Contacts of the helix formed by residues 376 - 401 (chain A) in PDB entry 4M3P
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 376 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A VAL* 1.3 84.2 - - + +
377A LYS* 1.3 64.5 + - - +
378A GLY* 3.7 3.6 + - - -
379A THR* 2.9 28.4 + - - +
380A ALA* 3.1 18.9 + - - +
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Residues in contact with LYS 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A VAL 3.7 0.8 + - - -
376A THR* 1.3 72.4 - - - +
378A GLY* 1.3 58.7 + - - +
380A ALA* 3.6 7.6 + - - +
381A GLU* 3.1 32.1 + - + +
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Residues in contact with GLY 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A THR* 3.2 4.3 + - - -
377A LYS* 1.3 78.6 - - - +
379A THR* 1.3 60.7 + - - +
381A GLU* 3.2 9.7 - - - +
382A LEU* 2.9 29.5 + - - +
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Residues in contact with THR 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A VAL* 3.2 31.1 - - + +
376A THR* 2.9 20.9 + - - +
378A GLY* 1.3 74.5 - - - +
380A ALA* 1.3 55.5 + - - +
382A LEU* 3.1 11.4 + - + +
383A MET* 2.7 56.2 + - + +
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Residues in contact with ALA 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A VAL* 3.8 14.5 - - + +
376A THR 3.1 13.8 + - - +
377A LYS* 3.6 11.7 - - - +
379A THR* 1.3 76.1 - - - +
381A GLU* 1.3 56.2 + - - +
383A MET* 4.1 6.4 - - - +
384A GLN* 3.0 37.2 + - - +
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Residues in contact with GLU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LYS* 3.1 23.5 + - + +
378A GLY* 3.2 14.4 - - - +
380A ALA* 1.3 74.7 - - - +
382A LEU* 1.3 65.6 + - - +
384A GLN* 3.5 7.0 - - - +
385A GLN* 3.0 53.8 + - - +
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Residues in contact with LEU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLY 2.9 17.9 + - - +
379A THR* 3.1 13.0 + - + +
381A GLU* 1.3 69.8 - - - +
383A MET* 1.3 68.3 + - + +
385A GLN* 3.0 10.3 + - + +
386A LYS* 2.9 47.0 + - - +
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Residues in contact with MET 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A VAL* 4.2 19.3 - - + -
379A THR* 2.7 45.1 + - + +
380A ALA* 4.1 4.9 - - - +
382A LEU* 1.3 72.1 - - + +
384A GLN* 1.3 62.6 + - - +
386A LYS* 3.5 9.9 + - - +
387A GLU* 3.0 41.4 + - - +
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Residues in contact with GLN 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ALA* 3.0 22.5 + - - +
381A GLU* 3.5 9.1 - - - +
382A LEU 3.1 0.2 + - - -
383A MET* 1.3 75.6 - - - +
385A GLN* 1.3 59.6 + - + +
387A GLU* 3.1 10.6 + - - +
388A ALA* 2.7 37.3 + - + +
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Residues in contact with GLN 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A GLU* 3.0 42.7 + - - +
382A LEU* 3.0 9.1 + - + +
384A GLN* 1.3 82.8 - - + +
386A LYS* 1.3 60.6 + - - +
388A ALA* 3.6 9.4 - - + +
389A THR* 2.8 36.2 + - - +
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Residues in contact with LYS 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A LEU* 2.9 39.2 + - - +
383A MET* 3.5 13.9 - - - +
385A GLN* 1.3 76.6 - - - +
387A GLU* 1.3 62.5 + - + +
389A THR* 3.3 5.6 + - - -
390A THR* 3.1 28.4 + - - +
290D ASN* 5.9 3.1 - - - +
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Residues in contact with GLU 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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383A MET* 3.0 31.1 + - - +
384A GLN* 3.5 8.4 + - - +
386A LYS* 1.3 73.2 - - + +
388A ALA* 1.3 66.8 + - - +
390A THR* 3.4 9.5 + - - -
391A GLU* 3.1 22.9 + - - +
286D ARG* 6.4 1.6 - - + -
349D LYS* 4.1 20.3 + - - +
353D GLU* 3.7 21.1 - - - +
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Residues in contact with ALA 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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384A GLN* 2.7 23.4 + - + +
385A GLN* 3.6 12.8 - - + +
387A GLU* 1.3 72.8 - - - +
389A THR* 1.3 62.9 + - - +
391A GLU* 3.2 10.5 + - - +
392A GLN* 3.0 22.4 + - - +
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Residues in contact with THR 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLN* 2.8 24.8 + - - +
386A LYS* 3.5 6.5 - - - -
387A GLU 3.3 0.2 - - - -
388A ALA* 1.3 73.3 - - - +
390A THR* 1.3 66.0 + - - +
392A GLN* 3.1 8.7 + - + +
393A GLN* 3.0 47.9 + - + +
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Residues in contact with THR 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A LYS* 3.1 15.5 + - - +
387A GLU* 3.6 11.5 - - - -
389A THR* 1.3 78.4 - - - +
391A GLU* 1.3 59.4 + - - +
393A GLN* 3.3 13.0 + - - +
394A LEU* 2.9 29.6 + - + +
286D ARG* 3.8 30.3 + - - +
313D GLU* 4.2 12.6 - - - +
316D PRO* 3.7 15.0 - - + +
317D GLU* 4.8 3.5 + - - -
349D LYS* 5.6 4.9 - - - +
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Residues in contact with GLU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A GLU 3.1 10.6 + - - +
388A ALA* 3.2 11.1 + - - +
390A THR* 1.3 79.9 - - - +
392A GLN* 1.3 57.0 + - - +
394A LEU* 3.4 6.5 + - + +
395A LYS* 3.0 58.4 + - - +
330D SER* 4.7 7.1 + - - +
331D TRP* 4.6 11.3 - - + +
348D ARG* 5.5 0.9 - - - -
349D LYS* 3.9 45.8 + - + +
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Residues in contact with GLN 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ALA 3.0 13.4 + - - +
389A THR* 3.1 11.6 + - + +
391A GLU* 1.3 74.4 - - - +
393A GLN* 1.3 65.3 + - + +
395A LYS* 3.5 15.4 + - - +
396A GLU* 3.2 38.5 + - - +
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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
----------------------------------------------------------
389A THR* 3.0 36.7 + - + +
390A THR* 3.6 11.1 + - - +
392A GLN* 1.3 75.4 - - + +
394A LEU* 1.3 61.7 + - - +
396A GLU* 3.2 21.9 + - - +
397A LEU* 2.9 34.7 + - + +
316D PRO* 3.2 30.8 - - + +
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Residues in contact with LEU 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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390A THR* 2.9 20.4 + - + +
391A GLU* 3.7 7.2 - - - +
393A GLN* 1.3 74.9 - - - +
395A LYS* 1.3 63.5 - - - +
397A LEU* 3.1 9.2 + - + +
398A PHE* 3.0 40.9 + - + -
282D GLN* 5.0 3.8 - - - +
312D GLU* 3.5 31.6 - - + +
313D GLU* 5.9 0.2 - - - -
315D ALA* 3.9 7.2 - - + -
316D PRO* 4.2 4.6 - - + +
321D LEU* 3.9 14.6 - - + -
330D SER* 3.2 33.9 - - - +
331D TRP* 3.9 20.2 - - + +
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Residues in contact with LYS 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A GLU* 3.0 44.6 + - - +
392A GLN* 3.7 18.2 - - - +
393A GLN 3.2 0.2 - - - -
394A LEU* 1.3 77.2 - - - +
396A GLU* 1.3 57.1 + - - +
398A PHE* 3.4 6.4 + - - +
399A GLU* 3.0 27.1 + - - +
330D SER* 4.6 15.0 - - - +
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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 GLN* 3.2 27.7 + - - +
393A GLN* 3.3 32.2 - - - +
395A LYS* 1.3 76.9 - - - +
397A LEU* 1.3 65.4 + - + +
399A GLU* 3.8 12.2 - - - +
400A LYS* 2.8 45.5 + - + +
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Residues in contact with LEU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A GLN* 2.9 19.9 + - + +
394A LEU* 3.5 9.0 - - - +
396A GLU* 1.3 76.7 - - + +
398A PHE* 1.3 63.1 + - - +
400A LYS* 3.3 4.9 + - + +
401A GLN* 3.1 29.4 + - + +
315D ALA* 3.5 45.3 - - + +
316D PRO* 3.8 10.3 - - + -
319D GLY* 3.8 26.5 - - - +
320D PHE* 4.2 5.8 - - - +
321D LEU* 3.7 20.1 - - + +
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Residues in contact with PHE 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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394A LEU* 3.0 39.7 + - + +
395A LYS* 3.7 9.0 - - - +
397A LEU* 1.3 78.7 - - - +
399A GLU* 1.3 62.0 + - - +
400A LYS 3.2 0.9 + - - -
401A GLN 3.7 14.6 + - - +
312D GLU* 3.6 24.0 - - - -
321D LEU* 3.8 14.1 - - + -
325D SER* 3.4 33.7 - - - -
328D HIS 3.8 2.0 - - - -
329D GLY* 3.5 30.1 - - - -
330D SER* 3.5 28.7 - - - +
333D SER* 5.8 0.2 - - - -
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Residues in contact with GLU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A LYS 3.0 17.9 + - - +
396A GLU* 3.8 13.2 - - - +
397A LEU 3.4 0.2 - - - -
398A PHE* 1.3 76.2 - - - +
400A LYS* 1.3 61.8 + - + +
401A GLN 4.4 2.3 - - - +
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Residues in contact with LYS 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A GLU* 2.8 36.9 + - - +
397A LEU* 3.9 6.3 - - + +
398A PHE 3.1 0.8 - - - -
399A GLU* 1.3 80.7 - - + +
401A GLN* 1.3 72.1 + - + +
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Residues in contact with GLN 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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397A LEU* 3.1 21.0 + - + +
398A PHE* 3.8 12.4 - - - +
399A GLU 4.4 2.1 - - - +
400A LYS* 1.3 87.3 - - + +
319D GLY 4.9 0.2 - - - +
320D PHE* 3.4 14.2 - - - +
321D LEU* 2.8 51.0 + - + +
326D GLU* 6.1 6.1 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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