Contacts of the helix formed by residues 255 - 274 (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 ASP 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A LEU* 3.6 9.1 + - + +
254A ASN* 1.3 75.6 - - - +
256A PRO* 1.3 68.6 - - - +
257A LEU* 3.1 23.4 + - - +
258A ALA* 3.1 28.2 + - + +
259A MET* 3.0 24.4 + - - +
286A ILE 4.2 4.5 - - - +
287A THR* 3.7 19.4 + - - +
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Residues in contact with PRO 256 (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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62A PRO* 5.8 9.9 - - + -
90A PRO* 5.8 10.3 - - + -
253A ARG 5.7 0.4 - - - +
254A ASN 3.0 12.7 - - - +
255A ASP* 1.3 84.4 - - - +
257A LEU* 1.3 67.1 + - + +
259A MET* 3.2 9.9 + - + +
260A GLN* 2.9 28.4 + - + +
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Residues in contact with LEU 257 (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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59A VAL* 4.2 30.5 - - + +
62A PRO* 6.4 0.6 - - - +
255A ASP* 3.1 11.8 + - - +
256A PRO* 1.3 81.5 - - + +
258A ALA* 1.3 64.9 + - + +
260A GLN* 3.0 13.9 + - - +
261A ARG* 3.0 53.9 + - + +
286A ILE 5.2 2.7 - - - +
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Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LEU* 4.2 14.1 - - + -
255A ASP* 3.1 32.7 + - + +
257A LEU* 1.3 84.5 - - - +
259A MET* 1.3 59.1 + - - +
261A ARG* 3.4 3.9 + - - +
262A LEU* 2.9 30.1 + - - +
286A ILE* 3.7 34.8 - - + +
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Residues in contact with MET 259 (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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237A ILE* 3.8 29.2 - - + -
241A VAL* 4.3 14.8 - - + -
252A LEU* 3.5 21.3 - - - +
253A ARG* 3.8 26.9 - - + +
255A ASP 3.0 19.7 + - - +
256A PRO* 3.5 10.1 - - + +
257A LEU 3.2 0.2 - - - -
258A ALA* 1.3 74.7 - - - +
260A GLN* 1.3 61.0 + - - +
262A LEU* 3.3 10.2 + - - +
263A LYS* 2.9 29.6 + - - +
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Residues in contact with GLN 260 (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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58A ALA* 3.5 16.8 + - - +
59A VAL* 3.3 35.0 - - + +
62A PRO* 3.3 32.8 + - - +
65A THR* 5.8 0.8 - - - -
67A PHE* 5.8 1.8 - - - -
90A PRO* 4.4 18.6 - - + +
256A PRO* 2.9 16.8 + - + +
257A LEU* 3.3 11.3 - - - +
259A MET* 1.3 74.5 - - + +
261A ARG* 1.3 67.5 + - + +
262A LEU 3.1 0.2 + - - -
263A LYS* 3.1 6.4 + - - +
264A GLU* 3.0 23.4 + - - +
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Residues in contact with ARG 261 (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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59A VAL* 5.4 7.4 - - + -
257A LEU* 3.0 39.9 + - + +
258A ALA 3.8 5.6 - - - +
260A GLN* 1.3 76.3 - - + +
262A LEU* 1.3 58.1 + - - +
264A GLU* 3.5 14.1 + - - +
265A ALA* 2.9 29.8 + - - +
283A LEU* 3.8 31.2 - - + +
284A PRO* 2.8 26.7 + - - +
285A TYR* 3.0 25.3 + - - +
286A ILE* 3.5 20.8 + - + +
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Residues in contact with LEU 262 (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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237A ILE* 4.5 10.3 - - + -
240A LEU* 3.7 28.5 - - + -
241A VAL* 3.7 30.1 - - + +
252A LEU* 4.1 19.5 - - + -
258A ALA 2.9 16.9 + - - +
259A MET* 3.6 13.7 - - - +
260A GLN 3.1 0.2 - - - -
261A ARG* 1.3 76.7 - - - +
263A LYS* 1.3 60.8 + - - +
265A ALA 3.9 0.4 - - - +
266A ALA* 2.9 29.5 + - - +
281A VAL* 4.6 1.8 - - + -
283A LEU* 4.0 7.0 - - + -
286A ILE* 5.3 0.7 - - + -
296A MET* 3.5 32.3 - - + -
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Residues in contact with LYS 263 (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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67A PHE* 4.6 21.5 - - + -
230A GLU* 2.7 38.8 + - - -
233A ASP* 3.7 25.7 + - + +
237A ILE* 3.9 27.0 - - + +
259A MET 2.9 16.2 + - - +
260A GLN* 3.1 6.0 + - - +
262A LEU* 1.3 72.6 - - - +
264A GLU* 1.3 67.6 + - - +
266A ALA* 3.6 0.8 - - - +
267A GLU* 2.9 32.3 + - + +
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Residues in contact with GLU 264 (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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55A LYS* 5.4 9.1 - - - -
260A GLN 3.0 12.1 + - - +
261A ARG* 3.7 15.7 - - - +
263A LYS* 1.3 78.0 - - - +
265A ALA* 1.3 63.7 + - - +
267A GLU* 4.0 4.0 - - - +
268A LYS* 3.0 29.5 + - + +
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Residues in contact with ALA 265 (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 ARG 2.9 19.1 + - - +
262A LEU* 4.0 3.4 - - - +
264A GLU* 1.3 77.1 - - - +
266A ALA* 1.3 56.8 + - - +
268A LYS* 3.4 16.9 + - - +
269A ALA* 2.9 29.7 + - - +
281A VAL* 4.0 18.9 - - + +
282A ASN 5.8 0.7 - - - +
283A LEU* 4.0 26.9 - - + -
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Residues in contact with ALA 266 (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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233A ASP* 4.5 5.2 - - + +
236A LEU* 3.4 31.7 - - + +
237A ILE* 3.8 22.7 - - + -
240A LEU* 4.4 9.4 - - + -
262A LEU 2.9 20.6 + - - +
263A LYS 3.2 4.7 + - - +
265A ALA* 1.3 73.6 - - - +
267A GLU* 1.3 66.5 + - - +
269A ALA* 3.0 3.2 + - - -
270A LYS* 2.9 20.4 + - - +
281A VAL* 5.4 0.2 - - - -
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Residues in contact with GLU 267 (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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12A THR* 5.0 6.5 - - - +
230A GLU* 5.5 1.8 - - - +
233A ASP* 3.6 33.2 + - - +
263A LYS* 2.9 23.3 + - + +
264A GLU* 4.1 4.1 - - - +
266A ALA* 1.3 74.9 - - - +
268A LYS* 1.3 63.0 + - - +
270A LYS* 3.2 3.9 + - - +
271A ILE* 3.0 36.3 + - + +
700A ATP 3.0 37.3 + - - +
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Residues in contact with LYS 268 (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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264A GLU* 3.0 23.9 + - + +
265A ALA* 3.6 14.1 - - - +
267A GLU* 1.3 77.2 - - - +
269A ALA* 1.3 57.8 + - - +
271A ILE* 3.9 6.0 - - - +
272A GLU* 2.9 67.0 + - + +
280A ASP 5.5 4.4 + - - -
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Residues in contact with ALA 269 (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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236A LEU* 4.2 8.5 - - + -
265A ALA 2.9 17.9 + - - +
266A ALA 3.0 4.5 + - - +
268A LYS* 1.3 75.5 - - - +
270A LYS* 1.3 59.5 + - - +
272A GLU* 3.3 10.0 + - - +
273A LEU* 2.9 38.1 + - + +
279A THR* 3.9 20.1 - - + +
280A ASP 5.7 1.1 - - - +
281A VAL* 4.0 20.0 - - + -
300A VAL* 5.8 1.1 - - + -
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Residues in contact with LYS 270 (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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229A GLY 3.6 5.7 + - - -
232A PHE* 3.9 17.7 - - + -
233A ASP* 2.6 31.0 + - - +
236A LEU* 4.3 8.2 - - + +
266A ALA 2.9 11.3 + - - +
267A GLU* 3.5 13.0 - - - +
269A ALA* 1.3 75.2 - - - +
271A ILE* 1.3 59.1 + - - +
273A LEU* 2.8 21.0 + - - +
274A SER* 3.0 12.3 + - - +
305A LEU* 3.9 29.2 - - + +
343A GLN* 3.0 30.4 + - - +
346A MET* 6.0 2.7 - - + -
700A ATP 2.7 42.7 + - + -
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Residues in contact with ILE 271 (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 GLU* 3.0 37.3 + - + +
268A LYS* 4.0 5.4 - - - +
270A LYS* 1.3 74.0 - - - +
272A GLU* 1.3 64.4 + - + +
274A SER* 3.1 17.2 + - - -
275A SER* 4.2 4.5 + - - -
700A ATP 3.7 63.8 + - + +
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Residues in contact with GLU 272 (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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268A LYS* 2.9 59.5 + - + +
269A ALA* 3.6 7.1 - - - +
271A ILE* 1.3 77.6 - - + +
273A LEU* 1.3 57.7 + - - +
275A SER* 3.5 6.5 + - - -
276A ALA* 3.1 30.4 + - + +
279A THR* 2.7 30.9 + - - +
280A ASP 5.2 0.5 - - - +
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Residues in contact with LEU 273 (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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236A LEU* 5.7 1.3 - - + -
269A ALA* 2.9 20.9 + - + +
270A LYS 2.8 8.4 + - - +
272A GLU* 1.3 73.6 - - - +
274A SER* 1.3 59.9 + - - +
275A SER 3.1 2.0 - - - -
276A ALA 3.9 7.0 - - - +
278A GLN* 3.9 15.7 - - - +
279A THR* 3.8 33.0 - - + +
300A VAL* 3.6 34.8 - - + +
301A THR 3.9 6.5 - - - +
302A ARG* 3.0 41.9 + - + +
305A LEU* 3.9 26.4 - - + +
347A PRO* 4.7 1.2 - - - +
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Residues in contact with SER 274 (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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270A LYS* 3.0 7.4 + - - +
271A ILE 3.1 9.9 + - - -
273A LEU* 1.3 77.7 - - - +
275A SER* 1.3 57.3 + - - +
302A ARG* 3.5 2.8 + - - -
345A ARG 4.2 6.6 - - - +
346A MET* 3.7 12.3 - - - +
347A PRO* 3.3 31.2 - - - +
700A ATP 2.5 45.8 + - - -
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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