Contacts of the helix formed by residues 378 - 403 (chain B) 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 GLY 378 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B LYS* 1.3 76.4 - - - +
379B THR* 1.3 57.4 + - - +
381B GLU* 3.4 31.4 - - - +
382B LEU* 3.0 39.2 + - - +
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Residues in contact with THR 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B VAL* 3.6 22.4 - - + -
376B THR* 2.8 27.1 + - - +
377B LYS 2.8 8.9 + - - -
378B GLY* 1.3 71.8 - - - +
380B ALA* 1.3 59.5 + - - +
382B LEU* 3.3 9.5 + - - +
383B MET* 3.0 47.3 + - + +
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Residues in contact with ALA 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B VAL* 3.7 17.9 - - + +
376B THR 3.0 16.1 + - - +
377B LYS* 4.5 4.3 - - - -
378B GLY 4.4 2.5 - - - +
379B THR* 1.3 77.2 - - - +
381B GLU* 1.3 58.6 + - + +
383B MET* 3.3 10.1 + - - +
384B GLN* 2.9 45.0 + - - +
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Residues in contact with GLU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B LYS* 3.2 39.7 - - + +
378B GLY* 3.4 20.6 + - - +
379B THR 3.3 0.4 - - - -
380B ALA* 1.3 79.8 - - + +
382B LEU* 1.3 58.9 + - + +
384B GLN* 3.4 21.3 + - - +
385B GLN* 3.1 43.8 + - - +
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Residues in contact with LEU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B GLY* 3.0 31.5 + - - +
379B THR* 3.5 7.9 - - - +
380B ALA 3.2 0.2 - - - -
381B GLU* 1.3 78.6 - - + +
383B MET* 1.3 65.4 + - - +
385B GLN* 3.4 19.3 + - - +
386B LYS* 3.2 37.1 + - - +
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Residues in contact with MET 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B VAL* 4.1 18.8 - - + -
379B THR* 3.0 39.3 + - + +
380B ALA* 3.6 13.5 - - - +
382B LEU* 1.3 75.0 - - - +
384B GLN* 1.3 59.0 + - + +
386B LYS* 3.4 18.4 + - - +
387B GLU* 2.9 30.7 + - - +
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Residues in contact with GLN 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ALA* 2.9 33.0 + - - +
381B GLU* 3.6 20.6 - - - +
382B LEU 3.2 0.2 - - - -
383B MET* 1.3 77.7 - - + +
385B GLN* 1.3 57.8 + - + +
387B GLU* 3.3 7.9 + - - +
388B ALA* 2.9 28.8 + - - +
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Residues in contact with GLN 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B GLU* 3.1 30.0 + - - +
382B LEU* 3.4 19.8 + - - +
383B MET 3.3 0.2 - - - -
384B GLN* 1.3 73.4 - - + +
386B LYS* 1.3 60.3 + - - +
388B ALA* 3.3 7.4 + - - +
389B THR* 2.9 31.7 + - - -
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Residues in contact with LYS 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B LEU* 3.2 29.3 + - - +
383B MET* 3.6 18.3 - - - +
385B GLN* 1.3 73.3 - - + +
387B GLU* 1.3 62.0 + - - +
389B THR* 3.5 6.8 - - - -
390B THR* 2.9 37.3 + - - +
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Residues in contact with GLU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B MET 2.9 18.8 + - - +
384B GLN* 3.5 8.7 - - - +
386B LYS* 1.3 75.3 - - - +
388B ALA* 1.3 57.7 + - - +
390B THR* 3.3 9.4 + - - +
391B GLU* 2.8 66.2 + - - +
349C LYS* 3.3 35.6 + - - +
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Residues in contact with ALA 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B GLN 2.9 17.2 + - - +
385B GLN* 3.7 7.2 - - - +
387B GLU* 1.3 73.7 - - - +
389B THR* 1.3 64.0 + - - +
391B GLU* 3.3 9.1 - - - +
392B GLN* 3.2 25.6 + - - +
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Residues in contact with THR 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B GLN 2.9 15.7 + - - -
386B LYS* 3.5 10.6 - - - -
388B ALA* 1.3 75.0 - - - +
390B THR* 1.3 65.5 + - - +
392B GLN* 3.0 9.7 + - - +
393B GLN* 2.9 45.4 + - + +
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Residues in contact with THR 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B LYS* 2.9 22.7 + - - +
387B GLU* 3.6 12.1 - - - +
389B THR* 1.3 73.3 - - - +
391B GLU* 1.3 52.2 + - - +
393B GLN* 3.1 14.5 + - - +
394B LEU* 2.8 49.5 + - + +
286C ARG* 5.7 5.8 - - - +
313C GLU 6.1 0.4 - - - +
316C PRO* 4.3 16.1 - - + +
349C LYS* 6.1 2.0 - - - +
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Residues in contact with GLU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B GLU* 2.8 43.2 + - - +
388B ALA* 3.3 15.2 - - - +
390B THR* 1.3 73.6 - - - +
392B GLN* 1.3 66.1 + - - +
394B LEU* 3.5 15.0 + - - +
395B LYS* 3.0 27.9 + - - +
330C SER* 5.3 1.7 + - - -
331C TRP* 5.0 2.6 - - - +
349C LYS* 4.1 22.7 - - - +
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Residues in contact with GLN 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ALA 3.2 10.3 + - - +
389B THR* 3.0 9.9 + - - +
391B GLU* 1.3 87.4 - - - +
393B GLN* 1.3 67.4 + - + +
395B LYS* 3.4 33.7 + - - +
396B GLU* 2.9 43.6 + - - +
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Residues in contact with GLN 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B THR* 2.9 39.3 + - + +
390B THR* 3.5 14.6 + - - +
392B GLN* 1.3 76.8 - - - +
394B LEU* 1.3 56.5 + - - +
396B GLU* 3.4 11.2 + - - +
397B LEU* 3.0 35.7 + - + +
316C PRO* 3.4 31.1 - - + +
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Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B THR* 2.8 37.5 + - + +
391B GLU* 3.7 16.4 - - - +
392B GLN 3.2 0.2 - - - -
393B GLN* 1.3 69.9 - - - +
395B LYS* 1.3 65.1 + - - +
397B LEU* 3.2 4.9 + - + +
398B PHE* 2.9 42.1 + - + -
282C GLN* 6.0 1.1 - - - +
312C GLU* 3.8 22.9 - - + +
313C GLU* 6.0 1.8 - - - +
315C ALA* 4.4 7.6 - - + -
316C PRO* 4.0 20.6 - - + -
321C LEU* 5.3 0.2 - - + -
330C SER* 3.8 24.5 - - - +
331C TRP* 4.6 13.2 - - + +
349C LYS* 6.1 1.3 - - + +
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Residues in contact with LYS 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B GLU 3.0 17.7 + - - +
392B GLN* 3.7 33.6 + - - +
394B LEU* 1.3 75.4 - - - +
396B GLU* 1.3 64.9 + - + +
398B PHE* 4.0 4.5 - - - +
399B GLU* 3.0 51.9 + - + +
330C SER* 5.3 3.7 + - - -
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Residues in contact with GLU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B GLN* 2.9 34.9 + - - +
393B GLN* 3.8 9.7 - - - +
395B LYS* 1.3 75.4 - - + +
397B LEU* 1.3 62.0 + - + +
399B GLU* 3.8 9.6 - - - +
400B LYS* 2.9 61.4 + - + +
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Residues in contact with LEU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B GLN* 3.0 25.6 + - + +
394B LEU* 3.2 7.1 + - + +
396B GLU* 1.3 77.6 - - + +
398B PHE* 1.3 62.6 + - - +
400B LYS* 3.9 8.4 - - + +
401B GLN* 3.0 25.6 + - - +
315C ALA* 3.7 41.7 - - + +
316C PRO* 4.1 9.2 - - + -
319C GLY* 3.7 25.4 - - - +
320C PHE* 4.3 6.7 - - - +
321C LEU* 3.6 15.8 - - + +
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Residues in contact with PHE 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B LEU* 2.9 36.1 + - + +
395B LYS* 4.0 4.7 - - - +
397B LEU* 1.3 76.2 - - - +
399B GLU* 1.3 58.7 - - + +
401B GLN* 3.5 4.5 + - - +
402B LYS* 2.9 34.6 + - + +
312C GLU* 3.5 28.9 - - + -
321C LEU* 3.6 27.6 - - + -
325C SER* 3.7 28.7 - - - -
328C HIS 4.4 1.6 - - - -
329C GLY* 3.6 26.7 - - - -
330C SER* 3.6 35.9 - - - -
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Residues in contact with GLU 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B LYS* 3.0 52.9 + - + +
396B GLU* 3.8 9.2 - - - +
398B PHE* 1.3 75.9 - - + +
400B LYS* 1.3 58.2 + - + +
402B LYS* 3.1 14.8 - - + +
403B PHE* 2.9 26.9 + - - +
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Residues in contact with LYS 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B GLU* 2.9 52.6 + - + +
397B LEU* 4.0 9.4 - - + +
399B GLU* 1.3 70.0 - - + +
401B GLN* 1.3 67.7 + - - +
403B PHE* 3.1 28.1 + - + +
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Residues in contact with GLN 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B LEU 3.0 17.6 + - - +
398B PHE* 3.7 5.9 - - - +
400B LYS* 1.3 77.3 - - - +
402B LYS* 1.3 64.4 + - - +
403B PHE 3.2 7.4 + - - +
321C LEU* 3.7 23.1 + - + +
322C PRO 2.9 29.9 + - - -
323C PRO* 4.1 2.8 - - - +
325C SER* 3.4 13.0 - - - +
326C GLU* 3.4 52.2 + - + +
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Residues in contact with LYS 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B PHE* 2.9 18.6 + - + +
399B GLU* 3.1 19.5 - - + +
401B GLN* 1.3 77.7 - - - +
403B PHE* 1.3 60.5 + - - +
326C GLU* 6.0 2.9 - - - +
40D LYS* 4.9 18.9 - - - +
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Residues in contact with PHE 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B GLU 2.9 12.5 + - - +
400B LYS* 3.1 24.5 + - + +
401B GLN 3.3 7.3 - - - +
402B LYS* 1.3 80.8 - - - +
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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