Contacts of the helix formed by residues 275 - 293 (chain A) in PDB entry 5ZUN
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 LEU 275 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ARG* 3.5 63.3 - - + +
187A ASN* 4.0 7.2 - - + +
274A GLU* 1.3 90.4 + - - +
276A PRO* 1.3 77.8 - - + +
277A GLU* 3.2 5.6 - - + +
278A VAL* 2.9 16.8 + - + -
279A THR 3.0 10.2 + - - -
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Residues in contact with PRO 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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187A ASN* 4.0 15.3 - - - +
274A GLU 4.3 1.6 - - - +
275A LEU* 1.3 90.8 - - + +
277A GLU* 1.3 56.7 + - + +
279A THR* 4.5 5.2 - - - +
280A ASN* 2.8 47.9 + - - +
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Residues in contact with GLU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LEU* 3.1 4.6 + - + +
276A PRO* 1.3 78.6 - - + +
278A VAL* 1.3 65.2 + - + +
280A ASN* 4.1 6.3 - - - +
281A SER* 3.2 22.3 + - - -
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Residues in contact with VAL 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ARG* 3.7 26.7 - - - +
264A TYR* 4.0 23.8 - - + -
265A GLU 6.0 1.1 - - - +
267A ALA* 4.3 6.5 - - + -
271A LEU* 3.7 30.7 - - + +
274A GLU* 3.7 13.7 - - + +
275A LEU* 2.9 10.3 + - + +
277A GLU* 1.3 78.0 - - + +
279A THR* 1.3 66.0 + - - +
281A SER* 3.0 7.2 + - - -
282A VAL* 2.9 27.4 + - + +
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Residues in contact with THR 279 (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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190A GLU* 5.3 0.4 + - - +
271A LEU 3.3 9.8 + - - -
272A HIS 3.5 19.8 + - - +
273A LYS* 3.8 0.5 - - - -
274A GLU 2.9 35.3 + - - -
275A LEU 3.0 8.8 + - - -
276A PRO* 4.0 5.4 - - - -
278A VAL* 1.3 76.2 - - - +
280A ASN* 1.3 67.7 + - - +
282A VAL* 3.2 2.2 + - - +
283A PHE* 3.0 41.6 + - + -
404A EDO 4.0 12.8 - - - -
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Residues in contact with ASN 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A PRO* 2.8 38.3 + - - +
277A GLU* 4.1 5.8 - - - +
279A THR* 1.3 79.2 - - - +
281A SER* 1.3 57.6 - - - +
283A PHE* 3.4 6.8 + - - +
284A HIS* 3.0 28.5 + - - +
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Residues in contact with SER 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LYS* 3.5 12.3 - - - -
264A TYR* 2.8 31.2 + - - -
277A GLU 3.2 13.1 + - - -
278A VAL* 3.0 8.6 + - - -
280A ASN* 1.3 77.1 - - - +
282A VAL* 1.3 59.8 + - - +
284A HIS* 3.1 7.4 + - - +
285A GLU* 2.8 35.0 + - - +
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 5.8 0.2 - - + -
145A ILE* 4.7 3.6 - - + -
234A LEU* 3.9 12.3 - - + -
264A TYR* 3.7 24.9 - - + +
271A LEU* 3.7 29.2 - - + +
272A HIS* 4.3 23.1 - - + +
278A VAL* 2.9 19.0 + - + +
279A THR* 3.6 9.4 - - - +
281A SER* 1.3 74.7 - - - +
283A PHE* 1.3 65.7 + - + +
285A GLU* 3.4 1.3 + - - +
286A ILE* 3.0 48.0 + - + +
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Residues in contact with PHE 283 (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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60A GLU* 3.6 12.3 - - + -
61A LEU* 3.6 50.9 - - + -
64A MET* 3.5 25.7 - - + +
272A HIS* 4.3 9.0 - - + -
279A THR* 3.0 35.8 + - + +
280A ASN* 3.8 6.3 - - - +
282A VAL* 1.3 80.0 - - + +
284A HIS* 1.3 58.4 + - - +
286A ILE* 4.7 0.9 - - - -
287A ASN* 2.9 31.2 + - - +
404A EDO 3.5 35.4 - - - -
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Residues in contact with HIS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ASN 3.0 18.3 + - - +
281A SER* 3.6 7.0 - - - +
283A PHE* 1.3 76.3 - - - +
285A GLU* 1.3 67.3 + - - +
287A ASN* 3.3 8.0 + - - +
288A MET* 2.9 77.5 + - + +
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Residues in contact with GLU 285 (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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232A LEU* 3.9 15.8 - - + +
234A LEU* 4.7 6.5 - - + -
262A LYS* 3.8 37.9 + - + +
264A TYR* 3.8 5.8 - - - +
281A SER* 2.8 26.8 + - - +
282A VAL* 3.9 3.1 - - - +
284A HIS* 1.3 77.4 - - + +
286A ILE* 1.3 59.9 + - - +
288A MET* 3.5 24.3 + - - +
289A TRP* 3.0 31.4 + - - +
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Residues in contact with ILE 286 (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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61A LEU* 4.1 17.3 - - + -
64A MET* 4.0 15.3 - - + -
65A LEU* 4.1 15.3 - - + -
119A LEU* 4.4 7.2 - - + -
143A VAL* 3.8 31.6 - - + -
145A ILE* 4.1 13.0 - - + -
232A LEU* 4.2 7.0 - - + -
234A LEU* 4.0 13.2 - - + -
282A VAL* 3.0 39.4 + - + +
283A PHE 3.9 3.1 - - - +
285A GLU* 1.3 73.7 - - - +
287A ASN* 1.3 65.8 + - - +
289A TRP* 4.6 0.2 - - - -
290A VAL* 3.0 32.6 + - + +
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Residues in contact with ASN 287 (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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64A MET* 3.8 27.9 - - + +
68A LEU* 3.6 24.3 - - - +
283A PHE 2.9 18.6 + - - +
284A HIS* 3.5 10.5 - - - +
286A ILE* 1.3 76.1 - - - +
288A MET* 1.3 61.5 + - - +
291A SER* 2.9 45.2 + - - -
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Residues in contact with MET 288 (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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284A HIS* 2.9 62.6 + - + +
285A GLU* 3.7 24.9 - - - +
287A ASN* 1.3 81.0 - - - +
289A TRP* 1.3 63.2 + - - +
291A SER* 3.7 4.4 - - - -
292A GLN* 3.0 48.8 + - - +
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Residues in contact with TRP 289 (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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117A PHE* 4.1 20.0 - + - -
141A GLY* 3.9 5.8 - - - -
142A MET 3.8 22.9 - - - -
143A VAL* 3.9 25.6 - - + -
230A PRO* 3.9 7.2 - - + -
231A PHE* 3.4 30.2 + - - -
232A LEU* 3.7 37.1 - - + +
258A ASP* 4.6 1.5 + - - -
260A THR* 4.5 9.5 + - + -
285A GLU 3.0 19.0 + - - +
286A ILE* 3.3 2.2 + - - +
288A MET* 1.3 79.2 - - - +
290A VAL* 1.3 68.1 + - + +
292A GLN* 4.8 1.8 - - - -
293A ARG* 3.1 80.9 + - - +
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Residues in contact with VAL 290 (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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45A ILE* 4.8 6.7 - - + -
65A LEU* 4.2 14.8 - - + -
68A LEU* 4.4 4.5 - - + -
70A LEU* 3.8 39.9 - - + -
117A PHE* 5.2 6.7 - - + -
143A VAL* 4.2 15.5 - - + -
286A ILE* 3.0 28.0 + - + +
287A ASN 4.2 1.3 - - - +
289A TRP* 1.3 90.9 - - + +
291A SER* 1.3 65.6 + - - +
293A ARG* 3.0 11.5 + - - -
294A THR* 2.8 24.1 + - + +
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Residues in contact with SER 291 (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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42A LYS* 5.8 0.2 + - - -
68A LEU* 3.5 20.2 - - - +
287A ASN* 2.9 35.6 + - - -
288A MET* 3.7 6.7 - - - -
290A VAL* 1.3 76.9 - - - +
292A GLN* 1.3 64.5 + - - +
294A THR* 3.3 7.6 + - - -
295A ALA* 3.1 25.1 + - - +
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Residues in contact with GLN 292 (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 MET* 3.0 43.0 + - - +
289A TRP* 3.9 4.6 - - - +
290A VAL 3.2 0.2 - - - -
291A SER* 1.3 78.1 - - - +
293A ARG* 1.3 75.7 + - - +
294A THR 3.4 0.6 + - - -
295A ALA* 4.3 10.4 + - - +
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Residues in contact with ARG 293 (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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115A PRO* 6.0 1.9 - - - +
117A PHE* 3.7 21.9 - - + -
140A ALA* 5.5 2.1 - - - +
230A PRO* 4.9 3.8 - - - -
258A ASP* 2.8 40.3 + - - +
260A THR* 5.0 3.2 + - - -
289A TRP* 3.1 80.3 + - - +
290A VAL 3.0 4.2 + - - +
292A GLN* 1.3 96.1 + - - +
294A THR* 1.3 64.7 + - - +
295A ALA 3.8 0.2 - - - -
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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
------------------------------------------------------------
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