Contacts of the helix formed by residues 330 - 343 (chain C) in PDB entry 1EQR
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 330 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328C SER 4.8 2.5 + - - -
329C LEU* 1.3 76.8 - - - +
331C ARG* 1.3 58.0 + - + +
332C LYS* 2.8 37.2 - - + +
333C GLN* 2.9 27.0 + - + +
334C ILE* 2.7 38.8 + - - +
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Residues in contact with ARG 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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115B VAL* 5.9 7.9 - - + -
116B ASN 6.0 0.7 - - - -
117B THR* 5.2 4.1 - - - +
118B GLU* 3.1 54.6 + - - +
119B GLU* 6.0 0.4 + - - -
547B ASN* 5.3 3.0 - - - +
329C LEU 4.3 0.2 + - - -
330C THR* 1.3 76.1 + - + +
332C LYS* 1.3 67.2 + - + +
334C ILE* 3.6 8.8 + - - +
335C ASP* 3.0 48.5 + - - +
351C TYR* 5.0 9.1 + - - -
353C LYS* 5.6 1.4 - - - +
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Residues in contact with LYS 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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330C THR* 2.8 15.6 - - + +
331C ARG* 1.3 84.0 - - + +
333C GLN* 1.3 57.8 + - + +
335C ASP* 3.2 9.3 + - + +
336C GLU* 3.0 30.5 + - - +
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Residues in contact with GLN 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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328C SER 4.8 1.4 - - - +
329C LEU* 3.4 30.0 - - + +
330C THR* 2.9 34.7 + - + +
332C LYS* 1.3 73.9 - - + +
334C ILE* 1.3 65.6 + - - +
336C GLU* 2.6 43.0 + - - +
337C TYR* 3.2 13.4 - - + -
417C LEU* 5.7 4.0 - - - +
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Residues in contact with ILE 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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329C LEU* 4.3 10.8 - - + +
330C THR 2.7 26.1 + - - +
331C ARG* 3.9 7.0 - - - +
333C GLN* 1.3 71.4 - - - +
335C ASP* 1.3 57.4 + - - +
337C TYR* 3.1 12.9 + - - +
338C GLY* 2.7 32.2 + - - -
349C LEU* 4.8 5.5 - - + +
351C TYR* 3.7 43.1 - - + +
353C LYS* 4.1 15.3 - - - +
391C MET* 3.6 30.3 - - + -
393C PHE* 4.3 11.7 - - + -
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Residues in contact with ASP 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 ARG* 3.0 47.1 + - - +
332C LYS* 3.6 7.2 - - + +
334C ILE* 1.3 79.1 - - - +
336C GLU* 1.3 64.9 + - - +
338C GLY* 3.1 4.4 + - - +
339C ASN* 2.9 32.4 + - - +
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Residues in contact with GLU 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 LYS* 3.0 10.0 + - - +
333C GLN* 2.6 57.2 + - - +
335C ASP* 1.3 74.1 - - - +
337C TYR* 1.3 77.6 + - + +
339C ASN* 2.7 29.7 + - - +
340C PHE* 2.8 14.0 + - - +
412C LYS* 5.7 1.7 + - - -
416C ASP* 4.7 4.3 - - - +
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Residues in contact with TYR 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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329C LEU* 3.3 32.5 - - + +
333C GLN* 3.2 16.6 - - + -
334C ILE* 3.1 5.8 + - - +
336C GLU* 1.3 94.3 + - + +
338C GLY* 1.3 64.8 + - - +
340C PHE* 2.9 20.4 + - + +
341C VAL* 3.0 18.5 + - - +
349C LEU* 3.8 16.6 - - + -
393C PHE* 4.2 9.9 - + - -
409C LEU* 3.7 17.5 - - + -
412C LYS* 4.4 8.5 - - + -
413C VAL* 3.4 32.7 - - + +
416C ASP* 3.1 38.4 + - - +
417C LEU* 4.5 7.6 - - - +
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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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334C ILE* 2.7 14.2 + - - -
335C ASP* 3.1 7.4 + - - -
336C GLU 3.0 0.6 - - - -
337C TYR* 1.3 76.2 - - - +
339C ASN* 1.3 58.2 + - - +
341C VAL* 2.9 22.9 - - - +
342C LYS* 3.5 12.4 - - - +
348C GLY* 4.8 3.2 - - - -
349C LEU* 4.2 19.9 - - - +
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Residues in contact with ASN 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 ASP* 2.9 26.9 + - - +
336C GLU* 2.7 15.3 + - - +
338C GLY* 1.3 71.0 - - - +
340C PHE* 1.3 63.0 + - - +
341C VAL 3.2 0.7 - - - -
342C LYS* 2.8 54.3 + - + +
343C ILE* 3.7 6.6 + - - +
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Residues in contact with PHE 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 GLU 2.8 15.8 + - - +
337C TYR* 3.5 15.3 - + + +
339C ASN* 1.3 74.3 - - - +
341C VAL* 1.3 67.0 + - + +
343C ILE* 3.3 39.2 + - + +
344C TYR* 3.4 38.8 - + - -
405C ALA 4.8 0.4 - - - -
408C ALA* 3.7 15.0 - - + -
409C LEU* 3.9 17.0 - - + -
412C LYS* 3.2 45.8 - - + -
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Residues in contact with VAL 341 (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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337C TYR 3.0 10.7 + - - +
338C GLY* 2.9 28.3 - - - +
340C PHE* 1.3 79.0 - - + +
342C LYS* 1.3 67.3 + - - +
344C TYR* 2.9 19.3 + - - +
346C ALA* 3.3 32.5 + - + +
348C GLY 3.6 18.4 - - - +
349C LEU* 3.9 14.8 - - + -
405C ALA* 4.1 12.8 - - + -
406C MET* 5.0 0.2 - - - -
409C LEU* 3.8 32.5 - - + -
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Residues in contact with LYS 342 (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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222B ARG* 5.7 7.0 - - - +
223B ALA* 5.6 7.7 - - - +
338C GLY 3.5 17.3 - - - +
339C ASN* 2.8 39.9 + - + +
341C VAL* 1.3 80.2 - - + +
343C ILE* 1.3 55.4 + - - +
345C GLY* 2.7 25.6 + - - -
346C ALA 3.3 22.2 - - - +
347C LYS* 5.5 1.8 - - - +
348C GLY* 5.0 7.0 - - - +
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Residues in contact with ILE 343 (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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343B ILE* 3.8 51.9 - - + +
339C ASN 4.1 6.1 - - - +
340C PHE* 3.3 39.7 - - + +
341C VAL 3.1 0.2 - - - -
342C LYS* 1.3 76.9 - - + +
344C TYR* 1.3 75.8 + - + +
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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