Contacts of the helix formed by residues 386 - 401 (chain A) in PDB entry 1N54
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 SER 386 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A ASN* 3.0 34.7 + - - -
383A GLN* 3.4 22.5 + - - +
384A PRO 3.3 1.0 - - - -
385A GLY* 1.3 78.7 - - - +
387A LEU* 1.3 73.2 + - - +
389A GLN* 2.9 20.7 + - - +
390A VAL* 3.2 18.8 - - - +
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Residues in contact with LEU 387 (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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348A ASN* 3.7 26.0 - - + +
351A ILE* 5.3 4.3 - - + -
352A VAL* 3.9 28.7 - - + -
376A LEU* 4.4 6.5 - - + +
379A LEU* 3.8 40.4 - - + +
380A CYS* 3.8 22.0 - - - -
383A GLN* 3.3 12.0 + - + +
386A SER* 1.3 76.5 + - - +
388A PRO* 1.3 81.1 - - + +
390A VAL* 3.2 5.6 + - + +
391A LEU* 3.1 26.2 + - + +
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Residues in contact with PRO 388 (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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380A CYS* 4.6 17.3 - - + +
383A GLN 3.2 8.1 - - - +
384A PRO* 3.1 31.9 - - + +
386A SER 3.4 2.0 - - - -
387A LEU* 1.3 97.3 - - + +
389A GLN* 1.3 59.7 + - + +
390A VAL 2.7 9.4 + - - -
391A LEU* 2.7 13.4 + - + +
392A ALA* 3.2 11.0 + - - +
1560A GOL 4.4 23.6 + - - +
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Residues in contact with GLN 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A TYR* 5.5 0.7 - - - +
384A PRO 3.8 1.4 - - - +
385A GLY 2.7 30.5 + - - +
386A SER* 2.9 19.2 - - - +
388A PRO* 1.3 80.3 - - + +
390A VAL* 1.3 63.0 + - + +
392A ALA* 3.8 8.5 + - - +
393A GLN* 3.3 20.8 + - - +
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Residues in contact with VAL 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A PHE* 4.9 4.7 - - + -
348A ASN* 4.1 16.2 - - + +
349A TYR* 3.6 65.3 - - + +
352A VAL* 4.4 16.2 - - + -
386A SER* 3.2 18.8 - - - +
387A LEU* 3.5 6.1 - - - +
388A PRO 2.7 4.6 + - - -
389A GLN* 1.3 72.5 - - + +
391A LEU* 1.3 57.3 + - - +
393A GLN* 2.6 28.9 + - - +
394A ALA* 2.7 11.7 + - + +
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Residues in contact with LEU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A VAL* 4.4 8.9 - - + +
356A PHE* 3.8 35.2 - - + -
376A LEU* 4.5 16.6 - - + -
380A CYS* 4.1 20.2 - - - -
387A LEU* 3.1 15.1 + - + +
388A PRO* 2.7 14.2 + - + +
390A VAL* 1.3 75.4 - - - +
392A ALA* 1.3 56.9 + - - +
394A ALA* 2.8 6.6 + - - +
395A THR* 2.7 32.3 + - - +
416A TRP* 4.0 15.3 - - + -
420A HIS* 3.5 27.6 - - + +
1560A GOL 3.7 11.2 - - - +
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Residues in contact with ALA 392 (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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388A PRO 3.2 7.9 + - - +
389A GLN* 4.0 10.8 - - - +
391A LEU* 1.3 78.4 - - - +
393A GLN* 1.3 60.1 + - - +
395A THR* 3.8 9.2 - - - -
396A GLU* 3.3 22.3 + - - +
428A TRP* 4.0 23.5 - - + -
1560A GOL 4.1 11.0 + - - +
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Residues in contact with GLN 393 (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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292A PHE* 4.6 2.2 - - - -
296A ASP* 3.7 30.2 + - - +
349A TYR* 3.3 40.3 + - - -
389A GLN 3.3 13.5 + - - +
390A VAL* 2.6 18.7 + - - +
392A ALA* 1.3 72.3 - - - +
394A ALA* 1.3 61.2 + - - +
396A GLU* 3.7 5.9 - - + +
397A MET* 3.3 37.6 + - + +
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Residues in contact with ALA 394 (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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291A MET* 3.7 25.7 - - + +
292A PHE* 4.3 8.5 - - + -
352A VAL* 4.3 13.2 - - + -
356A PHE* 4.3 8.1 - - + -
390A VAL 2.7 10.7 + - - +
391A LEU* 3.3 12.8 - - - +
393A GLN* 1.3 77.5 - - - +
395A THR* 1.3 66.0 + - - +
397A MET* 3.3 5.4 + - - +
398A LEU* 2.9 30.1 + - - +
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Residues in contact with THR 395 (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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391A LEU* 2.7 23.2 + - - +
392A ALA* 3.8 7.8 - - - -
393A GLN 3.3 0.2 - - - -
394A ALA* 1.3 76.0 - - - +
396A GLU* 1.3 66.6 + - - +
398A LEU* 2.9 14.2 + - - +
399A TYR* 2.9 22.8 + - - +
413A PHE* 4.3 12.5 - - + -
416A TRP* 4.0 17.2 - - + -
417A PHE* 4.1 24.9 - - + -
428A TRP* 4.2 8.8 - - + -
433A TRP* 4.0 24.7 - - + -
1560A GOL 5.0 2.4 + - - -
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Residues in contact with GLU 396 (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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392A ALA 3.3 15.7 + - - +
393A GLN* 3.7 8.3 - - + +
395A THR* 1.3 79.8 - - - +
397A MET* 1.3 60.7 + - + +
399A TYR* 3.1 2.6 + - - +
400A MET* 2.8 59.4 + - + +
428A TRP* 4.8 7.2 - - + -
432A ASP* 4.0 28.9 - - - +
433A TRP* 4.2 23.3 + - - +
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Residues in contact with MET 397 (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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291A MET* 3.0 28.5 - - + +
292A PHE* 3.8 20.2 - - + -
296A ASP* 3.4 21.8 - - - +
393A GLN* 3.3 31.7 + - + +
394A ALA* 3.6 5.8 - - - +
395A THR 3.2 0.8 - - - -
396A GLU* 1.3 80.8 - - + +
398A LEU* 1.3 63.3 + - - +
400A MET* 3.3 7.2 + - - +
401A ARG* 2.9 71.7 + - - +
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Residues in contact with LEU 398 (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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217A TRP* 4.1 28.1 + - + -
291A MET* 4.2 23.1 - - + -
356A PHE* 3.7 37.7 - - + -
360A PHE* 4.4 18.8 - - + -
394A ALA* 2.9 28.4 + - + +
395A THR* 2.9 9.8 + - - +
397A MET* 1.3 76.2 - - + +
399A TYR* 1.3 62.2 + - - +
401A ARG* 3.6 2.3 + - - +
402A LEU* 3.0 27.4 + - - +
405A MET* 4.6 4.7 - - + +
413A PHE* 3.7 24.9 - - + -
416A TRP* 5.0 0.7 - - + -
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Residues in contact with TYR 399 (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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395A THR 2.9 9.3 + - - +
396A GLU 3.3 5.6 - - - +
398A LEU* 1.3 76.4 - - - +
400A MET* 1.3 69.3 + - - +
402A LEU* 2.7 53.6 + - + +
413A PHE* 3.9 6.2 - - + -
433A TRP* 2.8 65.2 - + + +
435A ASP* 3.1 26.5 + - - -
436A CYS* 3.4 22.9 - - - +
445A LYS* 3.6 42.6 - - + +
448A PHE* 4.0 11.0 - + - -
449A VAL* 4.4 4.3 - - + -
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Residues in contact with MET 400 (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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396A GLU* 2.8 49.1 + - + +
397A MET* 3.3 7.6 + - - +
399A TYR* 1.3 90.9 - - + +
401A ARG* 1.3 63.1 + - + +
402A LEU 3.5 0.5 + - - -
403A ASP* 3.6 14.7 - - - +
432A ASP 5.7 1.6 - - - +
433A TRP* 5.2 0.4 - - - -
435A ASP* 4.6 7.6 - - - +
445A LYS* 3.8 26.5 + - - +
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Residues in contact with ARG 401 (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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217A TRP* 3.6 36.7 + - + +
222A PRO* 3.7 34.9 - - + +
223A HIS* 3.4 27.1 + - - +
290A ARG 4.7 0.8 + - - -
291A MET* 3.5 23.2 + - - +
296A ASP* 4.5 3.6 + - - -
397A MET* 2.9 55.5 + - - +
398A LEU 4.0 2.2 - - - +
399A TYR 3.1 0.4 - - - -
400A MET* 1.3 77.8 - - + +
402A LEU* 1.3 65.7 + - - +
403A ASP* 3.0 5.7 + - - +
404A THR* 3.3 19.5 + - - +
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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