Contacts of the helix formed by residues 268 - 282 (chain D) in PDB entry 1UMD
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 SER 268 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B HIS* 4.0 9.4 - - - -
267B ALA* 4.0 8.0 - - - +
135D ALA* 4.1 1.6 - - - -
261D SER* 6.0 0.2 - - - -
263D ALA* 4.8 8.5 - - - -
264D PRO 3.0 26.9 - - - -
265D ARG* 2.9 14.1 + - - -
266D HIS 3.1 0.2 - - - -
267D ALA* 1.3 81.6 - - - +
269D PHE* 1.3 64.9 + - - +
270D VAL* 3.2 22.3 - - - +
271D SER* 3.1 24.8 + - - -
272D GLU 3.3 4.3 + - - -
293D THR* 4.6 0.2 - - - +
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Residues in contact with PHE 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B HIS* 5.0 1.3 - + - -
267B ALA* 4.6 4.5 - - - -
134D GLU* 4.7 10.9 - - + +
135D ALA* 4.1 9.0 - - - +
138D VAL* 3.9 28.5 - - + -
210D TYR* 3.8 31.1 + + - +
236D LEU* 3.5 25.6 - - + -
239D LEU* 3.2 44.2 - - + -
242D TRP* 3.7 27.1 - + + -
263D ALA* 5.9 1.6 - - - +
268D SER* 1.3 74.7 - - - +
270D VAL* 1.3 59.4 + - + +
272D GLU* 2.9 26.9 + - + +
273D VAL* 3.1 31.6 + - + +
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Residues in contact with VAL 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D ILE* 5.5 4.5 - - + +
209D CYS* 6.1 0.4 - - - -
210D TYR* 4.1 16.1 + - + +
236D LEU* 6.2 0.4 - - + -
259D LEU* 3.5 26.4 - - + +
260D VAL 4.1 7.9 - - - +
261D SER* 3.7 26.7 - - - -
268D SER* 3.2 17.9 - - - +
269D PHE* 1.3 81.3 - - + +
271D SER* 1.3 56.4 + - - +
273D VAL* 4.4 7.0 - - + +
274D ALA* 2.9 29.6 + - - +
291D ARG* 4.1 7.5 - - + -
293D THR* 3.5 27.6 - - + -
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Residues in contact with SER 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B SER* 3.8 3.3 - - - +
272B GLU* 2.6 35.9 + - - -
275B ALA* 3.4 7.6 - - - +
265D ARG* 3.2 2.1 + - - +
267D ALA* 4.6 1.3 - - - -
268D SER* 3.1 27.4 + - - -
269D PHE 3.0 0.6 - - - -
270D VAL* 1.3 77.7 - - - +
272D GLU* 1.3 58.8 + - - +
274D ALA 3.4 0.3 + - - -
275D ALA* 2.9 30.7 + - - +
291D ARG* 2.8 26.9 + - - +
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Residues in contact with GLU 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ARG* 3.1 9.8 - - - +
266B HIS* 3.7 32.1 + - + +
267B ALA* 2.8 35.1 + - + +
271B SER* 2.6 29.6 + - - -
291B ARG* 2.8 20.7 + - - -
242D TRP* 4.7 5.3 - - - +
268D SER 3.3 2.0 + - - -
269D PHE* 2.9 16.1 + - + +
271D SER* 1.3 77.7 - - - +
273D VAL* 1.3 66.0 + - - +
275D ALA* 3.4 1.6 + - - +
276D THR* 2.8 41.2 + - - +
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Residues in contact with VAL 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D ILE* 4.2 6.7 - - + -
236D LEU* 4.5 4.7 - - + -
242D TRP* 4.0 37.5 - - + -
247D VAL* 4.2 8.5 - - + -
259D LEU* 3.7 22.7 - - + -
269D PHE* 3.1 44.5 + - + +
270D VAL* 3.8 2.9 - - + +
271D SER 3.4 0.2 - - - -
272D GLU* 1.3 76.7 - - - +
274D ALA* 1.3 57.7 + - - +
276D THR* 3.1 2.3 + - - -
277D ILE* 2.9 45.5 + - + +
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Residues in contact with ALA 274 (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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275B ALA* 3.9 9.4 - - + +
259D LEU* 3.8 15.1 - - + +
270D VAL 2.9 19.0 + - - +
271D SER 3.7 4.5 - - - +
273D VAL* 1.3 76.3 - - - +
275D ALA* 1.3 61.7 + - - +
277D ILE* 3.3 8.5 + - - +
278D ALA* 3.1 23.6 + - - +
289D PRO* 4.3 15.5 - - + +
291D ARG* 3.9 24.7 - - + -
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Residues in contact with ALA 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B SER* 3.4 20.4 - - - +
274B ALA* 4.0 10.1 - - + +
275B ALA* 3.9 13.0 - - - +
289B PRO* 4.9 1.7 - - - +
291B ARG* 3.9 23.0 + - - +
271D SER 2.9 18.5 + - - +
272D GLU 3.8 4.0 - - - +
274D ALA* 1.3 76.8 - - - +
276D THR* 1.3 57.7 + - - +
278D ALA* 3.6 5.4 + - - +
279D GLU* 3.0 28.8 + - - +
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Residues in contact with THR 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ARG* 3.2 13.4 + - - +
354C TRP* 4.9 3.5 - - + -
358C ARG* 4.8 3.8 - - - +
242D TRP* 3.9 18.9 - - + -
244D TYR* 3.8 18.4 - - + -
248D MET* 3.9 5.4 - - + -
272D GLU* 2.8 37.3 + - - -
273D VAL 3.1 4.7 + - - -
275D ALA* 1.3 75.4 - - - +
277D ILE* 1.3 65.7 + - - +
279D GLU* 3.3 2.1 + - - +
280D ASP* 2.9 41.3 + - - +
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Residues in contact with ILE 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D ILE* 3.7 29.6 - - + -
247D VAL* 3.9 9.2 - - + -
248D MET* 3.8 25.1 - - + -
251D VAL* 4.0 18.6 - - + -
257D VAL* 4.2 14.1 - - + -
259D LEU* 4.4 4.7 - - + -
273D VAL* 2.9 25.2 + - + +
274D ALA* 3.3 7.2 + - - +
276D THR* 1.3 75.2 - - - +
278D ALA* 1.3 56.6 + - - +
281D LEU* 2.7 37.6 + - + -
285D LEU* 4.0 28.0 - - + -
289D PRO* 5.0 3.6 - - + -
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Residues in contact with ALA 278 (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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274B ALA 5.3 0.2 - - - +
278B ALA* 3.5 32.3 - - + -
288B PRO* 3.5 5.0 - - - +
289B PRO* 3.8 14.7 - - + +
274D ALA 3.1 15.4 + - - +
275D ALA* 3.8 6.1 - - - +
277D ILE* 1.3 78.9 - - - +
279D GLU* 1.3 61.2 + - - +
282D LEU* 3.5 28.2 + - + +
285D LEU* 4.4 13.9 - - + -
289D PRO* 4.8 3.6 - - + +
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Residues in contact with GLU 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ARG* 2.7 29.3 + - - -
288B PRO* 3.4 19.6 - - - +
289B PRO* 3.4 21.9 - - - +
290B ILE* 3.3 17.3 - - + +
291B ARG* 2.8 47.5 + - - +
358C ARG* 5.7 1.2 + - - -
275D ALA 3.0 17.7 + - - +
276D THR* 3.3 3.4 + - - +
278D ALA* 1.3 76.5 - - - +
280D ASP* 1.3 73.2 + - - +
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Residues in contact with ASP 280 (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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288B PRO* 6.1 0.4 - - - -
358C ARG* 2.7 26.8 + - - -
244D TYR* 2.7 35.8 + - + +
248D MET* 5.1 1.3 - - - -
276D THR* 2.9 18.6 + - - +
279D GLU* 1.3 97.2 - - - +
281D LEU* 1.3 72.8 + - + +
282D LEU 3.7 1.3 - - - -
283D ASP* 4.1 5.7 - - - +
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Residues in contact with LEU 281 (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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244D TYR* 5.5 0.7 - - - +
248D MET* 3.6 59.5 - - + +
251D VAL* 4.0 19.1 - - + -
252D ALA* 4.1 10.5 - - + +
277D ILE* 2.7 24.3 + - + +
280D ASP* 1.3 85.4 - - + +
282D LEU* 1.3 66.2 + - - +
283D ASP* 3.1 8.1 - - - +
284D MET* 2.8 28.1 + - + -
285D LEU* 3.3 11.8 + - + +
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Residues in contact with LEU 282 (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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278B ALA* 6.5 0.2 - - + -
282B LEU* 3.4 33.2 - - + +
285B LEU* 4.5 19.3 - - + +
286B LEU 4.9 0.4 - - - -
287B ALA* 3.4 16.4 - - - +
288B PRO* 3.4 40.4 - - + -
289B PRO* 5.4 0.7 - - + -
324B TYR* 4.0 10.3 - - + +
277D ILE 3.8 0.2 + - - -
278D ALA* 3.5 22.9 + - + +
280D ASP 3.7 1.8 - - - -
281D LEU* 1.3 75.0 - - - +
283D ASP* 1.3 62.7 + - - +
284D MET 3.2 1.0 + - - -
285D LEU* 3.2 27.8 + - + +
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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
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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