Contacts of the strand formed by residues 278 - 284 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113G ILE* 4.5 7.4 - - + -
128G ILE* 4.3 11.9 - - + -
129G GLU 3.4 20.4 - - - +
130G THR* 3.6 16.7 - - + +
132G ALA 4.1 0.4 - - - -
233G LYS 2.8 16.4 + - - +
234G LEU* 3.4 16.2 - - + +
235G LEU 2.9 24.9 + - - -
277G ILE* 1.3 72.6 - - - +
279G VAL* 1.3 59.5 + - - +
280G PHE 4.0 0.4 - - - -
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Residues in contact with VAL 279 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G ILE* 5.5 0.9 - - - -
132G ALA 2.9 15.4 + - - +
133G ILE* 3.3 20.5 - - + -
134G THR* 2.7 35.4 + - - +
235G LEU* 3.4 24.2 - - + +
268G LEU* 4.2 28.0 - - + +
271G LEU* 5.5 0.7 - - + -
272G ALA* 3.8 26.9 - - + +
277G ILE* 4.4 2.7 - - + -
278G ALA* 1.3 74.1 - - - +
280G PHE* 1.3 57.1 + - - +
281G VAL* 3.9 18.8 - - + -
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Residues in contact with PHE 280 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G ILE* 4.1 18.2 - - + -
134G THR* 3.5 20.4 - - + -
136G VAL* 3.5 38.1 - - + -
144G LYS 4.0 2.5 - - - -
147G LEU* 3.7 25.8 - - + -
148G ALA* 3.9 35.0 - - + -
151G LEU* 3.7 21.8 - - + -
234G LEU* 4.2 17.0 - - + -
235G LEU 2.8 11.6 + - - +
236G ILE* 3.2 14.9 - - + +
237G VAL 2.9 23.7 + - - +
278G ALA 3.9 0.6 + - - -
279G VAL* 1.3 72.2 - - - +
281G VAL* 1.3 64.1 + - - +
282G THR* 4.2 5.2 - - + -
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Residues in contact with VAL 281 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G ILE* 4.1 11.9 - - + -
134G THR 2.9 17.1 + - - +
135G GLU* 3.7 19.5 - - + -
136G VAL* 2.9 28.0 + - - +
237G VAL* 3.3 25.6 - - + +
240G LEU* 3.9 27.1 - - + -
268G LEU* 4.3 9.6 - - + -
279G VAL* 3.9 20.9 - - + -
280G PHE* 1.3 80.8 - - - +
282G THR* 1.3 64.0 + - - +
306G ALA* 5.0 1.1 - - + -
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Residues in contact with THR 282 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G VAL* 3.3 24.2 - - + -
144G LYS* 3.7 33.2 - - + +
148G ALA* 5.1 0.7 - - + -
237G VAL 3.1 4.4 + - - -
238G ASP* 2.3 50.1 + - + +
239G SER* 3.4 5.4 + - - -
240G LEU* 3.1 29.6 + - - +
280G PHE* 4.2 8.5 - - + -
281G VAL* 1.3 76.3 - - - +
283G ASN* 1.3 64.2 + - - +
284G GLN 4.3 0.2 - - - -
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Residues in contact with ASN 283 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G GLU* 3.3 29.1 - - + +
136G VAL 3.0 7.0 + - - +
137G PHE* 3.1 31.0 - - + +
138G GLY 3.3 2.6 + - - -
144G LYS* 3.3 3.3 - - - +
239G SER* 4.4 0.2 - - - -
240G LEU* 5.8 1.1 - - + -
241G THR* 2.5 40.1 + - + +
245G ARG* 2.9 17.6 - - - +
282G THR* 1.3 79.1 - - - +
284G GLN* 1.3 66.3 + - - +
285G VAL* 5.6 2.2 - - - -
303G HIS* 5.3 0.9 - - - -
304G ILE 3.0 23.4 + - - +
305G LEU* 4.0 1.2 - - - -
306G ALA* 5.8 0.2 - - - +
312G ARG* 4.9 0.9 + - - -
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Residues in contact with GLN 284 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138G GLY 3.5 10.5 - - - +
140G PHE* 3.1 44.9 + - - +
144G LYS* 3.6 12.3 - - - +
174G GLU* 3.7 23.5 + - - +
239G SER* 4.5 6.5 + - - +
241G THR* 4.1 2.0 + - - -
245G ARG* 2.9 32.0 + - - +
282G THR 4.3 0.4 - - - -
283G ASN* 1.3 77.7 + - - +
285G VAL* 1.3 64.7 + - - +
286G GLN 4.8 6.5 - - - +
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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