Contacts of the helix formed by residues 268 - 288 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G GLN* 5.0 5.4 - - - +
87G ASP* 2.6 12.3 + - - -
55H GLY* 2.8 40.9 - - - +
56H ILE* 4.0 11.6 - - - +
59H PRO* 4.1 1.8 - - + -
261H LYS* 4.6 6.5 + - - -
266H SER 3.4 7.4 + - - -
267H ALA* 1.3 75.6 + - - +
269H LEU* 1.3 78.3 + - + +
270H SER 3.5 0.7 - - - -
271H MET* 3.4 3.9 + - - +
272H ALA* 2.9 27.9 + - - +
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Residues in contact with LEU 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G GLN* 3.7 55.6 - - + +
59G PRO* 4.4 1.6 - - + -
62G MET* 3.6 21.2 - - + +
84G VAL* 4.0 11.0 - - + +
87G ASP* 3.0 12.6 + - - +
88G ILE* 3.7 29.6 - - + -
91G MET* 4.8 0.4 - - - -
59H PRO* 4.3 17.3 - - + -
268H THR* 1.3 83.9 - - + +
270H SER* 1.3 62.9 + - - +
271H MET 3.0 1.3 - - - -
272H ALA* 2.9 3.6 + - - +
273H TYR* 2.8 30.9 + - - +
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Residues in contact with SER 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G ASP* 2.6 43.8 + - - -
90G HIS* 4.3 9.7 + - - +
91G MET* 3.9 21.7 - - - -
192H LEU* 3.5 19.1 - - - +
196H ARG* 4.9 0.9 + - - -
267H ALA* 3.4 17.8 - - - +
269H LEU* 1.3 72.6 - - - +
271H MET* 1.3 57.9 + - - +
273H TYR* 3.6 3.8 + - - +
274H ALA* 2.9 29.5 + - - +
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Residues in contact with MET 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H ILE* 3.6 30.7 - - + -
160H ILE* 3.9 22.7 - - + -
162H ASN* 5.4 6.7 - - - +
189H VAL* 5.4 6.7 - - - +
192H LEU* 3.5 42.2 - - + -
220H HIS* 4.2 22.2 - - + -
267H ALA* 4.1 14.6 - - + +
268H THR 3.4 8.6 + - - +
269H LEU 3.0 0.6 - - - -
270H SER* 1.3 80.0 + - - +
272H ALA* 1.3 65.0 + - - +
274H ALA* 4.4 2.7 - - - +
275H ALA* 2.8 28.3 + - + +
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Residues in contact with ALA 272 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G MET* 4.0 4.7 - - - -
56H ILE* 3.9 11.0 - - - +
59H PRO* 3.5 33.9 - - + -
60H LEU* 3.7 13.4 - - - +
63H LEU* 4.3 0.4 - - + -
268H THR 2.9 15.4 + - - +
269H LEU 2.9 7.8 + - - +
271H MET* 1.3 74.8 - - - +
273H TYR* 1.3 58.8 + - - +
275H ALA* 3.1 5.1 + - - +
276H VAL* 2.8 35.4 + - - +
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Residues in contact with TYR 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G MET* 4.3 4.5 - - - -
66G MET* 3.8 34.5 - - + -
91G MET* 3.5 38.8 - - + -
92G ASP* 2.8 25.2 + - - -
93G THR* 3.6 21.8 - - + +
63H LEU* 4.0 11.4 - - - +
195H VAL* 3.9 17.9 - - + -
269H LEU 2.8 16.0 + - - +
270H SER 3.6 6.1 - - - +
272H ALA* 1.3 76.0 - - - +
274H ALA* 1.3 61.4 + - - +
276H VAL* 3.2 4.2 + - - +
277H LYS* 2.7 66.5 + - + +
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Residues in contact with ALA 274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H VAL* 5.1 1.1 - - + -
191H MET* 3.4 16.1 - - + +
192H LEU* 3.6 39.0 - - + +
195H VAL* 3.8 12.3 - - + -
270H SER 2.9 21.3 + - - +
271H MET* 4.0 4.0 - - - +
273H TYR* 1.3 78.0 - - - +
275H ALA* 1.3 58.1 + - - +
277H LYS* 3.4 2.6 + - - +
278H PHE* 2.9 24.4 + - - +
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Residues in contact with ALA 275 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H ILE* 5.5 0.4 - - + -
60H LEU* 3.7 17.7 - - + -
117H ILE* 4.9 2.5 - - + +
158H ASN* 5.3 0.2 - - - +
160H ILE* 3.8 27.4 - - + -
189H VAL* 4.4 13.4 - - + +
271H MET* 2.8 22.1 + - + +
272H ALA* 3.4 4.9 - - - +
274H ALA* 1.3 75.1 - - - +
276H VAL* 1.3 54.8 + - - +
278H PHE* 3.1 2.4 + - - +
279H ALA* 2.7 36.8 + - - +
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Residues in contact with VAL 276 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G MET* 5.9 3.1 - - + -
60H LEU* 3.2 26.5 - - + +
63H LEU* 3.2 55.2 - - + +
64H MET* 4.3 13.8 - - - +
67H ASN* 5.0 7.9 - - - +
272H ALA 2.8 7.8 + - - +
273H TYR 3.6 6.1 - - - +
275H ALA* 1.3 74.5 - - - +
277H LYS* 1.3 55.8 + - - +
279H ALA* 3.2 5.4 + - - +
280H ASP* 2.7 35.5 + - + +
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Residues in contact with LYS 277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G ASP* 4.1 13.1 + - - +
191H MET* 4.2 18.4 - - - -
195H VAL* 4.9 5.6 - - + -
273H TYR* 2.7 56.9 + - + +
274H ALA* 3.7 6.3 - - - +
276H VAL* 1.3 79.5 - - - +
278H PHE* 1.3 61.3 + - - +
280H ASP* 3.7 8.2 + - - +
281H ALA* 3.4 18.7 + - - +
284H ARG* 5.5 0.3 + - - -
294H GLU* 5.6 4.3 - - - +
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Residues in contact with PHE 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158H ASN* 3.4 36.3 - - - -
187H LEU* 3.6 31.0 - - + -
188H GLY 5.1 0.7 - - - -
189H VAL* 3.9 25.8 - - + -
191H MET* 4.1 20.0 - - + -
274H ALA 2.9 17.9 + - - +
275H ALA 3.7 3.1 - - - +
277H LYS* 1.3 73.4 - - - +
279H ALA* 1.3 67.9 + - - +
281H ALA* 2.9 16.9 + - - +
282H CYS* 3.1 19.1 + - - -
294H GLU* 4.1 23.3 - - + -
295H CYS 3.9 9.2 - - - -
296H ALA* 3.8 23.3 - - + -
312H VAL* 5.6 0.4 - - + -
314H LEU* 4.3 8.3 - - + -
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Residues in contact with ALA 279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H MET* 3.7 12.8 - - + -
115H LEU* 3.9 6.1 - - + +
117H ILE* 3.5 31.9 - - + -
158H ASN* 3.7 14.3 + - - +
275H ALA 2.7 21.0 + - - +
276H VAL 3.5 4.9 - - - +
278H PHE* 1.3 73.8 - - - +
280H ASP* 1.3 63.3 + - - +
282H CYS* 2.9 15.8 + - - +
283H LEU* 3.0 15.6 + - - +
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Residues in contact with ASP 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64H MET* 5.0 0.2 - - - +
67H ASN* 3.3 30.0 + - - +
69H LEU* 3.7 15.4 - - - +
276H VAL* 2.7 23.2 + - + +
277H LYS* 3.8 7.9 - - - +
279H ALA* 1.3 72.8 - - - +
281H ALA* 1.3 57.5 + - - +
283H LEU* 3.4 6.5 + - - +
284H ARG* 3.0 55.8 + - - +
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Residues in contact with ALA 281 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277H LYS 3.4 9.6 + - - +
278H PHE* 2.9 12.6 + - - +
280H ASP* 1.3 77.2 + - - +
282H CYS* 1.3 60.0 + - - +
284H ARG* 3.6 26.0 - - - +
285H GLY* 3.0 21.3 + - - -
292H VAL* 3.3 21.3 - - + +
294H GLU* 3.9 22.4 - - + -
314H LEU* 3.9 6.7 - - + +
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Residues in contact with CYS 282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H LEU* 4.1 17.7 - - + -
156H ILE* 4.6 11.4 - - + -
158H ASN* 3.6 26.7 - - - -
187H LEU* 4.8 1.1 - - - -
278H PHE* 3.1 30.0 + - - -
279H ALA 2.9 7.9 + - - +
281H ALA* 1.3 77.3 - - - +
283H LEU* 1.3 59.0 + - - +
285H GLY* 3.1 3.1 + - - -
286H LEU* 2.8 33.5 + - + +
314H LEU* 3.7 24.2 - - - +
315H GLY 4.5 0.9 - - - +
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Residues in contact with LEU 283 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H PHE* 3.7 31.8 - - + -
47H VAL* 3.9 6.1 - - + -
64H MET* 4.4 8.7 - - + -
67H ASN* 4.0 9.0 - - - +
69H LEU* 3.8 26.5 - - + +
70H VAL* 3.4 33.0 - - + -
115H LEU* 3.7 21.5 - - + -
279H ALA 3.0 15.0 + - - +
280H ASP* 3.7 7.4 - - - +
282H CYS* 1.3 73.3 - - - +
284H ARG* 1.3 55.4 + - - +
285H GLY 2.9 1.6 - - - -
286H LEU* 2.7 17.7 + - + +
287H ARG* 2.6 34.3 + - - +
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Residues in contact with ARG 284 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H LEU* 3.5 19.7 - - + +
277H LYS 5.5 0.2 + - - -
280H ASP* 3.0 41.9 + - - +
281H ALA* 3.6 24.8 - - - +
283H LEU* 1.3 74.7 - - - +
285H GLY* 1.3 63.8 + - - +
287H ARG* 3.1 27.2 + - - +
288H GLY 3.2 0.2 + - - -
289H ASP* 3.1 38.0 + - + +
292H VAL* 3.9 20.2 - - + +
294H GLU* 4.8 8.3 + - - -
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Residues in contact with GLY 285 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281H ALA 3.0 14.6 + - - -
282H CYS 3.4 5.4 - - - -
283H LEU 2.9 1.0 - - - -
284H ARG* 1.3 77.3 - - - +
286H LEU* 1.3 62.6 + - - +
288H GLY* 2.9 14.4 + - - -
289H ASP 4.5 1.3 - - - -
292H VAL* 4.3 4.7 - - - +
314H LEU 3.4 25.8 - - - -
315H GLY* 3.0 23.6 - - - -
316H ARG 3.2 1.9 + - - -
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Residues in contact with LEU 286 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H PHE* 3.2 35.3 - - + -
114H ASP* 4.1 19.1 - - + +
115H LEU* 4.8 2.2 - - + -
156H ILE* 4.0 30.3 - - + -
282H CYS 2.8 16.1 + - - +
283H LEU* 2.7 32.7 + - + +
285H GLY* 1.3 72.3 - - - +
287H ARG* 1.3 60.1 + - - +
288H GLY 3.0 1.2 + - - -
315H GLY 3.3 8.8 + - - +
316H ARG* 3.6 39.4 + - - +
318H GLY* 5.4 0.2 - - - -
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Residues in contact with ARG 287 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H PHE* 3.2 20.3 - - + -
69H LEU* 2.9 38.6 - - + +
283H LEU 2.6 14.9 + - - +
284H ARG* 3.1 23.4 + - - +
286H LEU* 1.3 72.4 - - - +
288H GLY* 1.3 56.8 + - - +
289H ASP* 2.9 33.4 + - - +
316H ARG* 3.7 12.2 + - - -
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Residues in contact with GLY 288 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285H GLY 2.9 12.2 + - - -
286H LEU 3.0 0.6 - - - -
287H ARG* 1.3 80.2 - - - +
289H ASP* 1.3 71.1 + - - +
290H ALA* 3.5 3.3 + - - +
316H ARG* 3.6 30.5 + - - -
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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