Contacts of the helix formed by residues 391 - 403 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388A VAL 4.1 1.1 + - - -
389A ALA 2.8 0.8 + - - -
390A GLY* 1.3 71.5 - - - +
392A LEU* 1.3 57.7 + - - +
393A LYS 3.2 2.2 - - - -
394A LEU* 2.6 38.2 + - - +
395A PHE* 2.8 37.5 + - - -
451A VAL* 3.2 29.8 - - - +
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Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A ALA* 4.2 17.9 - - + -
158A LEU* 3.7 21.3 - - + -
389A ALA* 2.8 18.7 + - + +
391A SER* 1.3 79.8 + - - +
393A LYS* 1.3 65.0 + - - +
394A LEU 3.0 0.9 + - - -
395A PHE* 4.4 2.2 - - - -
396A LEU* 3.2 43.2 + - + +
426A LEU* 3.7 34.1 - - + +
430A LEU* 4.4 18.4 - - + -
447A ILE* 4.4 17.7 - - + -
451A VAL* 4.0 9.0 - - + +
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Residues in contact with LYS 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LEU* 3.8 17.5 - - + +
369A VAL* 5.7 3.4 - - + +
389A ALA 3.4 4.4 + - - +
390A GLY 3.6 13.9 - - - +
392A LEU* 1.3 80.1 - - - +
394A LEU* 1.3 61.3 + - + +
396A LEU* 4.4 1.7 - - - +
397A ALA* 3.2 25.8 + - - +
400A ARG* 4.8 2.8 + - - -
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Residues in contact with LEU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A GLY 5.2 1.6 - - - +
391A SER* 2.6 32.4 + - - +
393A LYS* 1.3 74.6 - - + +
395A PHE* 1.3 69.4 + - + +
396A LEU 3.2 1.3 - - - -
397A ALA* 3.0 9.8 + - + +
398A GLN* 2.8 46.8 + - + +
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Residues in contact with PHE 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A SER* 2.8 49.7 + - - -
392A LEU* 4.3 3.4 - - - +
394A LEU* 1.3 77.0 - - + +
396A LEU* 1.3 50.4 + - - +
398A GLN* 3.0 17.4 + - - +
399A TYR* 2.6 36.5 + - - +
419A THR* 5.1 4.3 - - + +
422A ARG* 4.4 23.3 - - + -
423A GLY* 5.7 2.7 - - - +
426A LEU* 3.8 29.4 - - + -
451A VAL* 3.3 30.1 - - + -
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Residues in contact with LEU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LEU* 4.0 14.4 - - + -
369A VAL* 4.4 9.0 - - + -
392A LEU* 3.2 36.8 + - + +
393A LYS* 4.4 1.3 - - - +
394A LEU 3.2 0.6 - - - -
395A PHE* 1.3 75.0 - - - +
397A ALA* 1.3 66.4 + - - +
399A TYR* 3.2 13.5 - - + +
400A ARG* 3.1 45.9 + - + +
423A GLY* 4.2 12.6 - - - +
426A LEU* 4.4 6.5 - - + -
427A THR* 3.7 28.0 - - - +
430A LEU* 3.8 25.8 - - + -
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Residues in contact with ALA 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A LYS* 3.2 17.3 + - + +
394A LEU* 3.0 15.4 + - + +
396A LEU* 1.3 79.5 - - - +
398A GLN* 1.3 63.7 + - + +
399A TYR 3.4 0.2 + - - -
400A ARG* 3.5 27.0 + - - +
401A GLU* 3.2 32.1 + - - +
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Residues in contact with GLN 398 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A LEU* 2.8 34.4 + - + +
395A PHE* 3.5 19.8 - - - +
397A ALA* 1.3 73.6 - - + +
399A TYR* 1.3 65.9 + - - +
401A GLU* 3.6 16.6 - - - +
402A VAL* 3.4 26.9 + - + +
419A THR* 4.3 16.1 - - + +
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Residues in contact with TYR 399 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A PHE 2.6 17.3 + - - +
396A LEU* 3.2 19.3 - - + +
398A GLN* 1.3 69.4 - - - +
400A ARG* 1.3 64.6 + - + +
401A GLU 3.0 3.8 - - - -
402A VAL* 2.9 22.7 + - + +
403A ALA* 2.9 19.2 + - + -
406A ALA* 5.5 3.2 - - + +
419A THR* 4.0 15.2 - - + +
420A LEU* 3.8 38.3 - - + +
423A GLY* 3.9 20.2 - - - -
424A GLU* 3.3 29.2 - - - +
427A THR* 3.9 21.5 - - + -
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Residues in contact with ARG 400 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368A ASN* 5.6 1.6 - - - -
369A VAL* 3.2 33.6 - - - +
370A GLY* 3.6 29.8 - - - +
393A LYS 4.8 1.6 + - - -
396A LEU* 3.1 15.7 + - + +
397A ALA* 3.5 41.8 + - - +
399A TYR* 1.3 80.9 - - + +
401A GLU* 1.3 58.4 + - - +
403A ALA* 4.0 17.2 - - - +
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Residues in contact with GLU 401 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397A ALA* 3.2 26.5 + - - +
398A GLN* 3.6 21.1 + - - +
399A TYR 2.9 0.8 + - - -
400A ARG* 1.3 80.0 - - - +
402A VAL* 1.3 62.7 + - + +
403A ALA 3.3 2.2 + - - -
404A ALA* 5.2 1.4 + - - +
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Residues in contact with VAL 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A GLN* 3.4 17.5 + - + +
399A TYR* 2.9 7.3 + - + +
401A GLU* 1.3 80.8 - - + +
403A ALA* 1.3 54.2 + - - +
404A ALA* 3.4 2.5 - - - -
405A SER* 2.8 47.7 + - - +
406A ALA 4.0 0.5 + - - -
416A THR* 4.0 25.8 - - + -
419A THR* 5.2 10.8 - - + -
420A LEU* 4.4 14.6 - - + +
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Residues in contact with ALA 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A TYR* 2.9 23.8 + - + +
400A ARG* 4.0 18.4 - - + +
401A GLU 3.3 1.6 - - - -
402A VAL* 1.3 71.0 - - - +
404A ALA* 1.3 52.9 + - - +
405A SER 2.6 17.1 + - - -
406A ALA* 2.6 28.2 + - - +
407A GLN* 4.1 1.6 - - - +
420A LEU* 5.7 0.9 - - - -
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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