Contacts of the helix formed by residues 323 - 334 (chain a) in PDB entry 4RO0
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 LYS 323 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261a THR* 3.4 21.1 - - - +
262a ARG* 4.0 26.6 - - + +
322a GLY* 1.3 73.3 - - - -
324a PRO* 1.3 65.1 - - + +
325a GLU* 3.2 30.2 + - - +
326a GLU* 2.8 41.7 + - + +
327a ILE* 2.8 25.9 + - - +
329a ARG* 5.8 1.0 - - - +
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Residues in contact with PRO 324 (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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261a THR 3.5 17.3 - - - +
262a ARG* 5.1 0.7 - - - -
263a ARG* 5.6 4.0 - - + +
322a GLY 3.9 3.1 - - - +
323a LYS* 1.3 84.1 - - + +
325a GLU* 1.3 65.1 + - + +
327a ILE* 3.3 13.3 + - + +
328a GLU* 2.9 29.8 + - - +
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Residues in contact with GLU 325 (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 LYS* 3.2 47.0 + - - +
324a PRO* 1.3 80.5 - - + +
326a GLU* 1.3 61.6 + - - +
328a GLU* 3.5 7.7 - - - +
329a ARG* 2.8 47.3 + - - +
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Residues in contact with GLU 326 (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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305A ASP* 3.8 3.3 - - - +
262a ARG* 3.3 25.0 + - - -
289a THR* 3.5 24.1 + - - +
290a GLY* 3.1 29.2 - - - +
291a VAL* 3.3 18.2 - - + +
321a ILE 4.5 0.2 - - - +
322a GLY* 3.5 4.9 - - - -
323a LYS* 2.8 62.8 + - + +
325a GLU* 1.3 73.5 - - - +
327a ILE* 1.3 58.4 + - - +
329a ARG* 3.4 9.8 + - - +
330a LEU 3.3 14.4 + - - -
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Residues in contact with ILE 327 (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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263a ARG* 4.3 16.6 - - + +
265a VAL* 3.7 43.7 - - + -
267a VAL* 5.0 5.2 - - + -
291a VAL* 4.0 7.0 - - + -
322a GLY* 3.2 37.2 - - - +
323a LYS 2.8 18.1 + - - +
324a PRO* 3.6 11.7 - - + +
326a GLU* 1.3 71.3 - - - +
328a GLU* 1.3 58.2 - - - +
330a LEU* 2.8 26.0 + - + +
331a LYS* 3.1 36.8 + - + +
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Residues in contact with GLU 328 (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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324a PRO 2.9 18.5 + - - +
325a GLU* 3.5 9.6 - - - +
327a ILE* 1.3 78.0 - - - +
329a ARG* 1.3 60.3 + - - +
330a LEU 3.4 0.7 + - - -
331a LYS* 3.4 28.2 + - - +
332a ASN* 3.5 23.7 + - - +
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Residues in contact with ARG 329 (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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288a VAL 3.9 19.4 + - - +
289a THR* 3.7 30.1 + - + +
290a GLY* 5.4 1.0 - - - -
323a LYS* 5.8 1.0 - - - +
325a GLU* 2.8 37.0 + - - +
326a GLU* 3.5 14.9 - - - +
328a GLU* 1.3 76.7 - - - +
330a LEU* 1.3 60.8 + - - +
332a ASN* 3.7 6.0 + - + +
333a TYR* 3.3 22.0 + - - +
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Residues in contact with LEU 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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265a VAL* 5.6 1.8 - - + -
267a VAL* 4.8 18.4 - - + -
275a LEU* 5.4 0.9 - - + -
285a ILE* 4.1 22.9 - - + -
289a THR* 3.8 18.4 - - + +
291a VAL* 3.7 33.9 - - + -
293a ILE* 6.5 0.7 - - + -
318a ILE* 4.5 20.9 - - + -
326a GLU 3.3 6.3 + - - +
327a ILE* 2.8 13.8 + - - +
329a ARG* 1.3 76.2 - - - +
331a LYS* 1.3 64.1 + - - +
332a ASN 3.1 0.2 - - - -
333a TYR* 3.1 15.1 + - + +
334a ILE* 3.2 35.3 + - + +
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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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263a ARG* 4.5 11.5 - - - +
265a VAL* 5.7 0.2 - - - +
267a VAL* 4.2 26.4 - - + +
327a ILE* 3.1 36.4 + - + +
328a GLU* 3.4 29.2 + - - +
330a LEU* 1.3 76.1 - - - +
332a ASN* 1.3 62.0 + - - +
334a ILE* 3.1 27.3 + - - +
335a SER* 3.7 8.1 + - - -
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Residues in contact with ASN 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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274a LYS* 4.4 4.7 + - - +
328a GLU* 3.5 20.4 + - - +
329a ARG* 4.1 8.1 - - + +
330a LEU 3.1 0.6 - - - -
331a LYS* 1.3 79.9 - - - +
333a TYR* 1.3 57.5 + - - +
334a ILE 2.9 9.6 + - - -
335a SER* 3.6 19.3 + - - +
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Residues in contact with TYR 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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274a LYS* 3.6 42.1 - - + +
275a LEU* 3.7 36.8 - - + +
282a ASP 4.8 1.4 + - - -
283a ALA* 2.8 30.7 + - - -
285a ILE* 4.2 13.9 - - + -
288a VAL* 4.1 28.1 - - + +
289a THR* 3.8 18.6 - - + -
329a ARG 3.3 16.3 + - - +
330a LEU* 3.1 7.5 + - + +
332a ASN* 1.3 77.5 - - - +
334a ILE* 1.3 57.3 + - - +
335a SER 3.6 0.2 - - - -
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Residues in contact with ILE 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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267a VAL* 4.8 10.1 - - + +
268a PRO 3.8 12.3 - - - +
269a ILE* 3.8 17.5 - - + -
270a PRO* 3.8 22.1 - - + +
273a SER* 2.9 32.8 + - - +
274a LYS 4.1 2.7 - - - -
275a LEU* 3.8 17.3 - - + -
318a ILE* 3.7 29.8 - - + -
330a LEU* 3.2 20.6 + - + +
331a LYS* 3.1 24.9 - - - +
332a ASN 2.9 1.6 - - - -
333a TYR* 1.3 81.2 - - - +
335a SER* 1.3 59.5 + - - +
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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