Contacts of the strand formed by residues 371 - 380 (chain A) in PDB entry 1FCP
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 ASP 371 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365A PHE 3.9 3.4 - - - +
366A ALA* 3.5 18.9 - - - +
369A ASP 4.6 6.7 - - - +
370A ILE* 1.3 71.6 - - - +
372A HIS* 1.3 61.9 + - - +
373A THR* 4.7 1.0 + - - -
448A GLN 3.5 2.8 - - - +
449A ALA* 3.2 3.3 - - - -
450A GLN* 2.9 44.6 + - + +
452A ASP* 5.5 3.1 - - - +
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Residues in contact with HIS 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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364A LYS* 3.6 8.7 - - - -
365A PHE* 2.6 73.4 + + + +
367A THR* 4.0 13.9 - - + -
370A ILE* 3.0 44.7 - - + +
371A ASP* 1.3 75.1 - - - +
373A THR* 1.3 65.1 + - - +
374A LEU 3.9 1.1 - - - +
447A ASP* 3.4 20.2 + - - +
448A GLN 3.8 2.0 - - - -
449A ALA* 3.8 8.5 - - + +
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Residues in contact with THR 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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39A THR* 4.9 6.5 - - + +
362A GLN* 4.6 12.6 - - + -
363A SER 3.6 3.8 - - - -
364A LYS* 3.4 29.8 - - + -
371A ASP 4.7 1.0 + - - -
372A HIS* 1.3 75.6 + - - +
374A LEU* 1.3 60.5 + - - +
375A LEU* 3.7 3.0 + - + +
446A GLN 3.8 0.3 - - - +
447A ASP* 3.2 5.8 + - - -
448A GLN* 2.7 67.3 + - - +
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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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361A LEU 3.6 1.2 - - - +
362A GLN* 3.4 4.1 - - - +
363A SER* 2.6 60.6 + - - +
365A PHE* 4.3 21.1 - - + -
372A HIS 3.9 0.2 - - - -
373A THR* 1.3 73.2 - - - +
375A LEU* 1.3 58.4 + - - +
376A THR* 3.8 16.3 - - + +
445A VAL* 3.7 25.1 - - + -
446A GLN 3.3 18.6 - - - +
447A ASP* 3.6 15.7 - - + +
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Residues in contact with LEU 375 (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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37A THR 3.4 13.0 - - - +
38A LYS* 3.3 32.1 - - + -
39A THR* 4.0 19.5 - - + -
139A LEU* 4.2 4.3 - - + -
297A ARG* 4.6 2.9 - - - +
360A GLN* 3.8 28.9 - - + +
361A LEU 3.5 16.2 - - - +
362A GLN* 4.6 4.0 - - - -
373A THR* 3.7 3.0 + - + +
374A LEU* 1.3 72.3 - - - +
376A THR* 1.3 63.6 + - - +
444A TYR* 3.9 19.6 - - + +
445A VAL* 3.2 3.5 - - - -
446A GLN* 2.5 54.2 + - + +
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Residues in contact with THR 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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360A GLN* 3.6 2.4 - - - -
361A LEU* 2.8 54.0 + - - +
363A SER* 5.2 1.7 + - - -
374A LEU* 3.8 25.4 - - + -
375A LEU* 1.3 81.2 - - - +
377A GLY* 1.3 57.2 + - - +
444A TYR 3.5 5.6 - - - -
445A VAL* 3.9 21.1 - - + -
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Residues in contact with GLY 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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359A THR 3.2 14.1 - - - -
360A GLN* 3.9 2.7 - - - -
376A THR* 1.3 75.8 - - - +
378A VAL* 1.3 65.6 + - - -
443A VAL* 3.5 2.6 - - - +
444A TYR* 3.0 49.1 + - - +
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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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357A VAL 4.2 1.0 - - - +
358A ASP* 3.2 3.4 - - - +
359A THR* 3.0 41.2 + - + +
377A GLY* 1.3 79.1 - - - +
379A ASP* 1.3 61.4 + - - +
380A PHE* 5.6 2.7 - - + +
441A THR* 5.7 4.7 - - + -
442A GLY 3.0 8.1 - - - +
443A VAL* 3.9 19.7 - - + -
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Residues in contact with ASP 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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38A LYS* 5.0 3.4 - - - +
108A GLY 5.5 1.3 - - - +
109A LEU* 4.7 5.4 - - - +
140A TYR* 3.8 8.7 - - - +
356A SER* 5.9 0.5 - - - -
357A VAL 3.5 10.1 - - - +
358A ASP* 3.6 21.6 - - - +
378A VAL* 1.3 74.5 - - - +
380A PHE* 1.3 73.7 + - - +
381A MSE 5.6 3.4 - - - +
440A GLN* 3.7 5.0 + - - +
441A THR* 3.1 6.5 - - - +
442A GLY 2.7 35.7 + - - -
444A TYR* 4.1 4.2 - - + -
461A ARG* 2.9 41.4 + - - +
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Residues in contact with PHE 380 (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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355A PHE* 4.0 16.4 - + - -
356A SER* 3.4 1.0 - - - -
357A VAL* 2.9 56.4 + - + +
378A VAL* 4.3 3.3 - - + -
379A ASP* 1.3 80.8 + - - +
381A MSE 1.3 83.9 + - - +
382A ARG* 4.1 8.1 - - + -
439A LYS* 4.8 15.7 - - + -
440A GLN 3.3 5.2 - - - -
441A THR* 3.3 25.8 - - + +
906A LIM 3.4 50.9 - - + -
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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