Contacts of the helix formed by residues 309 - 323 (chain A) in PDB entry 1NRX
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 309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A ARG* 4.2 0.2 - - - -
307A ILE 3.9 4.0 + - - +
308A LEU* 1.3 83.7 - - + +
310A GLY* 1.3 69.1 + - - +
311A VAL* 3.0 19.7 + - + +
312A ALA* 3.0 20.4 + - + +
313A VAL* 3.5 6.2 + - - +
369A SER 4.4 3.8 + - - +
370A ALA* 6.3 1.1 - - + -
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Residues in contact with GLY 310 (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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303A ARG* 3.4 28.1 - - - +
308A LEU 3.6 3.2 + - - -
309A LYS* 1.3 73.5 - - - +
311A VAL* 1.3 64.4 + - - +
313A VAL* 3.1 19.2 + - - +
314A SER* 3.5 8.5 + - - -
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Residues in contact with VAL 311 (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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309A LYS* 4.4 17.9 - - + -
310A GLY* 1.3 78.5 - - - +
312A ALA* 1.3 63.8 + - - +
314A SER* 3.3 6.9 + - - -
315A ARG* 3.1 23.0 + - + +
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Residues in contact with ALA 312 (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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308A LEU* 3.4 24.5 - - + -
309A LYS* 3.0 7.6 + - + +
311A VAL* 1.3 78.2 - - - +
313A VAL* 1.3 66.4 + - - +
315A ARG* 3.0 11.6 + - - +
316A ILE* 2.8 27.0 + - - +
370A ALA* 5.3 0.4 - - + -
371A ILE* 3.3 33.4 - - + +
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Residues in contact with VAL 313 (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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296A VAL* 5.3 2.9 - - + +
299A ALA* 4.2 10.8 - - + +
300A GLU* 4.6 18.2 - - + +
303A ARG* 3.9 27.8 - - + +
308A LEU* 4.0 19.5 - - + +
309A LYS 3.5 9.2 + - - +
310A GLY 3.1 12.7 + - - +
312A ALA* 1.3 79.1 - - - +
314A SER* 1.3 61.8 + - - +
316A ILE* 3.0 6.6 + - - +
317A VAL* 2.9 40.3 + - + +
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Residues in contact with SER 314 (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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310A GLY 3.7 7.6 + - - -
311A VAL* 3.3 9.3 + - - -
312A ALA 3.3 0.2 - - - -
313A VAL* 1.3 76.9 - - - +
315A ARG* 1.3 61.7 + - - +
317A VAL* 4.2 8.7 - - - -
318A LYS* 2.8 45.3 + - - +
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Residues in contact with ARG 315 (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 GLU* 2.8 27.6 + - - +
207A PHE* 3.8 14.5 - - + -
208A THR* 2.6 38.2 + - - +
211A GLU* 3.1 38.9 + - - +
311A VAL* 3.1 18.9 + - + +
312A ALA* 3.0 13.4 + - - +
314A SER* 1.3 78.8 - - - +
316A ILE* 1.3 57.3 + - - +
318A LYS* 3.6 6.1 - - - +
319A CYS* 3.0 28.6 + - - +
371A ILE* 3.9 25.7 - - + +
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Residues in contact with ILE 316 (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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196A ILE* 5.6 1.6 - - + -
200A ALA* 5.0 1.3 - - + -
207A PHE* 3.8 19.1 - - + -
269A TRP* 3.3 43.1 - - + -
295A MET* 4.9 2.5 - - + -
296A VAL* 5.0 4.3 - - + +
299A ALA* 4.0 17.0 - - + -
308A LEU* 5.0 2.2 - - + -
312A ALA 2.8 10.0 + - - +
313A VAL* 3.4 7.6 - - - +
315A ARG* 1.3 73.9 - - - +
317A VAL* 1.3 67.1 + - - +
319A CYS* 3.3 1.9 + - - +
320A LEU* 3.0 43.1 + - + +
368A LEU* 3.8 7.4 - - + -
371A ILE* 3.3 33.0 - - + -
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Residues in contact with VAL 317 (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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296A VAL* 4.1 28.3 - - + -
313A VAL* 2.9 29.9 + - + +
314A SER* 3.6 9.6 - - - +
316A ILE* 1.3 76.3 - - + +
318A LYS* 1.3 78.4 + - + +
320A LEU* 3.3 1.9 + - - +
321A ALA* 3.1 24.6 + - + +
327A THR* 3.4 27.8 - - + +
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Residues in contact with LYS 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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211A GLU* 5.2 3.1 - - - +
314A SER* 2.8 42.8 + - - +
315A ARG* 3.6 7.0 - - - +
317A VAL* 1.3 86.7 - - + +
319A CYS* 1.3 52.5 + - - +
321A ALA* 3.7 4.0 - - - +
322A ALA* 2.7 39.1 + - - +
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Residues in contact with CYS 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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196A ILE* 3.9 20.4 - - + -
207A PHE* 3.6 32.1 - - + -
210A LEU* 4.4 9.6 - - - -
211A GLU* 4.1 23.9 + - + +
315A ARG 3.0 9.2 + - - +
316A ILE 3.7 2.0 - - - +
318A LYS* 1.3 73.8 - - - +
320A LEU* 1.3 67.9 + - - +
322A ALA* 3.1 13.6 + - - +
323A TYR* 3.1 41.0 + - - -
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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
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196A ILE* 3.4 37.7 - - + -
292A ALA* 3.2 32.8 - - + +
295A MET* 4.0 15.0 - - + -
296A VAL* 3.6 21.3 - - + -
316A ILE* 3.0 27.5 + - + +
317A VAL 3.6 6.1 - - - +
319A CYS* 1.3 74.9 - - - +
321A ALA* 1.3 54.2 + - - +
323A TYR* 2.8 27.0 + - - +
325A LEU* 3.1 38.6 + - + +
327A THR* 4.2 5.8 - - + -
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Residues in contact with ALA 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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218A LEU* 5.6 0.2 - - - +
317A VAL* 3.1 14.7 + - + +
318A LYS* 3.9 4.5 - - - +
320A LEU* 1.3 74.4 - - - +
322A ALA* 1.3 57.3 + - - +
323A TYR 2.9 5.8 - - - -
324A GLY* 2.9 18.5 + - - -
325A LEU 3.4 13.0 + - - +
327A THR* 3.9 15.2 + - + +
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Residues in contact with ALA 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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211A GLU* 6.3 1.1 - - - -
214A ALA* 3.9 25.7 - - + +
218A LEU* 3.3 17.5 - - - +
318A LYS 2.7 25.1 + - - +
319A CYS* 3.1 11.0 + - - +
321A ALA* 1.3 72.9 - - - +
323A TYR* 1.3 57.8 + - + +
324A GLY 3.5 0.2 - - - -
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Residues in contact with TYR 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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188A PHE* 5.6 0.2 - + - -
189A ILE* 3.4 25.6 - - - +
192A MET* 3.8 40.8 - - + -
196A ILE* 4.1 15.0 - - + -
210A LEU* 2.7 43.6 + - + +
211A GLU* 4.9 0.2 - - - -
213A ASN* 4.0 5.0 - - - +
214A ALA* 3.6 25.7 + - + -
217A ILE* 4.3 21.6 - - + +
218A LEU* 3.8 17.7 - - + +
319A CYS* 3.1 38.0 + - - -
320A LEU 2.8 10.6 + - - +
322A ALA* 1.3 82.4 - - + +
324A GLY* 1.3 57.2 + - - +
325A LEU* 3.4 6.7 - - + +
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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