Contacts of the strand formed by residues 371 - 380 (chain A) in PDB entry 1PCU
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 THR 371 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A CYS 3.7 9.6 - - - +
142A GLY* 4.0 1.3 - - - -
143A ARG* 3.3 29.1 + - + +
277A CYS* 3.6 31.6 - - - -
367A SER* 4.4 0.7 - - - -
368A PHE 2.9 33.5 + - - -
369A HIS 3.5 3.6 + - - -
370A GLY* 1.3 76.3 - - - +
372A TRP* 1.3 63.0 + - - +
373A PHE* 3.4 23.6 + - + -
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Residues in contact with TRP 372 (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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142A GLY* 3.2 44.6 + - - +
144A PRO* 3.8 12.7 - - + +
148A MET* 5.6 1.2 - - - +
149A GLU* 3.0 31.6 + - - -
154A HIS* 5.8 0.7 - + - -
158A ASP* 3.5 25.2 + - - -
161A ASP* 3.7 25.1 - - + -
180A ASP 5.6 0.8 + - - -
183A TRP* 3.8 19.3 - + + -
276A ILE* 4.4 6.2 - - - +
277A CYS 3.7 8.1 + - - -
296A LEU* 3.7 25.4 - - + -
365A VAL* 3.4 40.6 - - + -
366A ALA 3.6 3.8 - - - -
367A SER* 3.6 33.4 - - - -
370A GLY 4.3 0.9 - - - -
371A THR* 1.3 68.9 - - - +
373A PHE* 1.3 61.6 + - - +
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Residues in contact with PHE 373 (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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138A LYS* 5.9 0.9 - - - -
277A CYS* 3.6 25.1 - - + -
278A LEU 3.3 28.7 - - - -
279A PRO* 4.7 1.8 - - + -
280A ASP* 3.4 33.2 - - + -
283A LEU* 3.5 21.1 - - + +
365A VAL* 3.5 3.6 - - - -
366A ALA* 2.9 32.6 + - - +
368A PHE* 3.6 21.8 - + + -
371A THR* 3.4 37.6 + - + -
372A TRP* 1.3 72.6 - - - +
374A LEU* 1.3 61.3 + - - +
375A VAL 3.6 0.3 + - - -
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Residues in contact with LEU 374 (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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199A VAL* 4.8 0.9 - - + -
207A LEU* 3.9 12.1 - - + -
276A ILE* 3.5 35.3 - - + +
277A CYS 3.5 9.5 + - - +
279A PRO* 3.4 33.4 - - + +
283A LEU* 5.6 1.6 - - - -
363A PRO* 3.7 15.0 - - + -
364A MET 3.6 19.7 - - - +
365A VAL* 3.9 11.6 - - + +
372A TRP 4.4 0.4 + - - -
373A PHE* 1.3 71.6 - - - +
375A VAL* 1.3 59.3 + - - +
376A GLY 3.3 24.9 - - - +
377A LEU* 4.0 6.1 - - + -
396A VAL* 3.7 31.5 - - + +
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Residues in contact with VAL 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PRO* 5.6 0.4 - - - -
283A LEU* 4.2 9.2 - - + -
288A LEU* 3.6 37.2 - - + -
295A THR* 4.0 13.7 - - + +
325A VAL* 5.7 0.7 - - + -
344A LEU* 3.9 24.5 - - + -
364A MET* 2.9 21.2 + - + +
366A ALA* 3.8 28.9 - - + -
373A PHE 3.6 0.6 + - - -
374A LEU* 1.3 74.6 - - - +
376A GLY* 1.3 56.7 + - - +
393A TYR* 5.9 1.3 - - + -
395A LYS* 3.6 13.1 - - + +
396A VAL 2.9 19.1 + - - -
397A SER* 3.8 5.0 + - - -
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Residues in contact with GLY 376 (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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364A MET* 3.2 31.5 + - - +
374A LEU* 3.3 13.7 - - - +
375A VAL* 1.3 82.4 - - - +
377A LEU* 1.3 64.2 + - - +
393A TYR* 4.8 5.6 - - - -
394A THR 3.2 16.4 - - - -
395A LYS* 4.1 0.9 - - - -
396A VAL* 3.8 6.7 - - - -
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Residues in contact with LEU 377 (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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199A VAL* 3.7 20.0 - - + -
207A LEU* 4.0 21.1 - - + -
208A THR 3.5 28.7 - - - +
209A ALA 4.5 1.1 - - - +
258A ILE* 4.2 19.7 - - + -
361A GLY* 3.6 24.7 - - - +
362A GLY 3.4 4.5 - - - +
374A LEU* 4.0 12.1 - - + -
376A GLY* 1.3 82.8 - - - +
378A VAL* 1.3 63.6 + - - +
379A SER 3.2 0.9 + - - -
393A TYR* 3.3 9.7 - - - -
394A THR* 3.0 42.7 + - + +
396A VAL* 4.2 6.7 - - + -
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Residues in contact with VAL 378 (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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170A LEU* 5.3 0.4 - - + -
209A ALA* 3.6 8.4 - - - +
297A VAL* 3.9 15.3 - - + -
298A THR 4.7 2.0 - - - +
355A ALA* 3.8 18.4 - - + -
356A CYS 4.6 2.7 - - - +
359A ASP* 3.4 47.8 - - + +
360A SER* 3.5 12.9 - - - +
361A GLY 2.9 22.9 + - - +
362A GLY* 3.3 17.1 + - - +
377A LEU* 1.3 70.3 - - - +
379A SER* 1.3 61.5 + - - +
380A TRP* 5.2 0.7 - - - +
392A VAL 5.4 0.9 - - - +
393A TYR* 3.7 24.9 - - + +
394A THR* 5.1 0.2 - - - -
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Residues in contact with SER 379 (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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211A HIS* 3.1 26.4 + - - -
254A THR* 3.4 20.6 + - - +
257A ASP* 2.9 28.8 + - - +
343A MET* 5.9 2.0 - - - +
360A SER* 4.2 3.7 + - - -
377A LEU 3.2 0.8 + - - -
378A VAL* 1.3 76.0 - - - +
380A TRP* 1.3 69.5 + - - +
392A VAL* 3.0 19.7 + - - -
394A THR* 4.0 17.4 - - - -
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Residues in contact with TRP 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A THR 3.4 12.0 + - - -
254A THR* 3.7 18.6 - - + +
335A MET* 4.0 12.1 - - + -
338A MET* 3.7 33.7 - - + -
339A VAL* 3.8 20.4 - - + -
343A MET* 3.2 36.6 - - - +
355A ALA* 5.4 6.0 - - - +
378A VAL* 5.2 1.6 - - - +
379A SER* 1.3 95.3 - - - +
381A GLY* 1.3 62.3 + - - +
382A GLU* 3.5 33.9 - - + -
390A TYR 3.7 1.2 - - - +
391A GLY* 3.9 2.6 - - - -
392A VAL* 2.9 54.7 + - + +
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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