Contacts of the helix formed by residues 258 - 272 (chain D) in PDB entry 1M54
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255D VAL* 3.7 7.6 - - - -
256D GLY 3.2 1.8 - - - -
257D THR* 1.3 79.0 - - - +
259D GLY* 1.3 58.5 + - - +
260D THR 3.2 2.9 - - - -
261D ILE* 4.5 4.0 - - - -
262D THR* 2.2 37.8 + - - -
314D VAL* 3.6 3.5 - - - +
315D LEU* 3.6 22.4 - - - -
1410D PLP 2.6 12.8 + - - -
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Residues in contact with GLY 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D ASN* 2.7 29.9 - - - +
229D PRO* 3.3 28.3 - - - +
232D HIS* 3.0 13.6 - - - +
257D THR* 3.0 8.7 + - - -
258D GLY* 1.3 78.4 - - - +
260D THR* 1.3 62.6 + - - +
262D THR 4.2 1.1 - - - -
263D GLY 3.7 3.2 + - - -
314D VAL* 4.0 2.0 - - - -
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Residues in contact with THR 260 (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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118D VAL* 4.5 11.0 - - + +
119D LYS* 6.1 0.2 - - - +
232D HIS* 3.1 26.9 + - + +
236D THR* 5.4 0.9 - - + -
253D ALA* 4.6 4.3 - - + -
254D SER 5.0 3.1 - - - -
258D GLY 3.2 0.6 - - - -
259D GLY* 1.3 79.9 - - - +
261D ILE* 1.3 66.5 + - - +
262D THR 3.4 0.2 + - - -
264D ILE* 3.1 34.3 + - + +
373D ILE* 3.8 34.3 - - + -
1410D PLP 2.5 36.1 + - - +
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Residues in contact with ILE 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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251D LEU* 4.6 11.2 - - + -
253D ALA* 4.3 16.2 - - + +
254D SER 4.8 2.9 + - - +
255D VAL* 4.2 21.3 - - + -
258D GLY* 4.2 10.3 - - - +
260D THR* 1.3 79.3 - - - +
262D THR* 1.3 59.4 + - - +
264D ILE* 4.5 5.2 - - - -
265D ALA* 2.6 43.7 + - + +
277D ILE* 3.3 23.8 - - + -
278D ILE 3.0 30.5 - - - +
279D GLY* 4.1 7.4 - - - -
315D LEU* 4.5 3.6 - - + -
320D VAL* 3.7 21.3 - - + -
1410D PLP 5.1 0.2 + - - -
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Residues in contact with THR 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D PRO* 4.7 7.2 - - + -
258D GLY 2.2 27.4 + - - -
259D GLY* 4.5 2.5 - - - -
260D THR 3.2 1.0 - - - -
261D ILE* 1.3 76.9 - - - +
263D GLY* 1.3 61.1 + - - +
265D ALA* 3.8 3.9 - - - +
266D ARG* 2.9 53.1 + - + +
314D VAL 3.2 17.4 + - - +
315D LEU* 3.6 5.7 - - - +
316D ASP* 3.2 40.7 + - + -
319D VAL* 4.2 3.8 - - + -
1420D HEM 5.0 0.2 - - + -
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Residues in contact with GLY 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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229D PRO* 3.3 25.7 - - - +
233D TYR* 2.9 38.8 - - - -
259D GLY 3.7 4.4 + - - -
260D THR 3.6 4.3 + - - -
261D ILE 3.4 0.2 - - - -
262D THR* 1.3 76.4 - - - +
264D ILE* 1.3 66.5 + - - +
266D ARG 3.3 0.7 + - - -
267D LYS* 3.1 5.7 + - - +
1420D HEM 4.0 8.3 - - - -
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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
----------------------------------------------------------
232D HIS* 3.5 15.7 + - + +
236D THR* 3.3 25.8 - - + -
237D ALA* 3.3 18.6 - - + +
240D ILE* 3.8 8.5 - - + -
251D LEU* 3.4 29.4 - - + -
260D THR* 3.1 22.5 + - + +
261D ILE* 4.0 3.8 - - - +
263D GLY* 1.3 75.1 - - - +
265D ALA* 1.3 53.2 + - - +
267D LYS* 3.4 1.6 + - - +
268D LEU* 2.7 45.7 + - + +
373D ILE* 3.6 29.2 - - + -
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Residues in contact with ALA 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D ILE* 2.6 27.3 + - + +
262D THR 3.8 0.2 - - - +
263D GLY 3.2 0.2 - - - -
264D ILE* 1.3 72.2 - - - +
266D ARG* 1.3 64.0 + - - +
268D LEU* 4.1 6.3 - - - -
269D LYS* 3.0 30.8 + - - +
277D ILE* 4.1 18.4 - - + -
319D VAL* 3.5 39.4 - - + +
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Residues in contact with ARG 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D SER* 5.7 4.4 - - - -
52D CYS* 3.6 11.7 - - - +
54D TRP* 2.9 77.4 - - + +
233D TYR* 3.6 10.5 - - + -
262D THR* 2.9 39.5 + - + +
263D GLY 3.9 3.8 - - - +
265D ALA* 1.3 73.4 - - - +
267D LYS* 1.3 51.7 + - - +
269D LYS* 4.1 0.5 + - - +
270D GLU* 2.7 36.2 + - - +
314D VAL 5.4 1.8 + - - -
316D ASP* 3.6 22.2 + - - +
319D VAL* 3.8 8.7 - - + -
1420D HEM 3.3 46.6 + - + +
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Residues in contact with LYS 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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233D TYR* 2.4 72.9 + - + +
234D ASP* 4.2 1.4 + - - +
237D ALA* 4.0 19.7 + - + +
238D ASP* 3.1 31.3 + - - +
241D LEU* 4.2 10.3 - - + -
263D GLY 3.1 9.8 + - - +
264D ILE 3.8 2.7 - - - +
266D ARG* 1.3 77.9 - - - +
268D LEU* 1.3 60.2 + - + +
270D GLU* 3.0 8.4 + - - +
271D LYS* 2.9 47.1 + - + +
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Residues in contact with LEU 268 (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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237D ALA 4.8 4.7 - - - +
240D ILE* 5.1 3.8 - - + -
241D LEU* 3.6 30.1 - - + -
248D LEU* 4.1 11.4 - - + -
251D LEU* 3.5 31.0 - - + -
264D ILE* 2.7 29.7 + - + +
265D ALA* 3.3 5.4 + - - +
267D LYS* 1.3 68.4 - - - +
269D LYS* 1.3 54.1 + - - +
270D GLU 2.9 4.9 + - - -
271D LYS 4.6 0.2 - - - +
272D CYS* 2.7 44.0 + - + +
275D CYS* 4.0 24.7 - - + +
277D ILE* 3.7 22.2 - - + -
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Residues in contact with LYS 269 (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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54D TRP* 5.6 0.4 - - + -
56D LEU* 3.3 34.7 - - + +
265D ALA 3.0 18.9 + - - +
266D ARG* 4.7 2.9 - - - +
268D LEU* 1.3 73.7 - - - +
270D GLU* 1.3 60.4 + - - +
272D CYS 4.0 5.6 - - - -
273D PRO* 4.0 21.0 - - - +
275D CYS 4.9 7.0 - - - +
277D ILE* 3.8 12.1 - - + +
318D THR 4.2 1.1 + - - -
319D VAL* 2.6 49.5 + - + +
321D ASP* 3.0 35.8 + - - -
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Residues in contact with GLU 270 (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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54D TRP* 4.0 15.8 + - + -
55D GLN 5.3 0.7 - - - +
56D LEU* 3.3 25.4 - - + +
57D GLY 5.1 3.3 + - - -
58D ARG 4.4 13.2 - - - +
60D ALA 5.9 0.3 + - - -
233D TYR* 2.6 29.0 + - - -
266D ARG 2.7 26.5 - - - +
267D LYS* 3.1 6.4 - - - +
268D LEU 2.9 1.4 - - - -
269D LYS* 1.3 81.5 - - - +
271D LYS* 1.3 68.5 + - + +
272D CYS 3.4 2.5 + - - -
273D PRO* 3.8 10.7 - - - +
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Residues in contact with LYS 271 (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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241D LEU* 4.0 28.4 - - + +
246D GLY 5.6 0.3 - - - +
267D LYS* 2.9 29.9 + - + +
268D LEU 3.9 0.2 - - - -
270D GLU* 1.3 80.6 - - + +
272D CYS* 1.3 58.9 + - - +
273D PRO* 3.9 3.9 - - - +
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Residues in contact with CYS 272 (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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241D LEU* 4.3 11.0 - - + -
246D GLY 3.6 24.2 - - - -
247D LYS* 5.0 0.7 - - - -
248D LEU* 3.7 28.9 - - - -
268D LEU* 2.7 29.7 + - + +
269D LYS* 4.0 0.7 - - - -
271D LYS* 1.3 78.4 - - - +
273D PRO* 1.3 70.1 - - - +
274D GLY 3.2 4.7 + - - -
275D CYS* 3.4 20.8 + - + +
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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
------------------------------------------------------------
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