Contacts of the helix formed by residues 382 - 398 (chain B) in PDB entry 3COG
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 ASP 382 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B GLU* 1.3 74.3 - - - +
383B GLU* 1.3 67.5 + - - +
384B GLU* 4.5 2.9 - - + +
385B ASP* 3.0 26.4 + - - +
386B LEU* 3.1 11.1 + - - +
15C PHE 4.9 3.1 - - - +
17C HIS* 3.0 22.8 + - - +
18C PHE* 4.3 2.4 + - - +
19C ALA* 2.9 34.2 + - - +
20C THR* 3.0 19.5 + - - +
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Residues in contact with GLU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LYS* 4.4 21.0 + - - +
272B ASN* 3.6 24.1 + - - +
275B ALA* 3.6 33.2 - - + +
276B VAL* 6.3 0.4 - - + -
381B GLU 3.4 3.8 + - - -
382B ASP* 1.3 71.3 - - - +
384B GLU* 1.3 60.2 + - - +
386B LEU* 3.2 7.0 + - - +
387B LEU* 3.0 42.9 + - + +
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Residues in contact with GLU 384 (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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382B ASP* 3.2 2.9 - - + +
383B GLU* 1.3 82.1 - - - +
385B ASP* 1.3 67.0 + - - +
387B LEU* 3.9 22.0 - - - +
388B GLU* 2.9 26.9 + - + +
16C GLN* 6.2 0.2 - - - +
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Residues in contact with ASP 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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334B LEU* 3.4 23.1 - - + +
382B ASP* 3.0 14.5 + - - +
384B GLU* 1.3 79.6 - - - +
386B LEU* 1.3 61.8 + - - +
388B GLU* 3.5 6.9 + - - +
389B ASP* 3.1 24.1 + - - +
17C HIS* 2.8 44.4 + - - -
20C THR* 2.7 27.2 + - - +
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Residues in contact with LEU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ASN* 3.8 28.3 - - + +
276B VAL* 4.7 8.5 - - + -
334B LEU* 3.9 20.0 - - + -
335B PHE* 3.7 21.3 - - + -
346B SER* 3.3 33.0 - - - +
378B VAL* 3.8 14.6 - - + -
379B GLY 4.2 0.4 - - - +
381B GLU* 3.8 21.3 - - + +
382B ASP 3.1 8.9 + - - +
383B GLU* 3.6 6.5 - - - +
385B ASP* 1.3 74.5 - - - +
387B LEU* 1.3 66.2 + - - +
389B ASP* 3.3 4.1 + - - +
390B LEU* 3.2 27.3 + - - +
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ALA* 3.7 27.6 - - + +
276B VAL* 3.9 21.3 - - + -
279B PHE* 3.8 31.9 - - + -
383B GLU* 3.0 40.4 + - + +
384B GLU* 3.9 23.3 - - - +
386B LEU* 1.3 75.1 - - - +
388B GLU* 1.3 62.4 + - - +
390B LEU* 3.3 7.3 + - + +
391B ASP* 3.0 24.6 + - - +
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Residues in contact with GLU 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 GLU* 2.9 20.6 + - + +
385B ASP* 3.6 7.6 - - - +
387B LEU* 1.3 76.0 - - - +
389B ASP* 1.3 60.0 + - - +
391B ASP* 4.3 13.6 - - - +
392B GLN* 2.9 54.7 + - - +
395B LYS* 6.1 0.2 - - - +
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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
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332B LEU* 3.6 7.2 - - - +
333B LYS* 2.8 28.7 + - - +
334B LEU* 2.9 33.7 + - + -
335B PHE* 2.9 24.6 + - + -
385B ASP 3.1 17.5 + - - +
386B LEU 3.6 4.7 - - - +
387B LEU 3.2 0.4 - - - -
388B GLU* 1.3 78.5 - - - +
390B LEU* 1.3 61.2 + - - +
392B GLN* 3.0 23.5 + - - +
393B ALA* 3.0 23.2 + - - +
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Residues in contact with LEU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B VAL* 3.5 40.4 - - + -
279B PHE* 3.9 21.3 - - + -
280B LEU* 4.6 8.7 - - + -
328B PHE* 3.8 28.6 - - + -
332B LEU* 4.2 4.5 - - + -
335B PHE* 3.8 20.4 - - + -
376B LEU* 3.9 16.8 - - + -
386B LEU 3.2 15.8 + - - +
387B LEU* 3.6 6.7 - - - +
389B ASP* 1.3 77.4 - - - +
391B ASP* 1.3 56.9 + - - +
393B ALA* 3.3 1.9 + - - +
394B LEU* 2.9 36.8 + - + +
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Residues in contact with ASP 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B PHE* 3.4 28.3 - - + -
283B ASN* 4.2 7.4 + - - -
387B LEU 3.0 16.4 + - - +
388B GLU* 3.6 15.7 - - - +
390B LEU* 1.3 77.7 - - - +
392B GLN* 1.3 56.9 + - - +
394B LEU* 3.4 4.3 + - - +
395B LYS* 3.0 66.2 + - - +
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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
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331B ASN* 3.2 25.9 + - - +
333B LYS* 3.3 31.1 + - + +
388B GLU* 2.9 36.4 + - - +
389B ASP* 3.0 34.7 + - - -
391B ASP* 1.3 75.6 + - - +
393B ALA* 1.3 62.6 + - - +
395B LYS* 3.5 12.7 + - - +
396B ALA* 3.2 20.3 + - - +
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Residues in contact with ALA 393 (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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328B PHE* 3.5 49.2 - - + +
331B ASN* 4.0 7.9 - - + -
332B LEU* 3.7 13.0 - - + +
389B ASP 3.0 18.3 + - - +
392B GLN* 1.3 83.4 - - - +
394B LEU* 1.3 64.6 + - - +
396B ALA* 3.2 5.4 + - - +
397B ALA 3.2 16.3 + - - -
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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
----------------------------------------------------------
279B PHE* 3.9 15.7 - - + -
280B LEU* 4.2 13.5 - - + -
283B ASN* 3.7 35.0 - - - +
285B TRP* 4.6 13.0 - - + +
286B VAL* 4.2 13.7 - - + -
316B PHE* 4.3 5.2 - - + -
318B ILE* 3.8 31.4 - - + -
328B PHE* 3.7 14.5 - - + -
390B LEU* 2.9 21.2 + - + +
391B ASP* 3.7 3.8 - - - +
393B ALA* 1.3 75.4 - - - +
395B LYS* 1.3 57.2 + - + +
397B ALA* 3.3 5.3 + - - +
398B HIS* 2.9 32.6 + - - +
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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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285B TRP* 6.2 0.4 - - - -
391B ASP* 3.0 51.9 + - - +
392B GLN* 3.7 9.4 - - - +
393B ALA 3.3 0.2 - - - -
394B LEU* 1.3 73.4 - - + +
396B ALA* 1.3 64.0 + - - +
398B HIS 3.9 8.3 - - - +
399B PRO* 3.2 28.8 - - + +
400B PRO* 4.9 4.5 - - + +
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Residues in contact with ALA 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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327B ILE* 3.5 12.3 - - + +
331B ASN* 3.4 38.4 - - + +
392B GLN* 3.2 14.3 + - - +
393B ALA 3.2 8.0 + - - +
395B LYS* 1.3 78.1 - - - +
397B ALA* 1.3 59.8 + - - +
399B PRO* 4.1 8.5 - - - +
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Residues in contact with ALA 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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318B ILE* 4.1 8.5 - - + -
324B HIS* 3.3 48.8 + - - +
327B ILE* 3.6 16.1 - - + +
328B PHE* 4.0 5.8 - - - +
393B ALA 3.2 12.3 + - - +
394B LEU 3.3 7.4 + - - +
396B ALA* 1.3 78.3 - - - +
398B HIS* 1.3 68.6 + - + +
399B PRO* 3.6 6.9 - - - +
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Residues in contact with HIS 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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285B TRP* 3.3 75.8 + + + -
318B ILE* 4.2 9.0 - - + +
319B LYS 2.6 32.0 + - - -
320B GLY* 4.7 0.7 - - - -
324B HIS* 3.5 28.0 + + - +
394B LEU* 2.9 10.4 + - + +
395B LYS* 3.2 13.2 - - - +
397B ALA* 1.3 89.6 + - + +
399B PRO* 1.3 70.8 - - - +
400B PRO* 3.9 0.3 - - - +
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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