Contacts of the helix formed by residues 317 - 328 (chain A) in PDB entry 5NRO
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 ILE 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A TYR* 5.0 0.4 - - + +
313A VAL* 3.8 12.3 - - + +
314A ASN* 3.0 18.0 + - - +
316A SER* 1.3 88.1 - - - +
318A GLU* 1.3 69.5 + - + +
320A LEU* 3.0 37.1 + - + +
321A LYS* 3.3 14.9 + - - +
352A LYS* 4.7 30.1 - - + +
353A VAL* 4.9 7.4 - - + -
356A PHE* 3.6 29.8 - - + -
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Residues in contact with GLU 318 (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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314A ASN* 4.1 13.1 - - - +
315A ARG* 4.3 7.4 - - - +
317A ILE* 1.3 78.1 - - - +
319A PRO* 1.3 68.1 - - + +
321A LYS* 3.0 30.4 + - - +
322A VAL* 3.0 27.2 + - + +
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Residues in contact with PRO 319 (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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200A PHE* 3.9 17.9 - - + -
202A ILE* 3.7 19.7 - - + +
222A ASN* 3.8 20.2 - - + +
223A GLY* 4.2 9.2 - - - +
224A ASP* 5.9 2.0 - - + -
315A ARG 3.4 13.9 - - - +
316A SER 3.3 12.6 - - - +
318A GLU* 1.3 93.9 - - + +
320A LEU* 1.3 55.1 + - - -
322A VAL* 3.8 9.6 - - + -
323A ALA* 2.9 31.4 + - - +
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Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TYR* 4.0 17.9 - - + -
200A PHE* 4.2 0.4 - - + -
202A ILE* 3.5 41.3 - - + -
316A SER 3.6 14.6 - - - +
317A ILE* 3.0 29.2 + - + +
319A PRO* 1.3 73.4 - - - +
321A LYS* 1.3 66.6 + - - +
323A ALA* 3.3 1.9 + - - +
324A LEU* 2.9 29.2 + - + +
353A VAL* 5.2 2.5 - - + -
356A PHE* 3.7 42.2 - - + -
357A PHE* 3.8 15.9 - - + -
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Residues in contact with LYS 321 (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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317A ILE* 3.9 15.7 - - - +
318A GLU* 3.0 29.4 + - - +
320A LEU* 1.3 77.9 - - - +
322A VAL* 1.3 63.4 + - + +
324A LEU* 3.3 5.0 + - - +
325A GLN* 2.9 24.7 + - - +
356A PHE* 3.9 29.8 - - + -
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Residues in contact with VAL 322 (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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222A ASN* 3.6 23.8 - - - +
318A GLU* 3.0 20.3 + - + +
319A PRO* 4.0 8.3 - - + +
321A LYS* 1.3 76.0 - - + +
323A ALA* 1.3 56.6 + - - +
325A GLN* 3.2 14.1 + - - +
326A ASP* 2.9 38.5 + - - +
414A LYS* 3.8 9.4 - - - +
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Residues in contact with ALA 323 (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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202A ILE* 4.3 18.4 - - + +
204A ILE* 4.4 11.9 - - + -
220A ALA* 3.3 20.1 - - + +
221A THR 4.8 1.8 - - - +
222A ASN* 4.3 17.0 - - + +
319A PRO 2.9 20.0 + - - +
320A LEU 3.8 2.2 - - - +
322A VAL* 1.3 77.9 - - - +
324A LEU* 1.3 56.5 + - - +
326A ASP* 3.3 3.9 + - - -
327A ALA* 2.9 26.7 + - - +
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Residues in contact with LEU 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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204A ILE* 3.8 28.0 - - + -
320A LEU* 2.9 16.5 + - - +
321A LYS* 3.8 4.5 - - - +
323A ALA* 1.3 75.0 - - - +
325A GLN* 1.3 62.9 + - - +
327A ALA* 3.5 2.3 + - - -
328A GLY 3.1 2.6 + - - -
329A LEU* 3.0 48.4 + - + +
330A SER* 4.6 1.3 - - - +
331A VAL* 3.7 38.4 - - + +
334A ILE* 4.0 19.7 - - + -
356A PHE* 3.8 21.1 - - + -
357A PHE* 4.6 6.5 - - + -
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Residues in contact with GLN 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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321A LYS 2.9 13.8 + - - +
322A VAL* 3.4 17.9 - - - +
323A ALA 3.2 0.2 - - - -
324A LEU* 1.3 77.6 - - - +
326A ASP* 1.3 68.4 - - - +
328A GLY* 3.0 15.5 + - - -
329A LEU 5.1 0.7 - - - -
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Residues in contact with ASP 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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219A LEU 4.8 2.4 - - - +
220A ALA* 4.1 6.5 - - + +
221A THR 5.0 0.7 - - - +
222A ASN* 4.3 4.7 + - - -
322A VAL* 2.9 26.0 + - - +
323A ALA* 3.3 5.0 + - - +
325A GLN* 1.3 83.6 - - - +
327A ALA* 1.3 62.1 + - - +
328A GLY* 3.3 1.0 + - - -
414A LYS* 2.6 38.1 + - - -
415A ASN* 3.2 25.7 + - - +
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Residues in contact with ALA 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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204A ILE* 4.2 7.0 - - + -
219A LEU* 4.0 25.7 - - + +
220A ALA* 3.8 14.8 - - + +
323A ALA 2.9 16.6 + - - +
324A LEU* 4.0 5.4 - - - +
325A GLN 3.2 0.2 - - - -
326A ASP* 1.3 76.2 - - - +
328A GLY* 1.3 61.6 + - - +
329A LEU* 3.4 24.4 + - + +
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Residues in contact with GLY 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 LEU 3.1 0.8 + - - -
325A GLN* 3.0 17.9 + - - -
326A ASP 3.1 1.8 - - - -
327A ALA* 1.3 78.3 - - - +
329A LEU* 1.3 63.9 + - - +
333A ASP* 4.7 0.9 - - - +
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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