Contacts of the helix formed by residues 371 - 392 (chain B) in PDB entry 3W8I
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 ASN 371 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ASN* 4.1 5.7 + - - -
368B ASP* 3.0 40.0 + - - +
369B GLU 3.4 0.4 - - - -
370B ASN* 1.3 74.8 - - - +
372B ALA* 1.3 64.2 + - - +
373B SER* 3.5 9.4 + - - -
374B ARG* 3.5 36.3 + - + +
375B ASN* 2.8 27.7 + - - +
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Residues in contact with ALA 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ASN 3.2 9.1 + - - +
371B ASN* 1.3 72.7 + - - +
373B SER* 1.3 58.3 + - - +
375B ASN* 3.3 6.4 + - - +
376B GLN* 2.9 29.9 + - - +
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Residues in contact with SER 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLU* 5.3 13.2 + - - +
55A ASN* 4.5 7.0 + - - +
371B ASN* 3.5 9.2 + - - -
372B ALA* 1.3 78.6 - - - +
374B ARG* 1.3 59.4 + - - +
376B GLN* 3.4 7.3 + - - +
377B ALA* 2.9 29.8 + - - +
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Residues in contact with ARG 374 (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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55A ASN* 3.3 40.9 - - + +
58A LEU* 3.9 18.7 - - + +
61A ASP* 3.0 30.1 + - - +
364B LEU* 2.6 31.1 + - - +
365B LYS* 4.4 2.0 - - - +
367B GLN* 3.2 18.1 + - - +
368B ASP* 4.0 21.8 - - - +
371B ASN* 3.5 27.9 + - + +
372B ALA 3.3 0.4 - - - -
373B SER* 1.3 82.1 + - - +
375B ASN* 1.3 59.5 + - - +
377B ALA* 3.2 6.6 + - - +
378B ILE* 2.9 39.4 + - + +
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Residues in contact with ASN 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LYS* 3.6 42.4 - - + +
368B ASP 3.6 10.2 - - - +
369B GLU* 3.5 26.7 + - - +
371B ASN 2.8 19.8 + - - +
372B ALA* 3.7 5.5 - - - +
374B ARG* 1.3 82.0 + - - +
376B GLN* 1.3 58.1 + - - +
378B ILE* 3.4 6.2 + - - +
379B GLU* 2.9 38.1 + - - +
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Residues in contact with GLN 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ALA 2.9 16.8 + - - +
373B SER* 3.7 8.3 - - - +
375B ASN* 1.3 74.5 - - - +
377B ALA* 1.3 59.5 + - - +
379B GLU* 3.1 23.8 + - - +
380B GLU* 2.9 64.4 + - - +
383B LYS* 5.0 7.4 + - - -
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Residues in contact with ALA 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ALA* 4.2 12.8 - - - +
54A GLU* 4.2 28.5 - - + +
55A ASN* 4.7 2.0 - - + -
58A LEU* 4.2 16.8 - - + -
373B SER 2.9 14.7 + - - +
374B ARG* 3.4 10.5 - - - +
376B GLN* 1.3 76.2 - - - +
378B ILE* 1.3 58.2 + - - +
380B GLU* 3.8 6.2 - - - +
381B LEU* 2.9 30.2 + - - +
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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
----------------------------------------------------------
58A LEU* 4.0 24.0 - - + -
62A ILE* 6.2 0.7 - - + -
361B PHE* 3.4 42.5 - - + +
364B LEU* 4.0 16.4 - - + -
365B LYS* 3.9 28.3 - - + +
374B ARG* 2.9 45.6 + - - +
375B ASN* 3.5 7.6 - - - +
376B GLN 3.2 0.2 - - - -
377B ALA* 1.3 75.9 - - - +
379B GLU* 1.3 57.8 + - - +
381B LEU* 3.2 8.1 + - + +
382B GLU* 2.9 24.7 + - - +
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Residues in contact with GLU 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LYS* 3.2 31.1 + - - +
375B ASN* 2.9 22.8 + - - +
376B GLN* 3.1 30.2 + - - +
378B ILE* 1.3 73.4 - - - +
380B GLU* 1.3 65.7 + - - +
382B GLU* 3.2 8.6 + - - +
383B LYS* 2.9 37.5 + - - +
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Residues in contact with GLU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LYS* 2.3 40.2 + - - +
54A GLU* 4.9 4.9 - - - +
376B GLN* 2.9 47.5 + - - +
377B ALA* 3.8 5.4 - - - +
379B GLU* 1.3 75.0 - - - +
381B LEU* 1.3 57.2 + - - +
383B LYS* 3.3 15.7 + - + +
384B SER* 2.9 33.4 + - - +
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Residues in contact with LEU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA* 3.6 37.9 - - + +
48A PHE* 3.9 24.5 - - + +
51A ALA* 3.9 16.6 - - + +
58A LEU* 5.3 1.8 - - + -
62A ILE* 3.5 31.4 - - + -
361B PHE* 3.8 18.8 - - + -
377B ALA 2.9 19.5 + - - +
378B ILE* 3.4 7.0 - - - +
379B GLU 3.2 0.2 - - - -
380B GLU* 1.3 77.6 - - - +
382B GLU* 1.3 57.9 + - - +
384B SER* 3.2 3.9 + - - -
385B ILE* 2.9 36.2 + - + +
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Residues in contact with GLU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B LEU* 4.6 8.3 - - + +
357B ILE* 4.6 9.4 - - + -
358B THR* 2.8 43.5 + - - +
361B PHE* 3.9 29.2 - - + +
365B LYS* 5.0 7.6 + - - -
378B ILE* 2.9 13.8 + - - +
379B GLU* 3.7 9.7 - - - +
381B LEU* 1.3 75.6 - - - +
383B LYS* 1.3 58.0 + - + +
385B ILE* 3.2 7.2 + - - +
386B ALA* 2.9 29.2 + - + +
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Residues in contact with LYS 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B GLN* 5.0 8.5 + - - -
379B GLU* 2.9 26.5 + - - +
380B GLU* 3.4 18.3 - - + +
382B GLU* 1.3 76.2 - - + +
384B SER* 1.3 57.3 + - - +
386B ALA* 3.2 9.2 + - - +
387B VAL* 2.9 32.6 + - + +
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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
----------------------------------------------------------
43A THR* 3.4 16.3 - - - +
44A LEU* 4.9 0.9 - - - -
47A ALA* 3.5 31.0 - - - +
380B GLU* 2.9 18.9 + - - +
381B LEU 3.2 1.5 + - - -
383B LYS* 1.3 74.3 - - - +
385B ILE* 1.3 61.0 + - - +
387B VAL* 3.2 12.2 + - - +
388B ALA* 2.9 23.4 + - - +
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Residues in contact with ILE 385 (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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44A LEU* 3.9 24.5 - - + -
47A ALA* 5.7 0.2 - - + -
48A PHE* 4.5 10.3 - - + -
353B LEU* 4.4 13.5 - - + -
357B ILE* 4.0 13.5 - - + -
361B PHE* 3.9 27.8 - - + -
381B LEU* 2.9 31.5 + - + +
382B GLU* 3.5 7.9 - - - +
384B SER* 1.3 76.3 - - - +
386B ALA* 1.3 57.2 + - - +
388B ALA* 3.3 3.5 + - - +
389B GLU* 2.9 26.2 + - - +
396B THR* 3.8 28.6 + - + +
399B MET* 4.7 9.6 - - + -
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Residues in contact with ALA 386 (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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353B LEU* 4.1 22.4 - - + +
382B GLU* 2.9 14.9 + - + +
383B LYS* 3.3 12.1 - - - +
384B SER 3.2 0.2 - - - -
385B ILE* 1.3 76.5 - - - +
387B VAL* 1.3 59.0 + - - +
389B GLU* 3.3 2.1 + - - +
390B ALA* 2.9 29.5 + - - +
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Residues in contact with VAL 387 (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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43A THR* 4.6 13.2 - - + +
383B LYS* 2.9 21.3 + - + +
384B SER* 3.4 13.5 - - - +
386B ALA* 1.3 76.6 - - + +
388B ALA* 1.3 58.2 + - - +
390B ALA* 3.2 8.0 + - + +
391B ALA* 2.9 29.5 + - + +
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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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40A ALA* 3.6 25.2 - - + +
43A THR* 3.9 7.6 - - + +
44A LEU* 3.7 35.0 - - + -
384B SER 2.9 13.0 + - - +
385B ILE* 3.5 8.1 - - + +
387B VAL* 1.3 77.1 - - - +
389B GLU* 1.3 57.8 + - - +
391B ALA* 3.2 5.0 + - - +
392B CYS 2.9 22.7 + - - -
395B ILE* 3.7 6.2 - - + +
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Residues in contact with GLU 389 (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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347B VAL* 6.0 1.7 - - - +
351B SER* 3.6 20.9 + - - +
353B LEU* 4.0 21.8 - - + -
385B ILE 2.9 17.4 + - - +
386B ALA 3.6 4.5 - - - +
388B ALA* 1.3 72.8 - - - +
390B ALA* 1.3 65.3 + - - +
392B CYS 4.1 1.8 - - - -
393B PRO* 3.1 30.2 - - + +
394B GLY* 2.7 29.9 + - - -
395B ILE* 3.6 2.8 + - - +
396B THR* 2.6 39.0 + - - +
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Residues in contact with ALA 390 (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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386B ALA 2.9 16.4 + - - +
387B VAL* 3.5 8.1 - - + +
389B GLU* 1.3 77.3 - - - +
391B ALA* 1.3 61.8 + - - +
393B PRO* 4.2 7.9 - - - +
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Residues in contact with ALA 391 (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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37A ASN* 4.7 9.7 + - - +
39A SER* 5.5 5.2 - - - +
40A ALA* 4.2 17.3 - - + +
387B VAL* 2.9 19.1 + - + +
388B ALA* 3.6 6.5 - - - +
389B GLU 3.2 0.2 - - - -
390B ALA* 1.3 80.2 - - - +
392B CYS* 1.3 60.6 + - - +
393B PRO* 4.1 1.9 - - - +
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Residues in contact with CYS 392 (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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36A VAL* 3.5 33.7 - - - -
37A ASN* 3.7 24.7 - - + -
40A ALA* 4.0 7.4 - - + -
388B ALA 2.9 9.9 + - - +
389B GLU 3.2 3.4 - - - +
390B ALA 3.3 0.4 - - - -
391B ALA* 1.3 81.7 - - - +
393B PRO* 1.3 75.4 - - - +
394B GLY 3.4 0.2 + - - -
395B ILE* 3.2 29.0 + - + +
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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
------------------------------------------------------------
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