Contacts of the helix formed by residues 329 - 340 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323C LEU* 4.7 1.6 - - - -
328C LEU* 1.3 77.9 - - - +
330C GLY* 1.3 65.0 + - - +
331C LYS* 3.7 5.6 + - - +
332C GLU* 2.9 48.3 + - - +
333C ALA* 3.0 13.0 + - - +
354C LYS* 3.5 28.5 - - + +
358C VAL* 3.7 19.0 - - + +
359C THR 3.3 11.7 - - - +
360C SER* 4.5 0.2 - - - +
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Residues in contact with GLY 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323C LEU* 4.6 0.2 - - - -
329C THR* 1.3 71.2 - - - +
331C LYS* 1.3 57.1 + - - +
333C ALA* 3.8 1.2 - - - +
334C ASP* 2.8 34.3 + - - +
346C LYS* 3.6 7.0 - - - +
359C THR* 2.8 20.6 + - - -
361C GLY* 3.2 33.1 - - - +
362C ILE* 4.1 5.9 - - - +
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Residues in contact with LYS 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C THR* 3.0 8.2 - - - +
330C GLY* 1.3 78.0 - - - +
332C GLU* 1.3 60.3 + - + +
334C ASP* 3.8 3.8 - - - +
335C ALA* 3.2 25.4 + - + +
346C LYS* 3.9 14.3 - - + +
357C PHE* 4.3 35.6 - - + +
358C VAL* 3.1 31.0 + - + +
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Residues in contact with GLU 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C ASN 4.2 3.1 - - - +
328C LEU* 3.5 18.7 - - + +
329C THR* 2.9 44.6 + - - +
331C LYS* 1.3 74.6 - - + +
333C ALA* 1.3 67.6 + - - +
335C ALA* 3.2 5.6 + - - +
336C ALA* 2.8 24.9 + - - +
393C ILE* 3.9 14.4 - - + +
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Residues in contact with ALA 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323C LEU* 3.6 31.0 - - + -
328C LEU* 5.3 1.5 - - + +
329C THR 3.0 5.4 + - - +
330C GLY 3.8 2.0 - - - +
332C GLU* 1.3 75.0 - - - +
334C ASP* 1.3 65.2 + - - +
336C ALA* 3.0 2.4 + - - +
337C LEU* 2.8 31.5 + - + +
362C ILE* 3.6 15.0 - - + -
390C LEU* 3.8 19.3 - - + -
393C ILE* 4.1 12.0 - - + +
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Residues in contact with ASP 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330C GLY 2.8 22.6 + - - +
331C LYS* 3.8 6.5 - - - +
333C ALA* 1.3 73.7 - - - +
335C ALA* 1.3 62.5 + - - +
337C LEU* 3.9 2.3 - - - +
338C GLY* 3.0 26.0 + - - -
342C ILE 4.8 0.3 - - - +
343C THR* 6.1 0.2 - - - -
344C VAL* 3.4 25.3 + - + +
345C ASN* 3.3 25.6 - - - -
346C LYS* 3.5 14.7 + - + +
362C ILE* 4.4 1.0 - - + +
65D PHE 4.6 0.9 - - - -
66D GLY* 4.0 18.0 + - - -
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Residues in contact with ALA 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C LYS* 3.2 18.1 + - + +
332C GLU* 3.7 4.9 - - - +
334C ASP* 1.3 83.9 + - - +
336C ALA* 1.3 61.8 + - - +
338C GLY* 3.4 2.5 + - - -
339C ARG* 3.3 29.6 + - - +
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Residues in contact with ALA 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C GLU 2.8 17.2 + - - +
333C ALA* 3.5 4.0 - - - +
335C ALA* 1.3 74.1 - - - +
337C LEU* 1.3 65.9 + - - +
339C ARG* 3.1 33.4 + - - +
340C ALA 3.6 6.1 + - - -
389C VAL* 4.1 16.2 - - + +
390C LEU* 5.7 0.4 - - + -
393C ILE* 3.5 28.7 - - + -
399C ILE* 4.1 10.7 - - + +
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Residues in contact with LEU 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C ALA 2.8 24.7 + - - +
334C ASP 4.0 2.5 - - - +
336C ALA* 1.3 73.0 - - - +
338C GLY* 1.3 61.0 + - - +
340C ALA* 3.0 10.0 + - - +
342C ILE* 3.0 45.7 + - + +
344C VAL* 3.9 20.9 - - + -
362C ILE* 4.0 14.8 - - + -
386C MET* 3.9 58.6 - - + +
389C VAL* 4.0 14.4 - - + -
390C LEU* 4.3 13.0 - - + -
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Residues in contact with GLY 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C HIS* 4.8 6.7 - - - -
334C ASP 3.0 16.9 + - - -
335C ALA* 3.8 2.9 - - - -
336C ALA 3.1 0.4 - - - -
337C LEU* 1.3 73.7 - - - +
339C ARG* 1.3 56.7 + - - +
340C ALA 2.9 5.4 - - - -
341C ASN* 2.8 24.3 + - - +
342C ILE 3.6 10.5 - - - -
343C THR* 5.2 4.7 - - - -
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Residues in contact with ARG 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C ALA* 3.3 16.8 + - - +
336C ALA* 3.1 16.7 + - - +
338C GLY* 1.3 74.7 - - - +
340C ALA* 1.3 55.9 + - - +
341C ASN 3.2 1.1 - - - -
393C ILE* 4.0 11.1 + - - +
394C ASN* 5.7 2.0 - - - +
396C GLU* 6.0 4.2 - - - +
399C ILE* 3.6 40.2 - - + +
403C LYS* 3.2 26.7 + - - +
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Residues in contact with ALA 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C ALA 3.6 4.2 + - - +
337C LEU 3.0 10.0 + - - +
338C GLY 2.9 1.4 - - - -
339C ARG* 1.3 77.6 - - - +
341C ASN* 1.3 71.0 + - - +
342C ILE* 3.2 6.1 + - + +
389C VAL* 4.3 11.4 - - + -
399C ILE* 3.9 27.8 - - + +
402C ILE* 4.1 17.5 - - + -
403C LYS* 3.8 7.0 - - - -
406C VAL* 3.3 20.8 - - - +
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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