Contacts of the strand formed by residues 142 - 149 (chain A) in PDB entry 2WA2
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 ASP 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A LYS* 3.3 45.7 + - + +
76A GLY* 3.5 6.3 - - - -
77A THR* 2.8 32.2 + - - -
140A GLN* 3.5 17.5 + - - +
141A ALA* 1.3 74.3 - - - +
143A THR* 1.3 61.0 + - - +
179A CYS* 3.4 7.0 - - - +
180A GLY* 3.0 21.5 + - - -
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Residues in contact with THR 143 (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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72A VAL* 4.0 9.0 - - + -
73A GLU 3.3 17.6 + - - +
74A LEU* 3.9 22.7 - - + -
75A LYS* 2.9 31.0 + - - +
77A THR 3.2 3.6 + - - +
78A VAL* 3.4 14.0 - - + -
79A VAL* 3.0 28.9 + - - +
141A ALA* 3.5 0.9 - - - +
142A ASP* 1.3 78.5 + - - +
144A VAL* 1.3 64.8 + - - +
145A LEU* 4.0 14.6 - - + -
180A GLY 3.4 7.0 - - - +
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Residues in contact with VAL 144 (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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79A VAL* 3.7 21.1 - - + -
81A LEU* 4.2 7.2 - - + -
141A ALA* 4.4 7.4 - - + -
143A THR* 1.3 74.3 - - - +
145A LEU* 1.3 63.5 + - - +
169A ILE* 3.9 29.4 - - + -
172A TRP* 4.3 25.6 - - + -
173A LEU* 4.4 5.2 - - + -
176A ASN* 4.6 2.7 - - - +
179A CYS* 4.0 20.6 - - - -
180A GLY 2.8 13.0 + - - +
181A PHE* 3.1 9.4 - - + +
182A CYS 3.0 25.5 + - - +
183A VAL* 4.6 1.2 - - + +
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Residues in contact with LEU 145 (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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63A LEU* 4.0 28.3 - - + -
72A VAL* 4.4 0.9 - - + -
74A LEU* 3.8 23.1 - - + -
78A VAL* 3.7 24.0 - - + -
79A VAL 2.9 16.5 + - - +
80A ASP* 4.1 8.7 - - + +
81A LEU* 2.9 28.3 + - - +
88A TRP* 3.8 20.4 - - + +
92A ALA* 4.4 7.4 - - + -
143A THR* 4.0 7.6 - - + -
144A VAL* 1.3 76.2 - - - +
146A CYS* 1.3 63.8 + - - +
182A CYS* 3.4 27.4 - - + +
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Residues in contact with CYS 146 (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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80A ASP* 4.9 0.4 - - - -
81A LEU* 3.4 19.3 - - + -
88A TRP* 3.8 4.1 - - - -
133A VAL* 5.6 0.4 - - - -
145A LEU* 1.3 77.6 - - - +
147A ASP* 1.3 62.9 + - - +
148A ILE* 3.5 22.0 - - - -
165A VAL* 3.8 26.7 - - - -
169A ILE* 3.6 26.0 - - + -
182A CYS 3.0 8.9 + - - +
183A VAL* 3.3 9.9 - - + -
184A LYS 2.8 26.5 + - - -
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Residues in contact with ASP 147 (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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59A GLY* 5.3 2.1 - - - -
62A LYS* 4.6 4.4 + - - -
80A ASP* 5.0 0.9 + - - +
81A LEU 3.3 7.9 + - - -
82A GLY 4.5 2.5 - - - +
88A TRP* 3.5 27.2 + - + -
146A CYS* 1.3 73.1 - - - +
148A ILE* 1.3 63.2 + - - +
149A GLY 3.8 1.0 + - - +
184A LYS* 3.3 19.4 + - - +
222A TYR* 2.9 28.8 + - - -
1248A SAM 2.8 65.0 + - + +
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Residues in contact with ILE 148 (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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82A GLY* 3.7 22.4 - - - -
133A VAL* 3.5 33.2 - - + -
134A THR* 5.7 2.0 - - + -
146A CYS* 3.5 20.1 + - - -
147A ASP* 1.3 78.0 - - - +
149A GLY* 1.3 61.6 + - - +
165A VAL* 3.7 30.5 - - + +
184A LYS* 3.8 21.7 - - - +
186A LEU* 5.1 1.9 + - - +
1248A SAM 3.7 35.4 - - + +
1249A SO4 3.5 21.3 - - - +
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Residues in contact with GLY 149 (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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147A ASP 3.8 2.1 + - - +
148A ILE* 1.3 80.2 - - - +
150A GLU* 1.3 61.1 + - - +
151A SER 3.9 0.7 + - - -
161A ARG* 5.8 2.7 - - - -
165A VAL* 5.7 0.9 - - - -
184A LYS* 2.8 29.8 + - - -
186A LEU* 4.0 21.9 - - - +
1248A SAM 5.1 2.9 - - - +
1249A SO4 3.4 11.3 + - - -
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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