Contacts of the helix formed by residues 329 - 340 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A LEU* 4.7 1.6 - - - -
328A LEU* 1.3 78.1 - - - +
330A GLY* 1.3 65.7 - - - +
331A LYS* 3.7 6.0 + - - +
332A GLU* 2.8 48.6 + - - +
333A ALA* 3.0 12.3 + - - +
354A LYS* 3.5 28.9 - - + +
358A VAL* 3.7 18.8 - - + +
359A THR 3.3 10.8 - - - +
360A SER* 5.5 0.4 - - - +
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Residues in contact with GLY 330 (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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323A LEU* 4.6 0.4 - - - -
329A THR* 1.3 71.6 - - - +
331A LYS* 1.3 56.1 + - - +
333A ALA* 3.8 1.6 - - - +
334A ASP* 2.8 34.1 + - - +
346A LYS* 3.6 7.6 - - - +
359A THR* 2.8 20.3 + - - -
361A GLY 3.2 34.0 - - - +
362A ILE* 4.1 5.5 - - - +
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Residues in contact with LYS 331 (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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329A THR* 3.0 8.2 - - - +
330A GLY* 1.3 76.8 - - - +
332A GLU* 1.3 60.1 + - + +
334A ASP* 3.9 3.2 - - - +
335A ALA* 3.2 24.1 + - + +
346A LYS* 3.9 15.0 - - + +
357A PHE* 4.3 34.4 - - + +
358A VAL* 3.1 29.9 + - + +
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Residues in contact with GLU 332 (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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327A ASN 4.2 2.9 - - - +
328A LEU* 3.4 19.3 - - + +
329A THR* 2.8 46.2 + - - +
331A LYS* 1.3 75.3 - - + +
333A ALA* 1.3 65.8 + - - +
335A ALA* 3.2 5.4 + - - +
336A ALA* 2.9 24.4 + - - +
393A ILE* 3.9 14.2 - - + +
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Residues in contact with ALA 333 (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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323A LEU* 3.6 31.2 - - + -
328A LEU* 5.3 1.5 - - + +
329A THR 3.0 5.4 + - - +
330A GLY 3.8 2.0 - - - +
332A GLU* 1.3 75.0 - - - +
334A ASP* 1.3 65.2 + - - +
336A ALA* 3.0 2.4 + - - +
337A LEU* 2.8 31.4 + - + +
362A ILE* 3.6 14.1 - - + -
390A LEU* 3.8 19.5 - - + -
393A ILE* 4.1 12.0 - - + +
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Residues in contact with ASP 334 (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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330A GLY 2.8 22.0 + - - +
331A LYS* 3.9 6.5 - - - +
333A ALA* 1.3 74.2 - - - +
335A ALA* 1.3 60.9 + - - +
337A LEU* 3.9 1.9 - - - +
338A GLY* 3.0 25.6 + - - -
342A ILE 4.8 0.5 - - - +
344A VAL* 3.4 25.0 + - + +
345A ASN* 3.3 26.0 + - - -
346A LYS* 3.5 15.4 + - + +
362A ILE* 4.4 1.2 - - + +
65B PHE 4.6 1.3 - - - -
66B GLY* 4.0 18.2 + - - -
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Residues in contact with ALA 335 (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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331A LYS* 3.2 17.4 + - + +
332A GLU* 3.2 5.1 + - - +
334A ASP* 1.3 83.7 + - - +
336A ALA* 1.3 62.4 + - - +
338A GLY* 3.4 2.2 + - - -
339A ARG* 3.3 29.5 + - - +
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Residues in contact with ALA 336 (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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332A GLU 2.9 17.0 + - - +
333A ALA* 3.6 3.6 - - - +
335A ALA* 1.3 74.1 - - - +
337A LEU* 1.3 67.0 + - + +
339A ARG* 3.1 34.3 + - - +
340A ALA* 3.6 5.9 + - - +
389A VAL* 4.1 16.0 - - + +
390A LEU* 5.8 0.7 - - + -
393A ILE* 3.5 29.6 - - + -
399A ILE* 4.1 10.6 - - + +
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Residues in contact with LEU 337 (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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333A ALA 2.8 25.2 + - - +
334A ASP 4.0 2.2 - - - +
336A ALA* 1.3 74.5 - - - +
338A GLY* 1.3 59.7 + - - +
340A ALA* 3.1 10.1 + - - +
342A ILE* 2.9 47.4 + - + +
344A VAL* 3.9 21.3 - - + -
362A ILE* 4.0 15.3 - - + -
386A MET* 3.9 55.0 - - + +
389A VAL* 4.0 17.5 - - + -
390A LEU* 4.3 12.3 - - + -
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Residues in contact with GLY 338 (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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29A HIS* 4.8 7.2 - - - -
334A ASP 3.0 18.1 + - - -
335A ALA* 3.4 3.3 + - - -
336A ALA 3.1 0.4 - - - -
337A LEU* 1.3 74.0 - - - +
339A ARG* 1.3 55.6 + - - +
340A ALA 2.9 4.9 - - - -
341A ASN* 2.8 24.3 + - - +
342A ILE 3.4 10.3 + - - -
343A THR* 5.2 4.9 - - - -
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Residues in contact with ARG 339 (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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335A ALA* 3.3 17.1 + - - +
336A ALA* 3.1 17.4 + - - +
338A GLY* 1.3 75.2 - - - +
340A ALA* 1.3 57.2 + - - +
341A ASN* 3.2 3.1 + - - +
393A ILE* 4.0 11.1 + - - +
394A ASN* 5.7 1.8 - - - +
396A GLU* 2.8 38.8 + - - +
399A ILE* 3.6 29.3 - - + +
403A LYS* 3.6 20.4 + - - +
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Residues in contact with ALA 340 (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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336A ALA 3.6 3.2 + - - +
337A LEU 3.1 8.5 + - - +
338A GLY 2.9 1.2 - - - -
339A ARG* 1.3 78.1 - - - +
341A ASN* 1.3 70.0 + - - +
342A ILE* 3.2 6.0 + - + +
389A VAL* 4.2 12.1 - - + -
399A ILE* 3.9 23.6 - - + +
402A ILE* 4.1 19.3 - - + -
403A LYS* 3.7 11.3 - - - +
406A VAL* 3.2 21.1 - - - +
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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