0 26.7 - - + +
133A LEU* 4.3 23.8 - - + -
134A GLY 5.3 0.4 - - - +
150A PHE* 3.4 40.6 - - + -
153A GLU* 1.3 74.3 - - - +
155A GLY* 1.3 66.2 + - - +
157A LEU* 4.7 7.0 - - + -
185A TRP* 3.6 7.9 - - + -
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Residues in contact with GLY 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LYS 4.1 1.1 - - - -
8A VAL* 4.0 13.7 - - - +
37A PHE* 3.6 3.6 - - - +
38A ARG* 2.8 38.6 + - - +
154A ILE* 1.3 76.0 - - - +
156A ASP* 1.3 66.0 + - - -
157A LEU* 3.2 4.0 + - - -
185A TRP* 3.5 14.4 - - - -
201A LEU* 6.0 1.3 - - - -
203A TRP* 4.8 0.8 - - - -
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Residues in contact with ASP 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A SER* 5.5 0.5 - - - -
6A GLY 5.0 6.4 + - - -
7A LYS 5.1 0.9 - - - +
36A CYS* 3.3 4.7 - - - +
37A PHE* 3.2 14.4 - - - -
38A ARG* 2.7 41.8 + - + +
93A HIS* 5.2 4.1 + - + +
155A GLY* 1.3 72.2 - - - +
157A LEU* 1.3 59.5 + - - +
158A TYR* 3.3 25.1 + - + -
185A TRP* 3.4 28.0 + - - +
201A LEU* 3.9 17.7 - - - +
204A VAL* 5.4 0.5 - - - +
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 4.5 8.7 - - + -
35A LEU* 3.7 20.4 - - + -
36A CYS 3.2 4.7 - - - -
37A PHE* 3.7 33.4 - - + -
49A LEU 5.9 0.2 - - - +
50A PHE* 4.1 13.9 - - + -
133A LEU* 4.4 12.1 - - + -
154A ILE* 4.7 7.2 - - + -
155A GLY 3.3 1.3 - - - +
156A ASP* 1.3 74.3 - - - +
158A TYR* 1.3 63.1 + - - +
183A LEU* 3.9 31.6 - - + -
184A ASP* 3.9 1.7 + - - -
185A TRP* 3.0 53.4 + - + +
188A LEU* 4.9 3.0 - - + +
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Residues in contact with TYR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A SER* 6.0 0.2 - - - -
35A LEU* 3.4 3.6 - - - +
36A CYS* 2.8 37.0 + - + +
156A ASP* 3.3 36.6 + - + -
157A LEU* 1.3 77.4 - - - +
159A MET* 1.3 61.6 + - - +
160A TRP* 3.4 24.7 - + + -
172A ALA* 5.9 0.7 - - + -
177A PRO* 3.5 34.4 - - + +
178A LEU 4.9 2.7 - - - -
180A ALA* 4.0 5.4 - - + -
183A LEU 3.4 4.0 - - - -
184A ASP* 3.5 32.5 - - - -
185A TRP* 3.6 20.9 - - + +
186A GLN* 2.8 33.3 + - - +
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Residues in contact with MET 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 3.8 29.2 - - + -
33A PHE* 4.0 15.0 - - + -
34A THR 3.2 13.2 - - - +
35A LEU* 4.0 11.4 - - + -
50A PHE* 3.9 26.0 - - + -
52A TYR* 4.7 7.4 - - + -
61A LEU* 3.8 21.1 - - + -
131A ILE* 5.5 0.4 - - - -
158A TYR* 1.3 76.6 - - - +
160A TRP* 1.3 62.9 + - - +
180A ALA* 3.4 6.4 - - - +
182A ILE* 3.0 46.9 + - + -
183A LEU* 2.9 29.2 + - + +
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Residues in contact with TRP 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PHE* 3.2 8.5 - - - +
34A THR* 2.8 40.0 + - - +
36A CYS* 3.6 24.9 - - + -
158A TYR* 3.4 36.3 - + + -
159A MET* 1.3 75.2 - - - +
161A ASP* 1.3 58.7 + - - +
162A SER* 3.2 14.1 - - - +
164A LEU* 3.6 48.7 - - + -
172A ALA* 4.5 3.4 - - + -
177A PRO* 4.1 9.0 - - + -
178A LEU* 2.9 46.4 + - + +
179A PRO 2.9 19.5 + - - -
180A ALA* 3.5 10.3 - - + -
181A ASN* 3.6 8.5 - - - +
182A ILE* 3.4 7.3 - - - +
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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