Contacts of the helix formed by residues 268 - 288 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A GLN* 4.4 5.7 + - - -
87A ASP* 2.8 12.2 + - - -
55B GLY* 3.5 41.1 - - - -
56B ILE* 3.9 13.0 - - + +
261B LYS* 3.6 8.6 + - - +
266B SER* 3.1 15.1 + - - +
267B ALA* 1.3 73.3 - - - +
269B LEU* 1.3 73.6 + - - +
270B SER 3.5 0.2 - - - -
271B MET* 3.2 4.4 + - - +
272B ALA* 2.8 30.3 + - - +
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Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLN* 3.7 54.3 - - + +
59A PRO* 4.4 2.7 - - + -
62A MET* 3.6 22.6 - - + +
84A VAL* 4.1 6.1 - - + -
87A ASP* 3.0 11.3 + - + +
88A ILE* 3.9 27.4 - - + -
59B PRO* 4.1 25.1 - - + -
268B THR* 1.3 88.4 + - - +
270B SER* 1.3 62.1 + - - +
272B ALA* 2.9 6.0 + - - +
273B TYR* 2.8 28.5 + - - +
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Residues in contact with SER 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASP* 2.6 44.8 + - - -
90A HIS* 4.3 9.8 + - - +
91A MET* 3.7 24.1 - - - -
192B LEU* 3.6 19.5 - - - +
267B ALA* 3.6 14.2 - - - +
269B LEU* 1.3 74.3 - - - +
271B MET* 1.3 58.5 + - - +
273B TYR* 3.5 4.1 - - - +
274B ALA* 2.9 28.4 + - - +
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Residues in contact with MET 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ILE* 3.3 30.7 - - + -
160B ILE* 3.8 24.7 - - + -
189B VAL* 4.0 19.1 - - + +
192B LEU* 4.0 29.4 - - + -
220B HIS* 5.5 6.3 - - - -
267B ALA 3.8 15.7 - - - +
268B THR 3.2 9.8 + - - +
269B LEU 3.0 0.4 - - - -
270B SER* 1.3 80.2 + - - +
272B ALA* 1.3 53.8 + - - +
274B ALA* 4.5 4.9 - - + -
275B ALA* 2.7 53.2 + - + +
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Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A MET* 4.3 3.1 - - - -
56B ILE* 3.8 6.5 - - - +
59B PRO* 3.7 17.3 - - + -
60B LEU* 3.6 36.6 - - - +
63B LEU* 4.0 1.1 - - + -
268B THR 2.8 13.7 + - - +
269B LEU 3.4 7.2 - - - +
271B MET* 1.3 76.2 - - - +
273B TYR* 1.3 57.8 + - - +
275B ALA* 3.3 3.1 + - - +
276B VAL* 2.9 37.2 + - - +
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Residues in contact with TYR 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A MET* 4.7 3.8 - - - -
66A MET* 3.8 33.7 - - + -
91A MET* 3.4 44.4 - - + -
92A ASP* 2.8 24.3 + - - -
93A THR* 3.3 20.5 - - + +
63B LEU* 4.0 10.4 - - - +
195B VAL* 4.0 10.3 - - + -
269B LEU 2.8 12.4 + - - +
270B SER* 3.5 9.2 - - - +
272B ALA* 1.3 78.5 - - - +
274B ALA* 1.3 66.4 + - - +
276B VAL* 3.2 2.3 + - - +
277B LYS* 2.7 73.7 + - + +
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Residues in contact with ALA 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B MET* 3.2 20.3 - - + +
192B LEU* 3.7 37.9 - - + +
195B VAL* 3.9 11.0 - - + -
270B SER 2.9 18.2 + - - +
271B MET* 3.8 4.7 - - + +
273B TYR* 1.3 82.6 - - - +
275B ALA* 1.3 58.2 + - - +
277B LYS* 3.3 2.3 + - - +
278B PHE* 2.9 24.1 + - - +
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Residues in contact with ALA 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ILE* 5.4 0.4 - - + -
60B LEU* 4.1 15.0 - - + +
117B ILE* 4.8 2.8 - - + +
158B ASN* 5.1 0.5 - - - +
160B ILE* 3.5 32.1 - - + -
189B VAL* 4.5 8.6 - - + +
271B MET* 2.7 27.9 + - + +
272B ALA* 3.7 4.9 - - - +
274B ALA* 1.3 72.9 - - - +
276B VAL* 1.3 59.0 + - - +
278B PHE* 3.3 1.7 + - - +
279B ALA* 2.8 30.6 + - - +
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Residues in contact with VAL 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A MET* 6.3 1.6 - - + -
60B LEU* 3.3 22.4 - - + +
63B LEU* 3.3 46.9 - - + +
64B MET* 4.0 14.4 - - - -
67B ASN* 5.0 9.2 - - + +
272B ALA 2.9 27.7 + - - +
273B TYR 3.7 4.0 - - - +
275B ALA* 1.3 74.1 - - - +
277B LYS* 1.3 62.5 + - + +
279B ALA* 3.7 5.3 - - - +
280B ASP* 2.8 31.1 + - + +
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Residues in contact with LYS 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A MET* 6.1 0.7 - - + -
92A ASP* 3.8 17.3 + - - +
191B MET* 3.5 15.2 - - + +
195B VAL* 5.0 5.8 - - + -
210B ARG* 6.0 2.0 - - - +
273B TYR* 2.7 67.1 + - + +
274B ALA* 3.7 5.8 - - - +
276B VAL* 1.3 77.7 - - + +
278B PHE* 1.3 62.1 + - - +
280B ASP* 3.5 6.9 + - - +
281B ALA* 3.1 21.1 + - - +
284B ARG* 4.7 1.6 + - - -
294B GLU* 4.6 0.9 - - - +
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Residues in contact with PHE 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B ASN* 3.6 28.3 - - - -
187B LEU* 3.6 31.0 - - + -
188B GLY 5.1 0.2 - - - -
189B VAL* 3.6 34.3 - - + -
191B MET* 3.3 26.0 - - + +
274B ALA 2.9 16.6 + - - +
275B ALA 3.7 3.6 - - - +
277B LYS* 1.3 76.8 - - - +
279B ALA* 1.3 64.9 + - - +
281B ALA* 3.1 12.2 + - - +
282B CYS* 3.2 20.9 + - - -
294B GLU* 4.0 19.1 - - + -
295B CYS 3.9 9.9 - - - -
296B ALA* 3.7 22.7 - - + -
312B VAL* 5.6 0.2 - - + -
314B LEU* 4.5 6.7 - - + -
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Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B MET* 4.0 12.3 - - + -
115B LEU* 3.9 7.7 - - + +
117B ILE* 3.8 28.7 - - + -
158B ASN* 3.5 17.2 + - - +
275B ALA 2.8 21.5 + - - +
276B VAL 3.7 2.9 - - - +
278B PHE* 1.3 71.8 - - - +
280B ASP* 1.3 63.1 + - - +
282B CYS* 3.1 6.2 + - - +
283B LEU* 3.0 26.7 + - - +
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Residues in contact with ASP 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B MET* 5.4 0.6 - - - -
67B ASN* 2.9 33.8 + - - +
69B LEU* 4.3 6.8 - - - +
276B VAL* 2.8 20.1 + - + +
277B LYS* 3.7 7.0 - - - +
279B ALA* 1.3 77.6 - - - +
281B ALA* 1.3 56.2 + - - +
283B LEU* 3.2 5.8 + - - +
284B ARG* 2.5 61.6 + - - +
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Residues in contact with ALA 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B LYS 3.1 10.1 + - - +
278B PHE* 3.1 11.7 + - + +
280B ASP* 1.3 76.6 - - - +
282B CYS* 1.3 56.6 + - - +
284B ARG* 3.2 16.9 + - - +
285B GLY* 2.9 23.7 + - - -
292B VAL* 3.3 15.5 - - + +
294B GLU* 3.6 38.6 - - + +
314B LEU* 3.7 8.9 - - + +
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Residues in contact with CYS 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LEU* 4.5 13.9 - - + -
156B ILE* 4.5 16.5 - - + +
158B ASN* 3.7 28.5 - - - -
187B LEU* 4.7 1.6 - - - -
278B PHE* 3.2 26.4 + - - -
279B ALA 3.1 8.0 + - - +
281B ALA* 1.3 79.3 - - - +
283B LEU* 1.3 52.0 + - + +
285B GLY* 2.9 3.5 + - - -
286B LEU* 2.7 39.1 + - + +
314B LEU* 3.7 24.8 - - + +
315B GLY 4.9 0.3 - - - +
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Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B PHE* 3.5 33.9 - - + -
47B VAL* 4.3 6.3 - - + -
64B MET* 4.1 13.0 - - + -
67B ASN* 4.2 8.1 - - - +
69B LEU* 3.6 27.4 - - + -
70B VAL* 3.8 27.8 - - + -
115B LEU* 4.1 16.2 - - + -
279B ALA 3.0 18.5 + - - +
280B ASP* 3.2 8.0 + - - +
282B CYS* 1.3 75.8 - - - +
284B ARG* 1.3 57.0 + - - +
286B LEU* 3.0 17.6 + - + +
287B ARG* 2.8 28.6 + - - +
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Residues in contact with ARG 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 3.7 16.6 - - + +
277B LYS 4.7 1.8 + - - -
280B ASP* 2.5 56.2 + - - +
281B ALA* 3.3 34.4 - - - +
283B LEU* 1.3 76.1 - - - +
285B GLY* 1.3 61.6 + - - +
287B ARG* 3.3 17.9 + - - +
288B GLY 3.3 0.2 + - - -
289B ASP* 3.1 50.0 + - + +
292B VAL* 3.9 21.9 - - + +
294B GLU* 4.1 9.1 + - - -
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Residues in contact with GLY 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B ALA 2.9 13.7 + - - -
282B CYS 2.9 5.1 + - - -
284B ARG* 1.3 78.5 - - - +
286B LEU* 1.3 62.8 + - - +
288B GLY* 2.9 13.7 + - - -
289B ASP 4.2 1.5 + - - -
292B VAL* 4.3 4.0 - - - +
314B LEU* 3.5 28.0 - - - -
315B GLY* 3.1 21.8 - - - -
316B ARG 3.2 1.6 + - - -
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Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B PHE* 3.6 30.1 - - + -
114B ASP* 4.1 21.8 - - + +
115B LEU* 5.0 2.5 - - + -
156B ILE* 3.2 33.0 - - + -
282B CYS* 2.7 17.9 + - + +
283B LEU* 3.0 28.7 + - + +
285B GLY* 1.3 72.4 - - - +
287B ARG* 1.3 61.1 + - - +
288B GLY 3.4 0.3 + - - -
315B GLY 3.7 2.4 + - - +
316B ARG* 3.2 42.6 + - - +
317B ASN* 5.0 0.4 - - - -
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Residues in contact with ARG 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B PHE* 3.5 15.0 - - + -
69B LEU* 3.4 38.2 - - + +
283B LEU 2.8 12.2 + - - +
284B ARG* 3.4 20.0 - - - +
285B GLY 3.1 0.4 - - - -
286B LEU* 1.3 78.5 - - - +
288B GLY* 1.3 56.0 + - - +
289B ASP* 3.0 36.9 + - - +
316B ARG* 3.5 15.2 + - - -
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Residues in contact with GLY 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLY 2.9 12.4 + - - -
286B LEU 3.2 0.4 - - - -
287B ARG* 1.3 79.9 - - - +
289B ASP* 1.3 69.4 + - - +
290B ALA* 3.6 2.1 + - - +
315B GLY* 6.3 0.2 - - - -
316B ARG* 3.8 26.9 + - - -
126H PRO* 6.0 2.1 - - - +
128H MET* 6.0 1.8 - - - +
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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
------------------------------------------------------------
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