Contacts of the helix formed by residues 319 - 331 (chain B) in PDB entry 3E6G
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 319 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284B ALA 4.6 0.6 + - - -
317B LEU 3.3 0.8 - - - -
318B LYS* 1.3 77.7 - - - +
320B GLY* 1.3 65.9 + - - +
322B ASP* 3.9 7.3 + - - +
323B ALA* 3.3 27.6 + - - +
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Residues in contact with GLY 320 (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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317B LEU* 3.8 3.6 + - - +
318B LYS 3.0 8.5 + - - -
319B GLY* 1.3 73.2 - - - +
321B PHE* 1.3 54.0 + - - -
322B ASP 2.5 4.9 + - - -
323B ALA* 2.5 32.9 + - - +
324B ALA 3.1 5.8 + - - -
371B ALA* 3.7 21.3 - - - -
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Residues in contact with PHE 321 (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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320B GLY* 1.3 67.6 - - - -
322B ASP* 1.3 70.3 + - - +
324B ALA* 3.3 4.3 + - - +
325B LYS* 2.9 57.1 + - + +
349B HIS* 3.6 13.8 - + - -
351B ALA* 3.6 22.0 - - + -
352B VAL* 4.8 9.0 - - + -
370B ASP* 3.4 46.0 + - + +
371B ALA* 3.7 9.2 - - - +
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Residues in contact with ASP 322 (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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319B GLY 4.2 6.7 - - - +
320B GLY 2.5 6.7 + - - -
321B PHE* 1.3 90.6 - - - +
323B ALA* 1.3 58.3 + - - +
325B LYS* 3.7 7.2 + - - +
326B ARG* 3.1 24.9 + - - +
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Residues in contact with ALA 323 (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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317B LEU* 3.2 19.3 - - + +
319B GLY* 3.3 38.0 + - - +
320B GLY 2.5 8.5 + - - +
322B ASP* 1.3 75.0 - - - +
324B ALA* 1.3 55.7 + - - +
326B ARG* 3.4 8.0 + - - +
327B PHE* 3.0 22.0 + - - +
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Residues in contact with ALA 324 (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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317B LEU* 3.5 12.0 - - + +
320B GLY 3.1 5.8 + - - +
321B PHE* 3.5 11.2 - - - +
323B ALA* 1.3 74.3 - - - +
325B LYS* 1.3 64.6 + - - +
326B ARG 3.1 1.1 - - - -
327B PHE* 3.1 1.8 + - - +
328B CYS* 3.0 29.1 + - - -
349B HIS* 3.7 19.5 - - + +
371B ALA 3.9 12.3 - - - +
373B VAL* 3.6 24.9 - - + -
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Residues in contact with LYS 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A SER* 5.0 10.6 + - - +
321B PHE* 2.9 50.1 + - + +
322B ASP* 4.0 8.7 - - - +
324B ALA* 1.3 73.5 - - - +
326B ARG* 1.3 63.1 + - - +
328B CYS* 3.6 3.4 + - - +
329B GLU* 3.2 56.4 + - - +
349B HIS* 4.1 12.0 - - - +
352B VAL* 5.8 7.6 - - + -
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Residues in contact with ARG 326 (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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322B ASP 3.1 18.8 + - - +
323B ALA* 3.5 9.6 - - - +
324B ALA 3.1 0.8 - - - -
325B LYS* 1.3 78.2 - - - +
327B PHE* 1.3 62.2 + - - +
329B GLU* 3.5 10.8 + - - +
330B LYS* 3.1 54.8 + - - +
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Residues in contact with PHE 327 (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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279B LEU* 6.2 2.2 - - + -
315B ILE* 4.1 13.7 - - + -
317B LEU* 3.6 18.6 - - + -
323B ALA 3.0 16.5 + - - +
324B ALA 3.1 4.2 + - - +
326B ARG* 1.3 77.2 - - - +
328B CYS* 1.3 63.1 + - - +
329B GLU 3.1 0.2 - - - -
330B LYS* 3.0 20.2 + - - +
331B THR* 3.2 28.2 + - + +
347B VAL* 4.1 6.5 - - + -
373B VAL* 3.5 37.2 - - + -
375B LEU* 4.0 12.8 - - + -
389B LEU* 3.9 42.8 - - + -
391B ARG 5.3 1.6 - - - -
392B ALA* 3.9 24.0 - - + +
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Residues in contact with CYS 328 (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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324B ALA 3.0 20.2 + - - +
325B LYS* 4.2 4.5 - - - +
327B PHE* 1.3 80.3 - - - +
329B GLU* 1.3 60.7 + - + +
331B THR* 3.7 14.1 + - - +
336B LEU* 3.6 42.7 - - + +
347B VAL* 4.1 20.0 - - - -
349B HIS* 3.8 30.3 - - + +
353B MET* 5.6 0.2 - - + -
373B VAL* 4.4 11.2 - - - -
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Residues in contact with GLU 329 (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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48A SER 3.4 27.5 - - - +
49A SER* 4.3 8.1 + - - -
325B LYS* 3.2 50.2 + - - +
326B ARG* 4.1 11.6 + - - +
327B PHE 3.1 1.2 - - - -
328B CYS* 1.3 82.6 - - + +
330B LYS* 1.3 60.8 + - - +
331B THR 3.6 4.3 - - - +
336B LEU* 5.0 2.2 - - + -
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Residues in contact with LYS 330 (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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326B ARG* 3.1 52.0 + - - +
327B PHE* 3.0 7.2 + - + +
329B GLU* 1.3 78.8 - - - +
331B THR* 1.3 66.4 + - + +
332B GLU* 3.7 10.9 + - - +
388B ASP* 5.2 0.5 - - - +
391B ARG* 3.7 31.6 - - + +
392B ALA* 5.0 9.1 - - - +
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Residues in contact with THR 331 (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 PHE* 3.2 39.5 + - + +
328B CYS* 3.7 15.5 + - - +
329B GLU 4.3 5.9 - - - +
330B LYS* 1.3 79.7 - - - +
332B GLU* 1.3 61.8 + - - +
334B PHE* 2.9 35.9 + - + +
347B VAL* 4.2 4.5 - - + +
388B ASP* 3.4 25.8 - - - +
389B LEU* 4.6 4.7 - - + -
391B ARG 5.2 1.8 + - - +
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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
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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