Contacts of the helix formed by residues 391 - 407 (chain B) in PDB entry 3OEE
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 SER 391 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389B ALA 2.7 5.2 + - - -
390B GLY* 1.3 68.7 - - - -
392B LEU* 1.3 55.1 + - - -
393B LYS* 2.9 6.3 - - - +
394B LEU* 2.5 53.4 + - - +
395B PHE* 2.7 19.3 + - - -
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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
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157B ALA* 5.0 6.7 - - + -
158B LEU* 3.8 22.6 - - + +
388B VAL 4.7 1.8 - - - +
389B ALA* 2.9 18.1 + - - +
390B GLY 2.6 12.6 + - - +
391B SER* 1.3 70.5 - - - +
393B LYS* 1.3 55.7 - - - +
395B PHE* 4.5 8.1 - - + -
396B LEU* 2.9 55.4 + - + +
426B LEU* 3.6 36.1 - - + -
429B LEU* 6.5 0.2 - - + -
430B LEU* 5.3 8.3 - - + -
447B ILE* 3.8 28.5 - - + -
451B VAL* 4.5 10.1 - - + -
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Residues in contact with LYS 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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158B LEU* 3.7 42.0 - - + +
369B VAL* 4.9 14.6 + - + +
370B GLY 5.9 0.2 + - - -
372B SER 3.7 20.4 + - - -
373B VAL* 4.5 17.5 - - - +
374B SER 5.5 1.6 - - - +
389B ALA 4.2 3.8 + - - +
391B SER* 4.2 4.5 - - - +
392B LEU* 1.3 78.9 - - - +
394B LEU* 1.3 65.7 + - + +
396B LEU* 4.8 0.2 - - - +
397B ALA* 3.7 20.8 + - - +
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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
----------------------------------------------------------
391B SER* 2.5 32.2 + - - +
393B LYS* 1.3 78.1 - - + +
395B PHE* 1.3 65.8 + - - +
397B ALA* 4.0 0.7 - - - +
398B GLN* 3.1 55.8 + - - +
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Residues in contact with PHE 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 SER* 2.7 22.9 + - - +
392B LEU* 4.2 5.4 - - + +
394B LEU* 1.3 71.9 - - - +
396B LEU* 1.3 73.5 + - + +
398B GLN* 2.8 11.4 + - + +
399B TYR* 2.6 39.9 + - + -
419B THR* 3.5 36.6 - - + -
422B ARG* 3.9 18.2 - - + -
423B GLY* 3.8 28.3 - - - -
426B LEU* 3.5 31.4 - - + -
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Residues in contact with LEU 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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158B LEU* 4.1 10.8 - - + -
369B VAL* 4.9 9.9 - - + -
392B LEU* 2.9 43.0 + - + +
393B LYS 4.8 0.4 - - - +
395B PHE* 1.3 81.5 - - + +
397B ALA* 1.3 55.7 + - - +
398B GLN 2.6 12.3 + - - -
399B TYR* 2.7 40.7 + - + +
400B ARG* 3.2 8.5 + - - +
423B GLY 4.3 1.6 - - - +
426B LEU* 4.2 21.5 - - + -
427B THR* 4.2 14.4 - - - +
430B LEU* 4.0 28.0 - - + -
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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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369B VAL* 4.2 12.5 - - + +
370B GLY* 3.9 32.7 - - - +
393B LYS 3.7 17.0 + - - +
394B LEU 4.0 1.6 - - - +
395B PHE 3.5 0.4 - - - -
396B LEU* 1.3 76.0 - - - +
398B GLN* 1.3 58.5 + - - +
400B ARG* 3.4 24.5 - - - +
401B GLU* 4.6 5.4 + - - +
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Residues in contact with GLN 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* 3.1 48.9 + - - +
395B PHE* 3.1 8.4 - - - +
396B LEU 2.6 6.1 + - - -
397B ALA* 1.3 75.9 - - - +
399B TYR* 1.3 51.4 + - - -
400B ARG 2.7 5.6 - - - -
401B GLU* 2.5 48.7 + - + +
402B VAL* 3.7 3.7 + - - +
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Residues in contact with TYR 399 (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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395B PHE* 2.6 36.5 + - + +
396B LEU* 2.7 23.2 + - + +
398B GLN* 1.3 71.2 - - - +
400B ARG* 1.3 56.8 + - + +
402B VAL* 3.2 10.8 + - + +
403B ALA* 2.8 53.8 + - + +
419B THR* 3.5 21.5 - - - +
420B LEU* 4.2 19.5 - - + -
423B GLY* 3.6 21.1 - - - -
424B GLU* 3.8 22.2 + - - +
427B THR* 3.6 22.6 + - + +
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Residues in contact with ARG 400 (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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355B GLU* 5.6 2.0 + - - -
368B ASN* 4.5 23.0 + - - +
370B GLY* 5.7 6.7 - - - +
371B LEU* 5.9 2.6 - - - +
396B LEU 3.2 9.6 + - - +
397B ALA* 3.4 24.9 - - - +
398B GLN 2.7 0.2 - - - -
399B TYR* 1.3 83.2 - - + +
401B GLU* 1.3 61.7 + - - +
403B ALA* 4.0 9.3 - - + +
404B ALA* 3.4 45.8 + - - +
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Residues in contact with GLU 401 (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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397B ALA 4.8 4.6 - - - +
398B GLN* 2.5 42.0 + - + +
400B ARG* 1.3 71.2 - - - +
402B VAL* 1.3 63.8 + - + +
404B ALA* 4.2 2.5 - - - +
405B SER* 2.9 27.4 + - - -
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Residues in contact with VAL 402 (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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398B GLN 4.6 4.7 - - - +
399B TYR* 3.2 12.4 + - + +
401B GLU* 1.3 76.7 - - + +
403B ALA* 1.3 55.1 + - - +
405B SER* 2.9 7.9 + - - -
406B ALA* 2.7 38.7 + - + +
416B THR* 3.8 40.2 - - + +
419B THR* 4.2 17.9 - - - +
420B LEU* 4.0 17.0 - - + +
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Residues in contact with ALA 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 TYR* 2.8 46.2 + - + +
400B ARG* 4.1 10.3 - - + +
401B GLU 3.4 0.2 - - - -
402B VAL* 1.3 73.9 - - - +
404B ALA* 1.3 61.1 + - - +
406B ALA* 3.5 12.5 + - - +
407B GLN* 4.3 6.4 + - - +
420B LEU* 4.1 13.2 - - + +
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Residues in contact with ALA 404 (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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400B ARG* 3.4 34.9 + - - +
401B GLU* 4.2 2.7 - - - +
402B VAL 3.3 0.8 - - - -
403B ALA* 1.3 79.9 - - - +
405B SER* 1.3 62.9 + - - +
407B GLN* 4.6 4.9 + - - +
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Residues in contact with SER 405 (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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401B GLU 2.9 14.2 + - - -
402B VAL* 2.9 10.6 + - - -
404B ALA* 1.3 79.5 - - - +
406B ALA* 1.3 68.0 + - - +
407B GLN 3.3 6.6 + - - -
410B SER* 4.7 7.3 + - - -
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Residues in contact with ALA 406 (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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402B VAL* 2.7 23.1 + - + +
403B ALA 3.5 9.4 - - - +
404B ALA 3.4 0.6 - - - -
405B SER* 1.3 74.2 - - - +
407B GLN* 1.3 73.0 + - + +
410B SER 3.4 16.2 + - - +
411B ASP 5.2 2.6 + - - +
420B LEU* 4.1 26.0 - - + -
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Residues in contact with GLN 407 (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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403B ALA 4.3 7.1 + - - +
404B ALA 4.6 3.4 + - - +
405B SER 3.3 7.0 + - - -
406B ALA* 1.3 90.7 - - + +
410B SER 4.3 8.7 + - - -
420B LEU* 6.0 3.6 - - - +
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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