Contacts of the helix formed by residues 262 - 282 (chain S) 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 ALA 262 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258S MET* 2.8 22.3 + - + +
261S VAL* 1.3 76.9 - - + +
263S PRO* 1.4 58.4 - - - +
264S ASN 3.3 2.9 + - - -
265S VAL* 3.4 15.9 + - + -
266S THR* 3.0 23.6 + - - -
284S LEU* 5.7 7.9 - - + -
352S ASP* 4.3 15.7 - - + -
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Residues in contact with PRO 263 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258S MET 3.6 1.9 - - - +
259S LYS* 3.4 23.6 - - + +
260S GLU 5.0 0.8 - - - +
261S VAL 4.1 0.4 - - - -
262S ALA* 1.4 74.0 - - - +
264S ASN* 1.3 58.5 + - - +
266S THR* 3.7 5.5 - - - -
267S ALA* 2.9 28.4 + - - +
352S ASP* 5.0 1.0 - - - -
358S PHE* 4.8 20.2 - - + +
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Residues in contact with ASN 264 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262S ALA 3.3 0.6 - - - -
263S PRO* 1.3 75.5 - - - +
265S VAL* 1.3 66.2 + - - +
267S ALA* 3.3 16.5 + - - +
268S LEU* 3.3 13.0 + - - +
348S ALA* 3.7 33.1 - - + +
351S VAL* 5.2 6.3 - - + -
352S ASP* 4.7 9.0 - - + +
358S PHE* 5.4 3.1 - - - +
359S ILE* 5.0 8.1 - - + +
360S GLY* 4.6 18.1 - - - +
363S LEU* 6.0 1.2 - - - +
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Residues in contact with VAL 265 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262S ALA* 3.4 20.9 + - + +
264S ASN* 1.3 75.2 - - - +
266S THR* 1.3 65.8 + - - +
268S LEU* 3.0 15.5 + - - +
269S VAL* 3.1 15.2 + - - +
270S GLY 4.5 1.0 - - - +
274S GLY* 5.1 14.2 - - - +
345S LEU* 5.7 1.6 - - + +
348S ALA* 3.9 19.4 + - + +
349S ALA* 5.2 5.8 - - + +
352S ASP* 5.1 0.8 - - + +
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Residues in contact with THR 266 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258S MET* 4.1 21.8 - - - -
259S LYS* 4.7 5.6 - - - -
262S ALA 3.0 17.9 + - - -
263S PRO* 3.7 7.2 - - - -
265S VAL* 1.3 77.4 - - - +
267S ALA* 1.3 59.4 + - - +
270S GLY* 2.8 44.6 + - - -
271S PRO* 4.8 1.8 - - - -
274S GLY* 5.6 1.1 - - - -
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Residues in contact with ALA 267 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263S PRO 2.9 14.3 + - - +
264S ASN 3.3 10.8 - - - +
266S THR* 1.3 76.0 - - - +
268S LEU* 1.3 61.4 + - - +
270S GLY 4.9 0.2 + - - -
360S GLY* 3.8 30.3 - - - +
364S ASN* 5.0 8.6 - - + +
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Residues in contact with LEU 268 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264S ASN 3.3 7.6 + - - +
265S VAL* 3.0 11.6 + - - +
267S ALA* 1.3 81.2 - - - +
269S VAL* 1.3 62.2 + - + +
270S GLY 3.8 0.7 - - - -
344S LYS* 6.0 5.2 - - + -
345S LEU* 5.7 8.3 - - + +
348S ALA* 5.2 6.5 - - + -
360S GLY 5.9 0.4 - - - -
363S LEU* 6.0 7.2 - - + -
364S ASN* 5.8 7.9 - - - +
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Residues in contact with VAL 269 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265S VAL 3.1 10.5 + - - +
268S LEU* 1.3 78.7 - - + +
270S GLY* 1.3 64.5 + - - +
273S LEU* 3.5 30.0 + - + +
274S GLY* 4.6 5.4 - - - +
323S TYR* 5.7 9.9 - - + -
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Residues in contact with GLY 270 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266S THR* 2.8 28.6 + - - -
267S ALA 4.9 0.2 + - - -
268S LEU 3.8 0.6 - - - -
269S VAL* 1.3 81.8 - - - +
271S PRO* 1.3 67.7 - - - +
272S ALA 3.5 1.8 - - - -
274S GLY* 3.3 10.4 + - - -
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Residues in contact with PRO 271 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251S ASN 5.0 1.3 - - - +
254S LEU* 4.4 5.6 - - + -
255S GLU* 3.7 37.0 - - + +
258S MET* 4.1 19.9 - - + +
266S THR* 4.8 4.8 - - - -
270S GLY* 1.3 71.1 - - - +
272S ALA* 1.3 59.8 + - - +
274S GLY* 3.2 2.4 + - - -
275S ALA* 2.9 31.8 + - - +
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Residues in contact with ALA 272 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923 A 4.4 27.6 - - + +
144S VAL* 4.7 5.8 - - + +
254S LEU* 5.7 4.9 - - - +
270S GLY 3.5 0.4 - - - -
271S PRO* 1.3 78.3 - - - +
273S LEU* 1.3 52.7 + - - +
275S ALA* 3.1 7.9 + - - +
276S ARG* 2.8 36.3 + - - +
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Residues in contact with LEU 273 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923 A 6.2 0.4 - - - -
269S VAL* 3.5 29.9 + - + +
270S GLY 4.1 1.0 + - - -
272S ALA* 1.3 78.8 - - - +
274S GLY* 1.3 61.6 + - - +
276S ARG* 3.5 9.1 - - - +
277S LEU* 3.1 22.2 + - - +
319S ILE 5.5 3.6 - - - +
322S GLN* 5.3 14.4 - - + -
323S TYR* 5.9 2.9 - - - +
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Residues in contact with GLY 274 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265S VAL* 5.1 17.6 - - - +
266S THR* 5.6 0.7 - - - -
269S VAL* 4.6 5.7 + - - +
270S GLY 3.3 12.4 + - - -
271S PRO 3.2 5.5 + - - -
272S ALA 3.2 0.8 - - - -
273S LEU* 1.3 76.2 - - - +
275S ALA* 1.3 58.2 + - - +
277S LEU* 3.2 9.3 + - - +
278S LEU* 3.0 25.3 + - - +
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Residues in contact with ALA 275 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140S ALA* 4.0 21.5 - - + +
141S ILE* 4.9 1.9 - - - -
144S VAL* 3.6 23.2 - - + +
254S LEU* 5.9 5.4 - - + -
258S MET* 5.6 6.3 - - + +
271S PRO 2.9 14.3 + - - +
272S ALA* 3.4 8.7 - - - +
274S GLY* 1.3 70.2 - - - +
276S ARG* 1.3 62.5 + - - +
278S LEU* 2.9 10.8 + - - +
279S SER* 2.8 29.5 + - - -
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Residues in contact with ARG 276 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923 A 4.2 24.9 - - + +
933 G 4.4 15.3 + - - +
144S VAL* 4.4 5.3 - - - +
272S ALA 2.8 19.6 + - - +
273S LEU* 3.5 12.3 - - - +
275S ALA* 1.3 72.4 - - - +
277S LEU* 1.3 57.6 + - - +
279S SER* 3.2 9.3 + - - -
280S ILE* 3.1 28.1 + - - +
319S ILE* 5.4 7.9 - - + -
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Residues in contact with LEU 277 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273S LEU 3.1 11.3 + - - +
274S GLY* 3.3 11.9 - - - +
275S ALA 3.2 0.2 - - - -
276S ARG* 1.3 76.5 - - - +
278S LEU* 1.3 64.0 + - - +
280S ILE* 3.6 5.1 + - - +
281S ALA* 3.1 25.8 + - - +
287S LEU* 4.9 5.7 - - + +
319S ILE* 6.0 2.9 - - + +
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Residues in contact with LEU 278 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137S ASP* 5.5 9.0 - - + +
140S ALA* 5.8 3.4 - - + -
141S ILE* 5.2 9.8 - - + +
274S GLY 3.0 11.7 + - - +
275S ALA* 2.9 14.4 + - - +
277S LEU* 1.3 76.8 - - - +
279S SER* 1.3 53.2 + - - +
281S ALA* 3.4 1.0 + - - -
282S GLY* 2.7 39.2 + - - -
283S SER* 3.5 17.6 + - - +
284S LEU* 5.2 3.6 - - + +
287S LEU* 5.3 3.8 - - - -
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Residues in contact with SER 279 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141S ILE* 4.4 28.0 - - - +
144S VAL* 5.7 2.7 - - - -
145S ARG* 5.7 5.6 - - - -
275S ALA 2.8 11.9 + - - -
276S ARG* 3.2 12.8 + - - -
278S LEU* 1.3 75.1 - - - +
280S ILE* 1.3 62.8 + - - +
282S GLY* 3.9 7.5 + - - +
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Residues in contact with ILE 280 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
933 G 5.8 5.4 - - - +
943 A 5.9 2.7 - - - +
276S ARG 3.1 15.5 + - - +
277S LEU* 4.2 5.2 - - - +
279S SER* 1.3 75.6 - - - +
281S ALA* 1.3 64.1 + - - +
282S GLY* 3.5 0.3 + - - -
298S LEU* 4.5 20.4 - - + -
299S GLY* 4.9 8.1 - - - +
319S ILE* 6.4 1.3 - - + -
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Residues in contact with ALA 281 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277S LEU 3.1 18.9 + - - +
278S LEU 3.9 0.2 - - - +
280S ILE* 1.3 78.6 - - - +
282S GLY* 1.3 56.8 + - - +
283S SER 3.4 17.3 - - - +
286S GLU* 3.6 17.1 - - - +
287S LEU* 3.8 22.9 - - + +
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Residues in contact with GLY 282 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141S ILE* 5.6 5.1 - - - +
278S LEU 2.7 16.7 + - - -
279S SER* 3.9 7.1 + - - -
280S ILE 3.3 3.4 - - - -
281S ALA* 1.3 72.8 - - - +
283S SER* 1.3 60.6 + - - -
286S GLU* 5.0 0.9 - - - -
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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
------------------------------------------------------------
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