Contacts of the helix formed by residues 251 - 270 (chain k) in PDB entry 5JPQ
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 GLU 251 (chain k).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250k TRP* 1.4 78.6 - - - +
252k PRO* 1.3 66.5 - - - +
253k GLU* 3.1 11.9 - - + +
254k LYS* 3.1 20.1 + - + +
255k LEU* 3.1 12.8 + - - +
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Residues in contact with PRO 252 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24k LEU* 5.1 12.0 - - + +
27k CYS* 4.6 19.7 - - + +
28k LYS* 5.3 6.7 - - + +
250k TRP 4.0 0.4 - - - -
251k GLU* 1.3 73.6 - - - +
253k GLU* 1.3 62.8 + - - +
255k LEU* 3.3 7.9 + - + +
256k ALA* 3.1 22.7 + - - +
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Residues in contact with GLU 253 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251k GLU* 3.1 7.7 - - + +
252k PRO* 1.3 79.2 - - - +
254k LYS* 1.3 61.9 + - - +
256k ALA* 3.3 8.0 + - - +
257k ALA* 3.1 21.5 + - - +
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Residues in contact with LYS 254 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250k TRP* 4.4 9.9 - - + -
251k GLU* 3.1 21.2 + - + +
253k GLU* 1.3 76.5 - - - +
255k LEU* 1.3 64.6 + - - +
257k ALA* 3.0 9.4 + - - +
258k ASN* 3.0 22.6 + - - +
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Residues in contact with LEU 255 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27k CYS* 5.0 11.2 - - + -
62k ILE* 5.6 9.2 - - + -
245k VAL* 4.5 15.3 - - + +
246k GLY* 5.8 3.1 - - - -
247k TYR 5.8 3.6 - - - +
250k TRP* 5.4 3.5 - - + +
251k GLU 3.1 11.6 + - - +
252k PRO* 3.3 11.4 + - + +
254k LYS* 1.3 75.8 - - - +
256k ALA* 1.3 56.9 + - - +
258k ASN* 3.3 8.8 + - - +
259k ILE* 3.0 27.3 + - - +
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Residues in contact with ALA 256 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20k PRO* 5.3 7.6 - - + +
23k THR* 4.8 19.0 - - - -
24k LEU* 5.2 9.9 - - + +
27k CYS* 5.8 1.3 - - + +
252k PRO 3.1 12.3 + - - +
253k GLU* 3.5 11.9 - - - +
255k LEU* 1.3 74.1 - - - +
257k ALA* 1.3 64.9 + - - +
259k ILE* 3.2 7.4 + - - +
260k GLU* 3.0 22.7 + - - +
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Residues in contact with ALA 257 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253k GLU 3.1 12.6 + - - +
254k LYS* 3.0 12.8 + - - +
256k ALA* 1.3 76.9 - - - +
258k ASN* 1.3 62.0 + - - +
260k GLU* 3.2 9.4 + - - +
261k THR* 3.2 18.5 + - - -
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Residues in contact with ASN 258 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84k ILE* 5.3 6.2 - - - +
245k VAL* 3.4 31.4 - - + +
254k LYS 3.0 11.1 + - - +
255k LEU 3.5 7.2 - - - +
257k ALA* 1.3 74.9 - - - +
259k ILE* 1.3 63.6 + - - +
261k THR* 3.0 17.6 + - - +
262k VAL* 3.2 10.9 + - - +
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Residues in contact with ILE 259 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23k THR* 5.7 7.2 - - - -
64k LEU* 5.4 11.0 - - + -
245k VAL* 4.8 8.9 - - + +
255k LEU 3.0 14.8 + - - +
256k ALA* 3.2 11.9 + - - +
258k ASN* 1.3 75.5 - - - +
260k GLU* 1.3 57.1 + - - +
262k VAL* 3.2 10.1 + - - +
263k ILE* 2.9 26.9 + - - +
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Residues in contact with GLU 260 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256k ALA 3.0 12.7 + - - +
257k ALA* 3.3 13.7 - - - +
259k ILE* 1.3 74.7 - - - +
261k THR* 1.3 60.4 + - - +
263k ILE* 3.1 8.3 + - - +
264k ARG* 2.8 29.1 + - - +
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Residues in contact with THR 261 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83k ILE* 4.1 23.3 - - - +
84k ILE* 5.6 1.6 - - - -
257k ALA 3.2 7.7 + - - -
258k ASN* 3.0 13.2 + - - -
260k GLU* 1.3 78.2 - - - +
262k VAL* 1.3 63.1 + - - +
264k ARG* 3.3 18.5 + - - +
265k GLU 3.6 3.3 + - - -
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Residues in contact with VAL 262 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64k LEU* 6.1 4.5 - - + -
83k ILE* 4.8 5.6 - - - -
84k ILE* 4.1 24.3 - - + +
243k ILE* 5.5 6.5 - - + -
258k ASN 3.2 7.3 + - - +
259k ILE* 3.2 12.9 + - - +
260k GLU 3.2 0.4 - - - -
261k THR* 1.3 78.7 - - - +
263k ILE* 1.3 63.0 + - - +
265k GLU* 3.0 20.1 + - - +
266k LEU* 3.7 4.3 + - - +
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Residues in contact with ILE 263 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259k ILE 2.9 13.2 + - - +
260k GLU* 3.1 11.2 + - - +
262k VAL* 1.3 75.4 - - - +
264k ARG* 1.3 63.9 + - - +
266k LEU* 3.1 9.8 + - - +
267k VAL* 3.0 21.5 + - - +
275k TRP* 6.1 0.7 - - - +
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Residues in contact with ARG 264 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260k GLU 2.8 12.7 + - - +
261k THR* 3.5 14.1 - - - +
262k VAL 3.1 0.4 - - - -
263k ILE* 1.3 77.2 - - - +
265k GLU* 1.3 61.3 + - - +
267k VAL* 3.2 9.1 + - - +
268k GLU* 3.1 22.5 + - - +
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Residues in contact with GLU 265 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83k ILE* 3.7 26.7 - - + +
261k THR 3.6 1.8 + - - -
262k VAL 3.0 11.6 + - - +
264k ARG* 1.3 77.8 - - - +
266k LEU* 1.3 62.3 + - - +
268k GLU* 3.1 8.5 + - - +
269k ARG* 3.0 22.3 + - - +
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Residues in contact with LEU 266 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262k VAL 3.7 4.4 + - - +
263k ILE* 3.1 11.7 + - - +
265k GLU* 1.3 78.0 - - - +
267k VAL* 1.3 65.4 + - - +
269k ARG* 3.0 14.9 + - - +
270k PHE* 3.5 10.2 + - - +
274k LYS* 4.4 9.9 - - - +
275k TRP* 5.7 4.3 - - - -
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Residues in contact with VAL 267 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263k ILE 3.0 12.4 + - - +
264k ARG* 3.2 13.0 + - - +
266k LEU* 1.3 77.4 - - - +
268k GLU* 1.3 63.7 + - - +
271k VAL* 3.8 10.0 - - - +
274k LYS* 3.7 32.1 - - + +
275k TRP* 4.3 10.3 - - + +
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Residues in contact with GLU 268 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264k ARG 3.1 12.1 + - - +
265k GLU* 3.1 9.8 + - - +
267k VAL* 1.3 76.9 - - - +
269k ARG* 1.4 66.2 + - - +
271k VAL* 3.3 14.1 + - - +
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Residues in contact with ARG 269 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77k ARG 6.0 1.6 - - - +
265k GLU 3.0 15.1 + - - +
266k LEU* 3.0 6.6 + - - +
268k GLU* 1.4 74.1 - - - +
270k PHE* 1.3 59.8 + - - +
271k VAL 2.9 10.5 + - - -
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Residues in contact with PHE 270 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266k LEU 3.5 7.3 + - - +
269k ARG* 1.3 76.9 - - - +
271k VAL* 1.3 48.9 + - - +
272k PRO* 2.3 9.5 - - + -
273k GLN* 2.1 47.0 + - + +
274k LYS* 2.6 20.1 + - - +
277k ASN* 5.3 6.3 - - + -
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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