Contacts of the strand formed by residues 232 - 238 (chain A) in PDB entry 1PZN
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 VAL 232 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A SER* 3.7 11.0 - - - +
169A ILE* 3.6 31.0 - - + +
221A LYS 4.5 0.2 - - - +
222A ILE* 3.8 37.5 + - + +
225A LEU* 4.2 23.7 + - + -
226A LEU* 5.5 0.4 - - - +
231A PRO* 1.3 75.8 - - - +
233A LYS* 1.3 74.3 + - - +
234A LEU 3.8 17.7 - - - +
235A LEU* 5.3 0.4 - - + -
275A TYR 4.4 1.7 - - - +
277A ILE* 3.5 28.0 - - + +
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Residues in contact with LYS 233 (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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113A ILE* 5.1 0.2 - - - +
130A THR* 4.5 2.1 - - - +
155A VAL* 3.6 22.1 - - + +
164A LEU* 3.5 36.4 - - + +
165A ASN 4.9 0.4 - - - +
166A GLY* 3.6 21.8 - - - -
167A SER 3.1 5.1 + - - -
231A PRO* 3.8 14.8 - - + +
232A VAL* 1.3 87.1 - - - +
234A LEU* 1.3 60.6 - - - +
275A TYR 4.2 4.0 + - - -
276A ASP* 2.9 49.5 + - - +
277A ILE* 3.8 4.6 - - - +
278A ALA* 2.8 32.6 + - - +
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Residues in contact with LEU 234 (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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113A ILE* 5.2 2.5 - - + -
128A ILE* 4.0 24.5 - - + -
151A LEU* 3.3 44.6 - - + +
152A ALA* 3.7 9.6 - - - +
155A VAL* 4.1 11.9 - - + -
167A SER 3.4 2.6 + - - -
168A VAL* 3.3 18.0 - - + +
169A ILE 2.9 24.4 + - - -
232A VAL* 3.8 3.4 - - - +
233A LYS* 1.3 82.5 - - - +
235A LEU* 1.3 61.0 + - - +
236A ILE* 4.0 16.2 - - + -
277A ILE* 4.2 1.1 - - - -
278A ALA* 3.3 18.2 - - + +
280A PHE* 4.2 14.6 - - + -
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Residues in contact with LEU 235 (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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169A ILE* 3.2 23.1 - - + +
171A ILE* 4.8 7.6 - - + -
215A VAL* 6.1 1.1 - - + -
218A ALA* 4.5 5.4 - - + -
222A ILE* 4.2 15.9 - - + -
232A VAL* 5.3 1.1 - - + -
234A LEU* 1.3 75.3 - - - +
236A ILE* 1.3 67.5 + - - +
237A VAL* 3.8 24.9 - - + -
268A LEU* 4.2 15.5 - - + -
271A LEU* 3.9 29.2 - - + -
277A ILE* 3.9 14.3 - - + +
278A ALA 2.9 9.0 + - - +
279A VAL* 3.4 12.8 - - + +
280A PHE 2.9 26.5 + - - +
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Residues in contact with ILE 236 (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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148A ALA* 3.5 27.1 - - + +
152A ALA* 4.4 2.0 - - + -
168A VAL* 4.6 2.2 - - + -
169A ILE 2.8 12.2 + - - +
170A TRP* 3.4 51.1 - - + +
171A ILE* 2.8 28.1 + - - +
234A LEU* 4.0 27.6 - - + -
235A LEU* 1.3 79.5 - - - +
237A VAL* 1.3 70.0 + - - +
238A ASP* 3.9 23.1 - - + +
280A PHE* 3.3 16.6 - - + +
282A THR* 5.8 0.4 - - + -
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Residues in contact with VAL 237 (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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171A ILE* 3.6 20.6 - - + +
211A GLN* 3.9 17.9 - - - +
215A VAL* 5.8 0.9 - - + -
235A LEU* 3.8 18.2 - - + -
236A ILE* 1.3 81.0 - - - +
238A ASP* 1.3 60.1 + - - +
239A SER 4.0 3.1 - - - +
240A LEU* 3.5 30.3 + - + -
264A HIS* 4.6 4.9 - - + +
268A LEU* 4.3 21.1 - - + -
279A VAL* 5.4 0.2 - - + -
280A PHE 2.9 9.1 + - - -
281A VAL* 3.3 14.0 - - + -
282A THR 3.1 24.1 + - - -
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Residues in contact with ASP 238 (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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144A LYS* 5.5 0.2 - - - +
145A THR* 3.2 40.3 + - - +
148A ALA* 4.7 0.6 - - - +
170A TRP* 4.3 11.6 + - + +
171A ILE 3.1 7.6 + - - -
172A ASP* 3.1 14.6 - - - +
173A THR* 2.9 24.1 + - - -
174A GLU* 3.9 5.7 + - - +
176A THR* 3.5 10.1 + - - -
236A ILE* 3.9 15.9 - - + -
237A VAL* 1.3 75.5 - - - +
239A SER* 1.3 54.8 + - - +
282A THR* 2.4 36.9 + - + +
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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