Contacts of the helix formed by residues 371 - 394 (chain B) in PDB entry 1MS4
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 LEU 371 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B SER* 4.9 2.2 - - - +
319B LEU* 4.5 14.6 - - + -
333B VAL* 3.7 29.2 - - + +
345B VAL* 4.8 4.7 - - + -
352B LEU* 2.8 48.8 + - + +
353B TYR 4.3 1.6 - - - +
354B CYS* 3.8 27.1 - - + +
369B ALA* 4.0 17.5 - - + -
370B ARG* 1.3 70.3 - - - +
372B VAL* 1.3 62.0 + - - +
374B GLU* 3.1 28.9 - - + +
375B LEU* 3.1 22.0 + - - +
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Residues in contact with VAL 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLY* 3.3 36.3 - - - +
5B SER* 3.1 1.2 + - - -
6B SER* 6.0 0.2 - - - +
351B LYS* 5.8 9.2 - - + -
370B ARG* 2.9 26.1 + - + +
371B LEU* 1.3 71.5 - - - +
373B GLY* 1.3 68.6 + - - +
374B GLU 3.1 0.9 + - - -
375B LEU* 3.3 10.2 + - - +
376B ARG* 3.3 27.3 + - + +
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Residues in contact with GLY 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ALA* 4.2 7.9 - - - -
3B PRO* 3.1 23.5 + - - -
5B SER* 2.9 13.4 + - - -
372B VAL* 1.3 76.6 - - - +
374B GLU* 1.3 63.1 + - - +
376B ARG* 3.4 14.3 + - - +
377B ILE* 3.1 31.9 + - - +
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Residues in contact with GLU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LEU* 5.7 0.9 - - - +
2B ALA* 3.1 22.6 - - + +
5B SER* 2.6 26.4 + - - -
319B LEU* 4.1 15.9 - - + -
330B VAL* 3.8 23.7 - - + +
331B GLY 5.9 1.8 - - - +
332B GLN 4.3 3.7 - - - +
333B VAL* 4.2 20.9 - - + +
352B LEU* 4.6 1.1 - - + -
371B LEU* 3.1 40.1 - - + +
372B VAL 3.2 0.4 - - - -
373B GLY* 1.3 71.8 - - - +
375B LEU* 1.3 58.4 + - - +
377B ILE* 3.2 8.5 + - + +
378B ILE* 2.9 33.1 + - - +
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Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ILE* 4.6 8.3 - - + -
347B TYR* 4.1 17.0 - - + -
350B ASP 3.5 30.7 - - - +
351B LYS* 4.1 12.3 - - + -
352B LEU* 4.2 17.0 - - + +
371B LEU 3.1 16.8 + - - +
372B VAL* 3.9 4.0 - - - +
374B GLU* 1.3 76.1 - - - +
376B ARG* 1.3 51.6 + - - +
378B ILE* 2.8 23.2 + - + +
379B LYS* 2.8 60.5 + - + +
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Residues in contact with ARG 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B PRO* 2.6 46.7 + - - +
4B GLY* 4.8 1.0 - - - -
372B VAL* 3.3 22.8 + - - +
373B GLY* 3.6 13.8 + - - +
375B LEU* 1.3 78.7 - - - +
377B ILE* 1.3 60.2 + - + +
379B LYS* 3.4 9.4 + - - +
380B SER* 3.0 27.0 + - - -
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Residues in contact with ILE 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ALA* 5.6 6.3 - - + -
3B PRO* 6.3 2.2 - - + -
328B TYR* 3.8 34.3 - - + +
330B VAL* 4.2 23.3 - - + +
373B GLY* 3.1 19.8 + - - +
374B GLU* 3.4 10.1 - - + +
376B ARG* 1.3 76.9 - - + +
378B ILE* 1.3 69.5 + - - +
380B SER* 3.2 6.8 + - - +
381B VAL* 3.0 24.2 + - + +
437B ARG* 6.0 1.6 - - - +
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Residues in contact with ILE 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ILE* 4.0 17.0 - - + -
301B LEU* 4.0 23.1 - - + -
319B LEU* 4.2 4.9 - - + -
321B LEU* 4.1 19.2 - - + +
328B TYR* 6.1 0.2 - - - -
330B VAL* 3.8 26.9 - - + -
352B LEU* 4.1 22.0 - - + -
374B GLU 2.9 18.9 + - - +
375B LEU* 2.8 15.8 + - + +
377B ILE* 1.3 81.5 - - - +
379B LYS* 1.3 56.9 + - - +
381B VAL* 3.3 2.9 + - - +
382B LEU* 3.1 45.7 + - + +
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Residues in contact with LYS 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ILE* 4.3 6.3 - - + -
295B GLU* 3.0 42.4 + - + +
350B ASP* 2.7 39.0 + - - -
375B LEU* 2.8 46.6 + - + +
376B ARG* 3.9 7.6 - - - +
378B ILE* 1.3 68.7 - - - +
380B SER* 1.3 66.7 + - - +
382B LEU* 3.4 8.1 + - - +
383B GLN* 3.2 26.3 + - - +
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Residues in contact with SER 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B ARG* 3.0 14.4 + - - -
377B ILE* 3.2 10.3 + - - -
379B LYS* 1.3 76.7 - - - +
381B VAL* 1.3 63.0 + - - +
383B GLN* 3.2 9.0 + - - +
384B SER* 3.1 21.3 + - - -
437B ARG* 2.8 33.1 + - - -
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Residues in contact with VAL 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B LEU* 4.0 13.0 - - + -
328B TYR* 3.7 44.0 - - + +
377B ILE* 3.0 19.5 + - + +
378B ILE 3.8 3.6 - - - +
380B SER* 1.3 74.8 - - - +
382B LEU* 1.3 56.5 + - - +
384B SER* 3.1 5.6 + - - -
385B TRP* 2.9 63.3 + - + +
436B TYR 4.7 2.0 - - - +
437B ARG* 3.9 24.0 - - + +
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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
----------------------------------------------------------
294B ILE* 3.7 46.0 - - + +
295B GLU* 5.2 5.6 - - + -
297B MET* 3.3 18.3 - - + +
299B VAL* 3.8 28.5 - - + -
321B LEU* 3.9 16.2 - - + -
378B ILE* 3.1 31.8 + - + +
379B LYS* 3.8 7.0 - - - +
380B SER 3.3 0.2 - - - -
381B VAL* 1.3 74.5 - - - +
383B GLN* 1.3 57.6 + - - +
385B TRP* 3.5 17.3 + - + +
386B LYS* 2.9 30.4 + - - +
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Residues in contact with GLN 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLU* 6.4 2.0 - - + -
379B LYS 3.2 11.5 + - - +
380B SER* 3.2 12.8 + - - +
382B LEU* 1.3 77.8 - - + +
384B SER* 1.3 55.5 + - - +
386B LYS* 3.3 21.5 + - - +
387B ASN* 2.4 84.2 + - - +
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Residues in contact with SER 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B SER 3.1 1.2 + - - -
381B VAL 3.1 9.3 + - - -
383B GLN* 1.3 76.0 - - - +
385B TRP* 1.3 66.8 + - - +
387B ASN* 4.4 5.4 - - - +
388B TRP* 3.0 37.9 + - - +
435B ALA 4.6 7.6 - - - -
437B ARG* 2.8 46.2 + - - -
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Residues in contact with TRP 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B MET* 4.3 10.5 - - - -
299B VAL* 4.8 1.3 - - + -
321B LEU* 3.7 28.5 - - + -
322B THR 4.3 2.0 - - - -
323B ASP* 3.7 37.0 - - + -
326B ARG* 3.6 38.8 - - + +
328B TYR* 4.2 5.2 - - + -
381B VAL* 2.9 35.7 + - + +
382B LEU* 3.7 28.5 - - + +
384B SER* 1.3 73.2 - - - +
386B LYS* 1.3 57.9 + - - +
388B TRP 4.0 0.2 - - - -
389B ASP* 2.9 37.1 + - - +
436B TYR* 2.9 52.0 + + + +
438B CYS* 4.1 10.1 - - - -
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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
----------------------------------------------------------
295B GLU 5.2 8.9 + - - +
297B MET* 3.7 19.0 - - + +
382B LEU 2.9 18.9 + - - +
383B GLN* 3.4 24.0 - - - +
385B TRP* 1.3 75.2 - - - +
387B ASN* 1.3 73.1 + - - +
389B ASP* 4.0 4.7 - - - +
390B SER* 3.0 28.6 + - - -
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Residues in contact with ASN 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B GLN* 2.4 59.1 + - - +
384B SER* 4.0 5.6 - - - +
386B LYS* 1.3 82.0 - - - +
388B TRP* 1.3 62.9 + - + +
390B SER* 3.6 5.2 - - - -
391B HIS* 3.0 29.2 + - - +
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Residues in contact with TRP 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B SER* 3.0 31.2 + - - +
387B ASN* 1.3 82.1 - - + +
389B ASP* 1.4 59.8 + - - +
391B HIS* 3.4 31.7 + + + +
392B LEU* 3.1 28.8 + - + +
422B PHE* 5.3 4.3 - + + -
435B ALA* 3.2 42.4 + - + +
436B TYR* 3.9 22.7 - + + +
629B THR* 3.4 46.9 - - + -
632B HIS* 4.7 16.6 - - + -
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Residues in contact with ASP 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B GLN* 4.8 2.4 + - - -
326B ARG* 2.7 41.7 + - - -
385B TRP 2.9 21.8 + - - +
386B LYS* 4.0 4.4 - - - +
388B TRP* 1.4 75.5 - - - +
390B SER* 1.3 57.2 + - - +
392B LEU 3.4 0.5 + - - -
393B SER* 3.0 33.9 + - - -
416B THR* 3.8 25.1 + - + +
436B TYR* 3.0 12.4 + - - -
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Residues in contact with SER 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B LYS* 3.0 22.2 + - - -
387B ASN* 3.6 6.1 - - - -
389B ASP* 1.3 75.1 - - - +
391B HIS* 1.3 58.5 + - - +
393B SER* 3.8 4.2 - - - -
394B SER* 2.9 37.5 + - - -
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Residues in contact with HIS 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B ASN 3.0 17.7 + - - +
388B TRP* 3.6 28.3 - + + +
389B ASP 3.3 0.2 - - - -
390B SER* 1.3 75.7 + - - +
392B LEU* 1.3 81.4 + - + +
394B SER* 3.1 20.3 + - - -
395B ILE* 3.3 16.4 - - + +
422B PHE* 5.3 0.9 - + - -
626B LEU 4.6 8.5 + - - -
627B ILE* 3.3 22.9 + - - -
628B GLY 3.6 9.9 + - - -
629B THR* 4.6 2.0 - - + -
632B HIS* 3.0 48.1 + + + -
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B TRP* 3.1 15.5 + - + +
389B ASP 3.8 3.1 - - - +
391B HIS* 1.3 95.0 - - + +
393B SER* 1.3 61.6 + - - +
395B ILE* 3.3 21.2 + - + +
414B VAL* 3.7 27.5 + - + +
416B THR* 3.9 11.4 - - + -
419B LEU* 3.6 31.9 - - + -
422B PHE* 4.6 18.8 - - + -
436B TYR* 3.7 9.6 - - - +
606B LEU* 4.8 7.9 - - + -
608B TYR* 5.7 0.4 - - - +
627B ILE* 3.9 36.1 - - + +
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Residues in contact with SER 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ASP 3.0 18.8 + - - -
390B SER* 4.0 4.5 - - - -
392B LEU* 1.3 75.5 - - - +
394B SER* 1.3 58.3 + - - +
395B ILE 3.2 5.8 + - - +
413B ALA* 4.3 15.9 - - - +
414B VAL 4.2 13.2 + - - -
416B THR* 4.1 16.4 + - - +
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Residues in contact with SER 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B SER* 2.9 20.3 + - - -
391B HIS* 3.1 15.4 + - - -
392B LEU 3.2 0.4 - - - -
393B SER* 1.3 75.8 - - - +
395B ILE* 1.3 67.1 + - - +
396B CYS* 3.3 4.2 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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