Contacts of the helix formed by residues 249 - 267 (chain D) in PDB entry 4K71
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 249 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D HIS* 2.6 35.2 + - - -
244D GLU* 2.8 20.3 + - + +
247D HIS* 2.7 34.8 + - - +
248D GLY* 1.3 76.1 - - - +
250D LEU* 1.3 59.9 + - - +
252D GLU* 3.3 34.9 - - + +
253D CYS* 3.1 27.5 + - - +
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Residues in contact with LEU 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU* 4.1 15.8 - - + +
25D ILE* 3.9 4.3 - - + -
26D ALA* 3.8 31.0 - - + +
29D GLN* 3.6 24.7 - - - +
70D PHE* 6.3 0.6 - - - -
106D LYS* 6.0 0.7 - - - +
149D PHE 6.0 0.7 - - - +
151D ALA* 3.8 24.6 - - + +
152D PRO* 5.7 0.2 - - - +
245D CYS* 3.4 41.0 - - - +
248D GLY* 3.1 19.2 + - - +
249D ASP* 1.3 72.7 - - - +
251D LEU* 1.3 62.3 + - + +
252D GLU* 3.7 0.4 + - - -
253D CYS* 3.5 3.8 - - - +
254D ALA* 2.9 31.7 + - - +
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Residues in contact with LEU 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ARG* 4.0 15.8 - - + -
14D LEU* 3.7 30.7 - - + +
19D PHE* 4.0 36.1 - - + +
22D LEU* 3.8 25.6 - - + -
23D VAL* 4.3 4.7 - - + +
66D LEU* 3.8 17.7 - - + -
70D PHE* 3.8 32.7 - - + -
250D LEU* 1.3 77.3 - - + +
252D GLU* 1.3 68.1 + - - +
255D ASP* 3.1 24.9 + - - +
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Residues in contact with GLU 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D GLU* 4.3 7.8 - - - +
10D ARG* 3.6 31.3 + - - +
66D LEU* 3.4 31.6 - - - +
70D PHE* 6.1 1.0 - - - -
244D GLU* 3.5 19.7 - - + +
249D ASP* 3.3 45.6 - - + +
250D LEU 3.7 0.2 + - - -
251D LEU* 1.3 78.7 + - - +
253D CYS* 1.3 58.5 + - - +
255D ASP* 3.7 1.0 - - - +
256D ASP* 3.0 35.1 + - - +
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Residues in contact with CYS 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D TYR* 4.1 4.3 - - - -
152D PRO* 4.2 4.7 - - - -
241D VAL* 3.5 22.9 - - - +
244D GLU* 3.6 11.1 + - - -
245D CYS* 2.0 58.1 - - - +
249D ASP 3.1 19.1 + - - +
250D LEU 3.5 3.1 - - - +
252D GLU* 1.3 74.2 - - - +
254D ALA* 1.3 61.2 + - - +
256D ASP* 3.8 0.6 - - - -
257D ARG* 2.9 31.0 + - - +
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Residues in contact with ALA 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 3.8 11.5 - - + +
22D LEU* 3.4 38.1 - - + -
152D PRO* 4.2 19.5 - - + -
155D LEU* 5.3 2.2 - - + -
250D LEU 2.9 15.9 + - - +
251D LEU 4.0 1.1 - - - +
253D CYS* 1.3 73.1 - - - +
255D ASP* 1.3 57.6 + - - +
257D ARG* 3.4 2.8 + - - +
258D ALA* 3.0 28.9 + - - +
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Residues in contact with ASP 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D HIS* 4.1 0.2 - - - -
10D ARG* 2.8 30.3 + - - +
13D ASP* 2.4 49.5 - - - +
14D LEU* 4.2 11.1 - - + +
251D LEU 3.1 18.3 + - - +
252D GLU 3.7 0.9 - - - +
254D ALA* 1.3 76.7 - - - +
256D ASP* 1.3 64.0 + - - +
258D ALA* 3.3 8.3 + - - +
259D ASP* 3.2 32.9 + - - +
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Residues in contact with ASP 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ARG* 4.9 8.1 + - - -
237D ASP 5.7 0.2 - - - +
240D LYS* 4.0 15.9 + - + -
241D VAL* 3.7 19.8 - - + +
244D GLU* 2.6 33.3 - - - +
252D GLU* 3.0 16.8 + - - +
253D CYS 4.0 0.7 - - - +
255D ASP* 1.3 74.4 - - - +
257D ARG* 1.3 63.7 + - - +
259D ASP* 3.5 15.4 + - - +
260D LEU* 3.0 23.2 + - - +
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Residues in contact with ARG 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D TYR* 3.1 40.0 + - - +
152D PRO* 3.6 35.7 + - + +
153D GLU* 4.3 8.1 - - - +
156D PHE* 6.3 0.2 - - - +
238D LEU* 6.1 1.8 - - + +
241D VAL* 3.7 13.6 - - + +
253D CYS 2.9 18.3 + - - +
254D ALA* 3.6 7.0 - - - +
256D ASP* 1.3 75.2 - - - +
258D ALA* 1.3 63.6 + - - +
260D LEU* 3.0 10.9 + - + +
261D ALA* 3.0 21.8 + - - +
284D LEU 5.4 0.8 + - - -
287D SER* 3.5 46.6 + - - -
288D HIS* 4.4 5.9 + - - +
291D ALA* 3.7 18.6 - - - +
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Residues in contact with ALA 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 5.9 2.7 - - + -
254D ALA 3.0 13.8 + - - +
255D ASP* 3.3 13.0 + - - +
257D ARG* 1.3 76.3 - - - +
259D ASP* 1.3 61.4 + - - +
261D ALA* 3.3 7.2 + - - +
262D LYS* 3.1 29.6 + - - +
283D LEU* 3.9 34.4 - - + +
287D SER* 4.6 3.8 - - - -
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Residues in contact with ASP 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D ASP* 3.2 22.9 + - - +
256D ASP* 3.6 19.9 - - - +
257D ARG 3.3 0.2 - - - -
258D ALA* 1.3 80.9 - - - +
260D LEU* 1.3 56.2 + - - +
262D LYS* 3.2 17.8 + - - +
263D TYR* 2.9 28.4 + - - +
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Residues in contact with LEU 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D LEU* 3.7 31.9 - - + +
237D ASP* 3.9 28.0 - - + +
238D LEU* 4.0 43.3 - - + +
241D VAL* 4.9 4.7 - - + -
256D ASP 3.0 13.9 + - - +
257D ARG* 3.0 13.6 + - + +
259D ASP* 1.3 71.9 - - - +
261D ALA* 1.3 60.9 + - - +
263D TYR* 3.3 8.6 + - + +
264D ILE* 2.9 39.1 + - + +
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Residues in contact with ALA 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D ARG 3.0 9.7 + - - +
258D ALA 3.3 9.2 + - - +
260D LEU* 1.3 76.1 - - - +
262D LYS* 1.3 55.8 + - - +
264D ILE* 3.1 6.3 + - - +
265D CYS* 2.9 34.9 + - - -
283D LEU* 4.6 4.7 - - + -
286D LYS* 4.4 9.0 - - + -
287D SER* 3.6 26.9 - - - +
290D ILE* 4.0 22.7 - - + -
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Residues in contact with LYS 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D ALA* 3.1 17.9 + - - +
259D ASP* 3.2 20.1 + - - +
261D ALA* 1.3 76.5 - - - +
263D TYR* 1.3 62.0 + - - +
265D CYS* 3.4 5.8 + - - +
266D GLU* 3.0 37.8 + - - +
283D LEU* 4.4 31.5 - - + +
286D LYS* 4.9 11.9 - - - +
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Residues in contact with TYR 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D GLU* 3.1 32.1 + - - -
233D LYS* 3.5 44.3 - - + +
234D LEU* 4.1 18.8 - - + -
237D ASP* 5.2 1.3 - - - +
259D ASP 2.9 13.7 + - - +
260D LEU* 3.6 12.6 - - + +
262D LYS* 1.3 73.9 - - - +
264D ILE* 1.3 69.3 + - + +
266D GLU* 3.1 15.0 + - - -
267D ASN* 3.0 51.1 + - + +
271D ILE* 4.6 0.9 - - + -
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Residues in contact with ILE 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D PHE* 5.1 8.3 - - + -
234D LEU* 3.8 35.2 - - + -
260D LEU* 2.9 31.7 + - + +
261D ALA* 3.1 9.8 + - - +
263D TYR* 1.3 77.2 - - - +
265D CYS* 1.3 61.7 + - - +
267D ASN 3.4 2.9 + - - -
268D GLN* 3.3 21.7 + - - +
271D ILE* 3.8 15.2 - - + +
275D LEU* 3.5 25.8 - - + -
290D ILE* 3.9 34.5 - - + -
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Residues in contact with CYS 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D ALA 2.9 18.7 + - - +
262D LYS* 3.9 5.4 - - - +
264D ILE* 1.3 76.2 - - - +
266D GLU* 1.3 58.9 + - + +
267D ASN 3.3 3.0 + - - -
268D GLN* 3.6 20.2 + - - +
279D CYS* 2.0 57.8 - - + +
286D LYS* 3.7 20.4 - - + +
290D ILE* 3.8 9.9 - - - -
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Residues in contact with GLU 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D LYS* 3.0 33.1 + - + +
263D TYR* 3.1 6.8 + - - -
265D CYS* 1.3 76.5 - - + +
267D ASN* 1.3 74.4 + - - +
268D GLN 3.8 0.4 - - - -
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Residues in contact with ASN 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D GLU* 4.6 4.7 - - - +
263D TYR* 3.0 61.4 + - + +
264D ILE 3.5 4.7 - - - +
265D CYS 3.3 0.2 - - - -
266D GLU* 1.3 91.4 + - - +
268D GLN* 1.3 65.1 + - - +
269D ASP* 3.2 3.8 - - - +
270D SER* 3.1 21.3 + - - +
271D ILE* 3.3 17.8 + - + +
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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