Contacts of the helix formed by residues 268 - 287 (chain D) in PDB entry 1SMK
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 THR 268 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C GLN* 4.6 6.5 - - - +
87C ASP* 2.7 12.4 + - - -
55D GLY* 3.1 37.3 - - - +
56D ILE* 4.1 11.2 + - - +
59D PRO* 4.2 0.9 - - + -
261D LYS* 3.6 12.1 + - - +
266D SER 3.0 9.2 + - - -
267D ALA* 1.3 72.9 + - - +
269D LEU* 1.3 80.7 + - + +
270D SER 3.4 0.7 - - - -
271D MET* 3.3 3.0 + - - +
272D ALA* 3.0 29.1 + - - +
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Residues in contact with LEU 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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58C GLN* 3.7 51.6 - - + +
59C PRO* 4.1 3.6 - - + -
62C MET* 3.3 25.7 - - + +
84C VAL* 3.8 16.4 - - + +
87C ASP* 2.9 12.8 + - - +
88C ILE* 3.6 34.1 - - + -
91C MET* 4.9 0.4 - - - -
59D PRO* 4.2 15.5 - - + -
261D LYS* 5.7 0.2 - - - +
268D THR* 1.3 84.8 - - + +
270D SER* 1.3 65.8 + - - +
272D ALA* 3.4 1.4 + - - -
273D TYR* 3.1 19.8 + - - +
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Residues in contact with SER 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ASP* 2.7 44.2 + - - -
90C HIS* 4.3 9.3 + - - +
91C MET* 3.8 22.4 - - - +
192D LEU* 3.7 19.0 - - - +
196D ARG* 4.8 1.0 + - - -
267D ALA* 3.7 13.3 - - - +
269D LEU* 1.3 70.8 - - - +
271D MET* 1.3 67.2 + - - +
273D TYR* 3.5 3.9 - - - +
274D ALA* 3.0 24.4 + - - +
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Residues in contact with MET 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D ILE* 3.3 36.3 - - + -
160D ILE* 3.8 24.9 - - + -
189D VAL* 4.2 15.7 - - + +
192D LEU* 3.7 30.3 - - + -
220D HIS* 5.7 5.8 - - - -
267D ALA* 4.0 12.6 - - + +
268D THR 3.3 9.3 + - - +
269D LEU 3.1 0.4 - - - -
270D SER* 1.3 78.5 + - - +
272D ALA* 1.3 67.3 + - - +
274D ALA* 3.0 6.7 + - + -
275D ALA* 2.8 46.0 + - + +
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Residues in contact with ALA 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C MET* 4.2 3.6 - - - -
56D ILE* 3.8 10.9 - - - +
59D PRO* 3.8 18.6 - - + +
60D LEU* 3.5 32.5 - - - +
63D LEU* 4.1 0.2 - - - -
268D THR 3.0 16.2 + - - +
269D LEU 3.4 5.4 + - - +
271D MET* 1.3 74.5 - - - +
273D TYR* 1.3 57.2 + - - +
275D ALA* 3.7 2.4 - - - +
276D VAL* 2.8 37.2 + - - +
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Residues in contact with TYR 273 (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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62C MET* 4.5 4.7 - - - -
66C MET* 3.9 33.9 - - + -
91C MET* 3.8 26.0 - - + -
92C ASP* 2.6 35.6 + - - -
93C THR* 3.7 27.2 - - + +
63D LEU* 4.0 11.1 - - + +
195D VAL* 3.7 18.6 - - + -
269D LEU 3.1 12.0 + - - +
270D SER 3.5 9.2 - - - +
272D ALA* 1.3 79.8 - - - +
274D ALA* 1.3 60.2 + - - +
276D VAL* 3.3 2.6 + - - +
277D LYS* 2.6 60.3 + - - +
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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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191D MET* 3.4 23.6 - - + +
192D LEU* 3.7 38.8 - - + +
195D VAL* 4.2 7.0 - - + -
270D SER 3.0 15.1 + - - +
271D MET* 3.0 6.7 + - + +
273D TYR* 1.3 78.4 - - - +
275D ALA* 1.3 67.2 + - - +
277D LYS* 3.2 4.1 + - - +
278D PHE* 3.0 19.2 + - - +
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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
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60D LEU* 3.9 16.8 - - + -
117D ILE* 4.9 3.6 - - + +
158D ASN* 4.6 2.3 + - - -
160D ILE* 3.5 31.6 - - + -
189D VAL* 4.4 9.6 - - + -
271D MET* 2.8 26.1 + - + +
272D ALA* 3.7 3.8 - - - +
274D ALA* 1.3 72.7 - - - +
276D VAL* 1.3 58.5 + - - +
278D PHE* 3.3 1.7 + - - +
279D ALA* 2.8 31.5 + - - +
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Residues in contact with VAL 276 (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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66C MET* 6.2 1.6 - - + -
60D LEU* 3.1 24.9 - - + +
63D LEU* 3.3 47.1 - - + +
64D MET* 4.2 12.5 - - - +
67D ASN* 5.1 7.9 - - - +
272D ALA 2.8 26.6 + - - +
273D TYR 3.6 4.9 - - - +
275D ALA* 1.3 74.8 - - - +
277D LYS* 1.3 60.1 + - - +
279D ALA* 3.8 4.6 - - - +
280D ASP* 2.9 30.3 + - + +
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Residues in contact with LYS 277 (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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92C ASP* 3.9 14.1 + - - +
191D MET* 4.5 16.8 - - + -
195D VAL* 5.2 3.8 - - + -
210D ARG* 6.4 0.2 - - - +
273D TYR* 2.6 54.3 + - + +
274D ALA* 3.2 9.4 + - - +
276D VAL* 1.3 76.3 - - - +
278D PHE* 1.3 60.4 + - - +
280D ASP* 3.9 6.3 - - - +
281D ALA* 3.2 20.4 + - - +
284D ARG* 4.2 8.7 + - - +
294D GLU* 4.6 7.8 - - - +
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Residues in contact with PHE 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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158D ASN* 3.1 36.8 - - - +
187D LEU* 3.5 26.2 - - + -
189D VAL* 3.9 28.0 - - + -
191D MET* 4.3 13.2 - - + -
274D ALA 3.0 15.3 + - - +
275D ALA 3.6 3.8 - - - +
277D LYS* 1.3 76.1 - - - +
279D ALA* 1.3 66.7 + - - +
281D ALA* 2.9 14.9 + - - +
282D CYS* 3.0 21.3 + - - -
294D GLU* 3.7 33.9 - - + -
295D CYS 3.8 5.6 - - - -
296D ALA* 3.5 29.8 - - + -
312D VAL* 5.4 0.4 - - + -
314D LEU* 4.4 5.8 - - + -
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Residues in contact with ALA 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D MET* 3.9 15.7 - - + -
115D LEU* 4.0 7.3 - - + +
117D ILE* 3.6 29.4 - - + -
158D ASN* 3.5 13.6 - - - +
275D ALA 2.8 21.0 + - - +
276D VAL 3.8 3.6 - - - +
278D PHE* 1.3 72.3 - - - +
280D ASP* 1.3 63.3 + - - +
282D CYS* 2.9 7.4 + - - +
283D LEU* 2.9 25.9 + - - +
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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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64D MET* 5.3 0.2 - - - +
67D ASN* 2.9 35.7 + - - +
69D LEU* 4.0 12.0 - - - +
276D VAL* 2.9 19.0 + - + +
277D LYS* 3.9 6.5 - - - +
279D ALA* 1.3 76.4 - - - +
281D ALA* 1.3 57.4 + - - +
283D LEU* 3.2 7.7 + - - +
284D ARG* 2.8 62.2 + - - -
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Residues in contact with ALA 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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277D LYS 3.2 12.4 + - - +
278D PHE 2.9 11.1 + - - +
280D ASP* 1.3 78.7 - - - +
282D CYS* 1.3 63.1 + - - +
284D ARG* 3.3 14.7 + - - +
285D GLY* 2.9 17.5 + - - -
292D VAL* 3.1 16.4 - - + +
294D GLU* 3.7 34.8 - - + +
314D LEU* 3.8 8.9 - - + +
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Residues in contact with CYS 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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115D LEU* 4.5 12.3 - - + -
156D ILE* 4.3 14.8 - - + -
158D ASN* 3.5 27.6 - - - -
187D LEU* 4.9 2.0 - - - -
278D PHE* 3.0 28.8 + - - -
279D ALA* 2.9 8.9 + - - +
281D ALA* 1.3 77.3 - - - +
283D LEU* 1.3 52.8 + - + +
285D GLY* 2.9 4.3 + - - -
286D LEU* 2.7 41.4 + - + +
314D LEU* 3.9 22.6 - - - +
315D GLY 4.7 0.7 - - - +
318D GLY* 6.4 1.8 - - - -
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Residues in contact with LEU 283 (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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45D PHE* 3.7 34.0 - - + -
47D VAL* 4.4 2.7 - - + -
64D MET* 4.4 11.7 - - + -
67D ASN* 4.4 4.3 - - - +
69D LEU* 3.7 27.8 - - + +
70D VAL* 3.9 27.4 - - + -
115D LEU* 4.1 19.3 - - + -
279D ALA 2.9 17.0 + - - +
280D ASP* 3.5 10.5 - - - +
282D CYS* 1.3 73.4 - - - +
284D ARG* 1.3 56.1 + - - +
286D LEU* 2.9 17.2 + - + +
287D ARG* 2.7 35.7 + - - +
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Residues in contact with ARG 284 (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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69D LEU* 4.0 12.1 - - + +
277D LYS* 4.2 10.9 + - - +
280D ASP* 2.8 45.0 + - - +
281D ALA* 3.6 21.9 - - - +
283D LEU* 1.3 71.8 - - - +
285D GLY* 1.3 58.4 + - - +
287D ARG* 3.5 12.5 + - - +
288D GLY 3.3 2.6 + - - -
289D ASP* 2.9 52.9 + - - +
292D VAL* 4.0 25.5 - - + +
293D ILE 5.6 0.6 - - - +
294D GLU* 3.9 17.6 + - - -
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Residues in contact with GLY 285 (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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281D ALA 2.9 10.0 + - - -
282D CYS 2.9 8.1 + - - -
284D ARG* 1.3 76.8 - - - +
286D LEU* 1.3 56.0 + - - +
288D GLY* 3.0 14.9 + - - -
289D ASP 4.5 1.6 - - - -
292D VAL* 4.1 4.9 - - - +
314D LEU* 3.6 24.9 - - - -
315D GLY* 2.8 27.7 - - - -
316D ARG 3.0 3.5 + - - -
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Residues in contact with LEU 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D PHE* 3.7 27.9 - - + -
114D ASP* 4.4 14.8 - - + +
115D LEU* 5.1 1.6 - - + -
156D ILE* 4.1 31.6 - - + -
185D ARG* 6.0 0.9 - - - +
282D CYS* 2.7 19.9 + - + +
283D LEU* 2.9 28.7 + - + +
285D GLY* 1.3 68.4 - - - +
287D ARG* 1.3 61.6 + - - +
288D GLY 3.0 6.0 + - - -
315D GLY 3.7 10.1 - - - +
316D ARG* 3.4 39.8 + - - +
318D GLY* 4.2 3.4 - - - +
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Residues in contact with ARG 287 (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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45D PHE* 3.6 16.8 - - + -
69D LEU* 3.3 37.8 - - + +
283D LEU 2.7 18.6 + - - +
284D ARG* 3.7 16.1 - - - +
286D LEU* 1.3 72.5 - - - +
288D GLY* 1.3 59.5 + - - +
289D ASP* 2.7 36.0 + - - +
316D ARG* 3.9 11.7 + - - -
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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
------------------------------------------------------------
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