Contacts of the helix formed by residues 329 - 340 (chain B) in PDB entry 1EQB
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 THR 329 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B LEU* 4.7 1.8 - - - -
328B LEU* 1.3 77.8 - - - +
330B GLY* 1.3 66.4 + - - +
331B LYS* 3.7 5.4 + - - +
332B GLU* 2.9 46.8 + - - +
333B ALA* 3.0 13.0 + - - +
354B LYS* 3.5 29.2 - - + +
358B VAL* 3.7 19.6 - - + +
359B THR 3.3 11.0 - - - +
360B SER* 4.5 0.2 - - - +
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Residues in contact with GLY 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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323B LEU* 4.6 0.2 - - - -
329B THR* 1.3 71.3 - - - +
331B LYS* 1.3 55.9 + - - +
333B ALA* 3.8 1.4 - - - +
334B ASP* 2.8 34.1 + - - +
346B LYS* 3.6 7.6 - - - +
359B THR* 2.8 20.8 + - - -
361B GLY* 3.2 34.2 - - - +
362B ILE* 4.1 5.4 - - - +
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Residues in contact with LYS 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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329B THR* 3.0 7.5 - - - +
330B GLY* 1.3 76.1 - - - +
332B GLU* 1.3 60.5 + - + +
334B ASP* 3.8 3.4 - - - +
335B ALA* 3.2 24.1 + - + +
346B LYS* 3.9 15.6 - - + +
357B PHE* 4.3 35.3 - - + +
358B VAL* 3.1 31.8 + - + +
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Residues in contact with GLU 332 (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 ASN 4.1 3.1 - - - +
328B LEU* 3.4 19.6 - - + +
329B THR* 2.9 45.1 + - - +
331B LYS* 1.3 75.9 - - + +
333B ALA* 1.3 66.4 + - - +
335B ALA* 3.2 5.3 + - - +
336B ALA* 2.9 25.1 + - - +
393B ILE* 3.9 13.3 - - + +
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Residues in contact with ALA 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B LEU* 3.6 31.6 - - + -
328B LEU* 5.3 2.4 - - + +
329B THR 3.0 5.4 + - - +
330B GLY 3.8 2.0 - - - +
332B GLU* 1.3 75.4 - - - +
334B ASP* 1.3 64.3 + - - +
336B ALA* 3.1 2.1 + - - +
337B LEU* 2.9 31.9 + - + +
362B ILE* 3.6 13.9 - - + -
390B LEU* 3.8 19.1 - - + -
393B ILE* 4.1 11.1 - - + +
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Residues in contact with ASP 334 (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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65A PHE 4.6 1.3 - - - -
66A GLY* 4.0 19.6 + - - -
330B GLY 2.8 22.1 + - - +
331B LYS* 3.8 6.8 - - - +
333B ALA* 1.3 73.8 - - - +
335B ALA* 1.3 61.5 + - - +
337B LEU* 3.5 1.9 + - - +
338B GLY* 3.0 26.5 + - - -
342B ILE 4.8 0.5 - - - +
344B VAL* 3.4 26.6 + - + +
345B ASN* 3.3 25.1 - - - -
346B LYS* 3.6 14.5 + - + +
362B ILE* 4.4 1.0 - - + +
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Residues in contact with ALA 335 (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 LYS* 3.2 17.8 + - + +
332B GLU* 3.7 4.9 - - - +
334B ASP* 1.3 81.2 + - - +
336B ALA* 1.3 64.9 + - - +
338B GLY* 3.4 2.3 + - - -
339B ARG* 3.3 30.4 + - - +
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Residues in contact with ALA 336 (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 GLU 2.9 17.7 + - - +
333B ALA* 3.1 3.3 + - - +
335B ALA* 1.3 76.0 - - - +
337B LEU* 1.3 65.5 + - + +
339B ARG* 3.2 34.4 + - - +
340B ALA* 3.6 5.9 + - - +
389B VAL* 4.1 18.7 - - + +
390B LEU* 5.8 0.7 - - + -
393B ILE* 3.5 30.5 - - + +
399B ILE* 4.1 6.1 - - + +
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Residues in contact with LEU 337 (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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333B ALA 2.9 21.8 + - - +
334B ASP 3.9 2.7 - - - +
336B ALA* 1.3 76.4 - - - +
338B GLY* 1.3 60.6 + - - +
340B ALA* 3.1 10.2 + - - +
342B ILE* 2.9 47.7 + - + +
344B VAL* 3.9 20.9 - - + -
362B ILE* 4.0 14.4 - - + -
386B MET* 3.9 53.6 - - + +
389B VAL* 4.0 17.9 - - + -
390B LEU* 4.3 13.2 - - + -
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Residues in contact with GLY 338 (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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29B HIS* 4.8 7.3 - - - -
334B ASP 3.0 17.1 + - - -
335B ALA* 3.8 3.8 - - - -
336B ALA 3.1 0.8 - - - -
337B LEU* 1.3 73.5 - - - +
339B ARG* 1.3 56.1 + - - +
340B ALA 3.0 5.4 - - - -
341B ASN* 2.8 24.3 + - - +
342B ILE 3.4 10.1 + - - -
343B THR* 5.3 5.6 - - - -
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Residues in contact with ARG 339 (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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335B ALA* 3.3 17.6 + - - +
336B ALA* 3.2 18.2 + - - +
338B GLY* 1.3 76.2 - - - +
340B ALA* 1.3 55.7 + - - +
341B ASN* 3.3 1.8 - - - -
393B ILE 4.0 10.7 + - - -
394B ASN* 5.7 1.6 - - - +
396B GLU* 2.8 38.0 + - - +
399B ILE* 3.7 29.4 - - + +
400B GLU* 5.3 2.3 - - - +
403B LYS* 3.5 24.6 + - - +
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Residues in contact with ALA 340 (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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336B ALA 3.6 4.4 + - - +
337B LEU 3.1 9.6 + - - +
338B GLY 3.0 1.2 - - - -
339B ARG* 1.3 77.0 - - - +
341B ASN* 1.3 67.5 + - - +
342B ILE* 3.2 5.4 + - + +
389B VAL* 4.3 10.3 - - + -
399B ILE* 3.9 17.9 - - + +
402B ILE* 3.9 23.6 - - + -
403B LYS* 3.6 12.4 - - - -
406B VAL* 3.0 22.9 - - - +
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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