Contacts of the strand formed by residues 278 - 284 (chain D) 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 ALA 278 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113D ILE* 4.6 6.7 - - + -
128D ILE* 4.2 20.2 - - + -
129D GLU 3.2 27.4 - - - +
130D THR* 3.7 11.7 - - + +
132D ALA 4.0 0.2 - - - -
233D LYS 2.9 17.0 + - - +
234D LEU* 3.3 7.4 - - + +
235D LEU 2.9 25.1 + - - -
277D ILE* 1.3 73.6 - - - +
279D VAL* 1.3 59.4 + - - +
280D PHE 4.0 0.2 - - - -
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Residues in contact with VAL 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ILE* 5.4 1.3 - - - +
132D ALA 2.9 15.3 + - - +
133D ILE* 3.2 21.8 - - + -
134D THR* 2.7 35.4 + - - +
235D LEU* 3.4 24.2 - - + +
268D LEU* 4.1 28.3 - - + +
271D LEU* 5.4 0.7 - - + -
272D ALA* 3.8 26.5 - - + +
277D ILE* 4.4 3.4 - - + -
278D ALA* 1.3 75.0 - - - +
280D PHE* 1.3 57.9 + - - +
281D VAL* 4.0 18.4 - - + -
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Residues in contact with PHE 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ILE* 4.2 15.0 - - + -
134D THR* 3.5 24.5 - - + -
136D VAL* 3.5 36.8 - - + -
144D LYS 4.0 2.9 - - - -
147D LEU* 3.7 24.9 - - + -
148D ALA* 3.8 35.4 - - + -
151D LEU* 3.8 23.3 - - + -
234D LEU* 4.2 19.5 - - + -
235D LEU 2.9 9.2 + - - +
236D ILE* 3.2 14.4 - - + +
237D VAL 2.9 24.9 + - - +
278D ALA 4.0 1.0 + - - -
279D VAL* 1.3 71.6 - - - +
281D VAL* 1.3 62.3 + - - +
282D THR* 4.3 4.3 - - + -
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Residues in contact with VAL 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ILE* 4.1 12.3 - - + -
134D THR 2.9 9.1 + - - +
135D GLU* 3.6 27.8 - - + -
136D VAL* 2.9 29.6 + - - +
237D VAL* 3.3 25.1 - - + +
240D LEU* 3.9 31.0 - - + -
265D LEU* 5.9 0.2 - - + -
268D LEU* 4.3 8.1 - - + -
279D VAL* 4.0 19.7 - - + -
280D PHE* 1.3 80.5 - - - +
282D THR* 1.3 63.4 + - - +
306D ALA* 5.0 0.7 - - + -
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Residues in contact with THR 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D VAL* 3.3 22.4 - - + -
144D LYS* 3.8 33.4 - - + +
148D ALA* 5.1 1.1 - - + -
236D ILE* 5.8 0.2 - - + -
237D VAL 3.1 4.0 + - - -
238D ASP* 2.3 49.2 + - + +
239D SER* 3.3 6.6 + - - -
240D LEU* 3.0 29.6 + - - +
241D THR 4.0 0.2 + - - -
280D PHE* 4.3 8.1 - - + -
281D VAL* 1.3 76.5 - - - +
283D ASN* 1.3 64.8 + - - +
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Residues in contact with ASN 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D GLU* 3.2 22.6 - - + +
136D VAL 3.0 5.8 + - - +
137D PHE* 3.0 31.6 - - + +
138D GLY 3.4 2.8 + - - -
144D LYS* 3.5 3.1 - - - +
239D SER* 4.3 0.7 - - - -
240D LEU* 5.7 1.1 - - + -
241D THR* 2.5 39.4 + - + +
245D ARG* 3.7 6.7 - - - +
282D THR* 1.3 79.0 - - - +
284D GLN* 1.3 77.1 + - - +
285D VAL* 5.5 2.3 - - - +
304D ILE 3.2 4.4 - - - +
305D LEU* 3.2 30.8 - - - +
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Residues in contact with GLN 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D GLY 3.6 5.6 - - - +
140D PHE* 3.2 50.0 + - - +
144D LYS* 3.6 11.2 - - - +
174D GLU* 3.8 23.9 + - - +
239D SER* 4.5 6.5 + - - +
241D THR* 4.1 2.4 + - - -
245D ARG* 3.1 23.7 + - - +
283D ASN* 1.3 87.5 + - - +
285D VAL* 1.3 65.6 + - - +
286D GLN 5.9 2.9 - - - -
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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