Contacts of the helix formed by residues 258 - 278 (chain A) in PDB entry 5JNQ
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 GLY 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A VAL* 6.2 0.9 - - - -
254A ILE* 2.8 27.4 + - - +
255A PRO 4.1 0.2 - - - -
257A ILE* 1.3 76.4 - - - +
259A LEU* 1.4 57.4 + - - -
260A ILE* 3.2 4.3 - - - -
261A TYR* 3.1 32.3 + - - +
262A LEU* 2.9 26.7 + - - +
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Residues in contact with LEU 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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255A PRO 3.3 25.0 + - - +
256A VAL* 3.6 4.7 + - - +
257A ILE 3.6 1.4 + - - -
258A GLY* 1.4 75.3 - - - +
260A ILE* 1.4 54.8 + - + +
262A LEU* 3.2 18.6 + - + +
263A VAL* 2.8 49.2 + - + +
310A VAL* 4.9 7.9 - - + -
314A LEU* 3.7 34.8 - - + -
403A PLM 6.3 2.7 - - + -
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Residues in contact with ILE 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A THR* 4.2 16.4 - - + +
184A VAL* 4.2 21.8 - - + -
257A ILE 5.5 0.2 + - - -
258A GLY* 3.2 1.3 - - - -
259A LEU* 1.4 82.1 - - + +
261A TYR* 1.4 62.5 + - + +
263A VAL* 3.4 8.0 + - + +
264A GLU* 3.0 29.1 + - + +
307A PHE* 3.6 49.3 - - + +
310A VAL* 3.7 26.7 - - + -
311A THR* 3.5 22.0 - - - +
314A LEU* 6.1 0.4 - - + -
403A PLM 4.3 15.5 - - + -
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Residues in contact with TYR 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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166A GLY 5.5 0.4 - - - -
167A THR* 4.8 9.9 - - + +
170A GLY* 3.3 29.1 - - - -
171A VAL* 3.6 36.3 - - + +
174A THR* 3.7 21.8 - - + -
184A VAL* 3.9 20.4 - - + -
185A THR* 2.8 44.6 + - - +
188A VAL* 3.7 20.8 - - + +
241A VAL* 4.2 21.5 - - + +
254A ILE* 5.3 3.4 - - + -
258A GLY* 3.1 21.9 + - - +
260A ILE* 1.4 75.6 - - + +
262A LEU* 1.4 61.8 + - - +
264A GLU* 3.4 2.3 + - - +
265A VAL* 3.3 18.5 + - - +
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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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254A ILE 6.1 0.2 - - - -
255A PRO* 4.0 26.5 - - + +
258A GLY 2.9 12.4 + - - +
259A LEU* 3.5 28.9 - - + +
261A TYR* 1.4 75.9 - - - +
263A VAL* 1.3 59.2 + - + +
265A VAL* 3.4 13.7 - - + +
266A LEU* 3.0 50.4 + - + +
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Residues in contact with VAL 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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259A LEU* 2.8 44.5 + - + +
260A ILE* 3.9 7.0 - - + +
262A LEU* 1.3 73.3 - - + +
264A GLU* 1.4 56.0 + - - +
266A LEU* 4.0 10.3 - - + +
267A SER* 2.9 30.8 + - - -
289A ILE* 3.6 39.5 - - + -
403A PLM 5.6 8.7 - - + -
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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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170A GLY 3.9 6.3 - - - +
173A PHE* 2.9 27.8 - - + +
174A THR* 3.3 23.3 - - - +
180A LEU* 5.5 0.2 - - - -
260A ILE* 3.0 23.1 + - + +
261A TYR 3.6 8.1 - - - +
262A LEU 3.3 0.2 - - - -
263A VAL* 1.4 73.5 - - - +
265A VAL* 1.4 61.9 + - - +
267A SER* 2.9 18.2 + - - -
268A VAL* 3.5 14.7 + - - +
288A PRO* 3.3 8.5 - - - +
289A ILE* 3.4 23.5 - - + +
290A HIS* 2.7 36.9 + - - -
307A PHE* 3.4 11.6 - - - -
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Residues in contact with VAL 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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166A GLY* 3.8 21.1 - - - +
169A ASN* 3.7 12.3 - - + -
170A GLY 3.5 22.2 - - - +
173A PHE* 3.7 23.6 - - + -
261A TYR 3.3 15.2 + - - +
262A LEU* 3.4 20.6 - - + +
264A GLU* 1.4 75.1 - - - +
266A LEU* 1.4 57.0 + - - +
268A VAL* 3.1 7.4 + - - +
269A ILE* 2.9 39.9 + - + +
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Residues in contact with LEU 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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262A LEU* 3.0 40.3 + - + +
263A VAL* 4.0 9.6 - - + +
265A VAL* 1.4 77.6 - - - +
267A SER* 1.4 55.1 + - - +
269A ILE* 3.3 14.2 + - + +
270A ILE* 2.9 55.4 + - + +
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Residues in contact with SER 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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263A VAL* 2.9 17.5 + - - -
264A GLU 2.9 21.1 + - - -
266A LEU* 1.4 74.0 - - - +
268A VAL* 1.4 56.2 + - - +
270A ILE* 3.6 1.3 + - - -
271A GLN* 2.9 33.3 + - - +
284A PHE* 3.7 29.5 - - - -
287A ALA* 4.1 2.0 - - - -
288A PRO* 3.5 2.8 - - - +
289A ILE* 3.2 35.0 + - - -
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Residues in contact with VAL 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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173A PHE* 3.8 26.9 - - + -
264A GLU 3.6 12.8 - - - +
265A VAL 3.1 9.2 + - - +
267A SER* 1.4 74.3 + - - +
269A ILE* 1.4 63.6 + - + +
271A GLN* 3.2 0.7 + - - -
272A VAL* 2.8 51.9 + - + +
287A ALA* 4.0 8.7 - - + -
288A PRO* 3.9 21.8 - - + -
401A TUM 3.7 31.4 - - + +
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Residues in contact with ILE 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A PHE* 5.8 1.6 - - + -
265A VAL* 2.9 32.1 + - + +
266A LEU* 3.3 17.5 + - + +
268A VAL* 1.4 80.3 - - + +
270A ILE* 1.4 57.1 + - + +
272A VAL* 4.5 2.2 - - - +
273A THR* 2.7 44.2 + - - +
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Residues in contact with ILE 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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266A LEU* 2.9 46.9 + - + +
267A SER* 4.0 6.7 - - - +
269A ILE* 1.4 73.7 - - + +
271A GLN* 1.4 58.4 + - - +
273A THR* 4.9 2.0 - - - -
274A TYR* 2.9 39.5 + - + +
283A ILE* 3.6 28.5 - - + -
284A PHE* 4.4 11.4 - - + -
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Residues in contact with GLN 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 SER 2.9 20.1 + - - +
268A VAL* 3.8 1.6 - - - +
270A ILE* 1.4 71.5 - - - +
272A VAL* 1.4 59.1 + - + +
274A TYR* 4.2 0.9 - - - +
275A PHE* 3.0 33.4 + - - +
281A LYS 5.0 0.5 - - - +
282A ARG* 3.6 16.0 - - - +
283A ILE* 2.8 34.1 + - - +
284A PHE* 2.8 37.0 + - + +
286A MET* 4.1 4.6 - - - +
287A ALA* 3.5 38.1 - - + +
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Residues in contact with VAL 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 VAL* 2.8 41.6 + - + +
269A ILE* 4.5 2.9 - - - +
271A GLN* 1.4 72.3 - - + +
273A THR* 1.4 61.4 + - - +
275A PHE* 3.8 5.9 - - + +
276A LYS* 3.4 46.9 + - + +
287A ALA* 6.3 0.4 - - + -
401A TUM 5.5 4.0 - - + -
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Residues in contact with THR 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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269A ILE* 2.7 33.6 + - - +
270A ILE* 4.2 2.7 - - - -
272A VAL* 1.4 74.4 - - - +
274A TYR* 1.4 58.5 + - - +
276A LYS* 3.3 7.6 + - - +
277A ARG* 3.0 42.6 + - + +
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Residues in contact with TYR 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 ILE* 2.9 28.9 + - + +
271A GLN 4.2 1.3 - - - +
273A THR* 1.4 71.5 - - - +
275A PHE* 1.4 52.1 + - - +
277A ARG* 3.3 7.0 + - + +
278A THR* 2.7 56.8 + - + +
281A LYS* 3.6 42.6 + - + +
282A ARG 3.8 12.0 + - - -
283A ILE* 3.7 44.6 - - + +
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Residues in contact with PHE 275 (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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271A GLN* 3.0 20.7 + - - +
272A VAL* 3.8 6.1 - - - +
273A THR 3.4 0.2 - - - -
274A TYR* 1.4 73.8 - - - +
276A LYS* 1.3 71.6 + - + +
278A THR* 3.2 17.4 - - - +
280A GLY* 3.3 49.8 + - - -
281A LYS 3.5 16.9 + - - +
282A ARG* 5.1 10.8 - - + -
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Residues in contact with LYS 276 (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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272A VAL* 3.4 36.5 + - + +
273A THR* 3.3 6.0 + - - +
274A TYR 3.3 0.4 - - - -
275A PHE* 1.3 88.2 - - + +
277A ARG* 1.3 62.0 + - + +
278A THR 3.2 7.9 - - - +
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Residues in contact with ARG 277 (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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273A THR* 3.0 31.7 + - + +
274A TYR* 3.3 9.8 + - + +
276A LYS* 1.3 74.2 - - + +
278A THR* 1.3 62.2 + - + +
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Residues in contact with THR 278 (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 TYR* 2.7 51.8 + - + +
275A PHE 3.2 7.1 + - - +
276A LYS* 3.2 9.7 - - - +
277A ARG* 1.3 79.8 - - + +
279A GLY* 1.3 58.2 + - - +
280A GLY 3.1 6.1 + - - -
281A LYS* 3.2 41.8 + - + +
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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