Contacts of the strand formed by residues 178 - 183 (chain A) in PDB entry 2PWA
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 CYS 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A GLN* 5.0 0.2 + - - -
154A MET* 3.7 15.3 - - + -
155A VAL 2.9 19.1 + - - +
156A ALA* 3.3 4.4 - - + -
157A VAL* 2.8 28.6 + - - +
177A VAL* 1.3 70.8 - - - +
179A THR* 1.3 61.7 + - - +
180A VAL* 3.6 2.4 - - - +
200A ASP* 4.0 6.3 - - - -
201A ILE* 4.0 16.8 - - - -
230A VAL* 4.2 7.6 - - - -
249A CYS* 2.0 53.2 - - + -
252A ILE* 5.6 1.1 - - - -
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Residues in contact with THR 179 (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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157A VAL* 3.5 10.7 - - - +
159A ALA* 3.9 27.6 - - + +
172A ALA* 2.7 36.0 + - + +
174A GLU 4.1 3.6 + - - -
177A VAL* 4.1 6.9 - - - +
178A CYS* 1.3 70.6 - - - +
180A VAL* 1.3 61.6 + - - +
198A VAL* 3.6 18.1 + - + +
199A LEU* 3.7 14.8 - - + -
200A ASP* 2.8 35.2 + - - +
201A ILE* 3.4 8.7 + - - +
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Residues in contact with VAL 180 (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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156A ALA* 4.5 4.3 - - + -
157A VAL 2.9 14.7 + - - +
158A ALA* 3.8 0.5 - - - -
159A ALA* 2.9 26.9 + - - +
178A CYS 3.6 13.5 - - - +
179A THR* 1.3 76.4 - - - +
181A GLY* 1.3 74.2 + - - +
201A ILE* 3.3 17.3 - - + +
203A GLY 4.0 4.5 - - - +
223A THR* 3.8 7.1 - - - -
226A ALA* 3.7 26.2 - - + +
227A THR* 3.8 11.4 - - - +
230A VAL* 3.7 31.2 - - + -
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Residues in contact with GLY 181 (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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159A ALA* 4.0 3.4 - - - -
180A VAL* 1.3 73.4 - - - +
182A ALA* 1.3 58.9 + - - -
193A SER* 3.5 11.7 - - - -
199A LEU* 3.8 15.5 - - - +
201A ILE 2.9 10.7 + - - -
202A PHE* 3.4 16.6 - - - -
203A GLY 2.9 23.7 + - - -
223A THR* 4.2 1.1 - - - -
226A ALA* 3.3 8.7 - - - +
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Residues in contact with ALA 182 (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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181A GLY* 1.3 73.3 - - - -
183A SER* 1.3 54.3 + - - +
189A ARG 3.7 0.7 - - - -
190A SER* 2.8 43.7 + - - +
192A PHE* 3.8 17.3 - - + -
193A SER* 3.0 11.9 + - - +
202A PHE* 3.5 11.9 - - - -
203A GLY 3.3 4.5 - - - -
205A GLY* 3.8 15.7 - - - -
222A GLY 4.0 3.4 - - - +
223A THR* 3.8 10.7 - - + +
226A ALA* 3.9 2.2 - - + -
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Residues in contact with SER 183 (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 TRP* 3.5 5.2 - - - -
12A ARG* 5.8 0.2 - - - +
182A ALA* 1.3 74.1 - - - +
184A ASP* 1.3 65.1 + - - +
187A ASP* 5.1 0.6 + - - -
188A ARG 3.2 13.5 - - - -
190A SER* 3.1 7.0 - - - -
202A PHE* 4.8 0.7 - - - -
203A GLY 2.9 16.3 + - - -
204A PRO* 3.7 4.0 - - - +
205A GLY 2.8 22.9 + - - -
206A THR 3.2 5.9 + - - -
261A LEU* 3.8 27.8 - - - -
272A LEU* 3.5 19.6 - - - +
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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