Contacts of the helix formed by residues 261 - 282 (chain H) in PDB entry 5EIG
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 261 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217E HIS* 3.8 23.1 + - - +
261E THR* 4.2 7.8 - - - +
265E ARG* 4.0 27.1 - - + -
344E PHE* 5.6 0.9 - - + -
380E LEU* 4.5 4.7 - - + -
217H HIS* 3.9 9.4 - - - -
257H ARG 4.5 0.3 + - - -
258H GLY* 3.2 7.0 + - - -
259H LEU 3.0 0.2 - - - -
260H LYS* 1.3 83.6 - - + +
262H LEU* 1.3 62.4 + - - +
263H HIS* 3.2 3.6 - - - -
264H VAL* 3.2 15.7 - - + +
265H ARG* 3.0 46.6 + - - +
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Residues in contact with LEU 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H PHE* 3.5 32.5 - - + -
78H LEU* 4.3 8.7 - - + -
192H SER* 4.5 5.4 - - - +
193H PRO* 4.4 6.3 - - + -
194H TYR* 4.6 0.7 - - + -
213H TYR 3.6 17.7 - - - +
214H MET* 4.1 24.0 - - + +
258H GLY 3.4 2.0 + - - -
259H LEU* 3.1 22.3 + - + +
260H LYS 3.6 0.2 - - - -
261H THR* 1.3 78.0 - - - +
263H HIS* 1.3 57.0 + - - +
265H ARG* 3.4 22.2 - - - +
266H MET* 3.0 58.6 + - + +
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Residues in contact with HIS 263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E LYS* 4.6 10.7 - - - +
380E LEU* 2.9 33.1 + - + +
18H PHE* 4.2 8.9 - - + -
19H ALA* 3.5 27.1 + - + +
22H ALA* 5.3 2.6 - - - +
23H ILE* 4.4 4.7 - - + -
194H TYR* 3.5 35.0 - - + +
259H LEU 4.7 1.6 + - - -
260H LYS 3.2 27.5 + - - -
261H THR* 4.3 2.7 - - - -
262H LEU* 1.3 81.1 + - - +
264H VAL* 1.3 86.2 + - + +
267H GLU* 3.2 29.6 + - - +
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Residues in contact with VAL 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264E VAL* 4.0 34.8 - - + +
265E ARG* 5.0 0.2 - - + -
268E LYS* 3.9 31.6 - - + -
380E LEU* 4.9 7.4 - - + -
261H THR* 3.2 35.0 - - + +
263H HIS* 1.3 99.4 - - + +
265H ARG* 1.3 63.0 + - - +
267H GLU* 3.8 6.3 + - - +
268H LYS* 3.5 19.2 + - - +
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Residues in contact with ARG 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E THR* 3.9 21.8 - - + -
264E VAL* 4.9 2.7 - - + -
213H TYR* 3.0 20.4 + - - +
214H MET 3.2 19.8 + - - -
215H ASN 3.7 7.5 + - - -
216H GLY* 3.5 15.9 + - - -
217H HIS* 3.8 8.6 - - - -
258H GLY 2.9 23.0 + - - -
261H THR* 3.0 31.4 + - - +
262H LEU* 3.4 19.7 - - - +
264H VAL* 1.3 77.0 - - + +
266H MET* 1.3 64.3 + - - +
267H GLU 3.2 0.2 - - - -
268H LYS 3.0 2.9 + - - -
269H HIS* 2.9 40.1 + - + -
342H GLY 4.5 4.0 + - - -
344H PHE* 5.6 0.4 - - - -
380H LEU* 3.5 30.2 - - + +
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Residues in contact with MET 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191H MET 3.3 24.5 - - - +
192H SER* 3.8 9.2 - - - +
194H TYR* 3.8 14.4 - - + -
195H PHE* 3.5 22.8 - - + -
213H TYR* 3.4 40.8 - - + -
262H LEU* 3.0 46.9 + - + +
263H HIS 4.2 0.2 - - - +
265H ARG* 1.3 79.2 - - - +
267H GLU* 1.3 57.0 + - - +
269H HIS* 3.6 6.1 - - + +
270H PHE* 2.9 28.2 + - - +
311H THR* 3.7 21.8 - - + -
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Residues in contact with GLU 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H HIS* 3.2 23.8 + - - -
194H TYR* 2.6 29.3 + - + +
195H PHE* 4.7 3.6 - - - -
263H HIS 3.2 19.4 + - - +
264H VAL* 4.0 7.6 - - - +
265H ARG 3.2 0.4 - - - -
266H MET* 1.3 79.3 - - - +
268H LYS* 1.3 56.4 + - - +
270H PHE* 3.4 15.9 + - - +
271H LYS* 3.0 27.4 + - - +
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Residues in contact with LYS 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E ALA* 4.7 2.4 - - - +
263E HIS* 3.3 31.3 + - - -
264E VAL* 3.9 13.6 - - + +
264H VAL 3.5 11.2 + - - +
265H ARG 3.0 8.3 + - - +
267H GLU* 1.3 75.8 - - - +
269H HIS* 1.3 60.9 + - - +
270H PHE 3.2 0.4 - - - -
271H LYS* 4.4 13.7 - - + +
272H ASN* 2.9 50.8 + - - +
380H LEU* 3.6 30.9 + - + -
381H GLU 4.2 4.7 + - - -
382H ASP* 5.3 2.2 + - - +
383H GLU* 5.6 2.5 - - - +
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Residues in contact with HIS 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213H TYR* 3.5 35.2 + + + -
265H ARG* 2.9 36.9 + - + +
266H MET* 3.6 13.2 - - + +
268H LYS* 1.3 77.0 - - - +
270H PHE* 1.3 52.3 + - - +
272H ASN* 4.3 0.2 - - - +
273H GLY* 2.7 33.0 + - - +
311H THR 4.5 1.1 - - - -
312H GLY* 3.5 20.8 - - - +
342H GLY* 4.1 4.3 + - - -
343H GLY 3.2 28.7 + - - -
377H SER* 5.6 0.4 - - - -
378H VAL 2.8 28.7 + - - +
379H GLY* 3.8 4.7 - - - -
380H LEU* 3.5 22.6 - - + +
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Residues in contact with PHE 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H PHE* 4.2 21.5 - + - -
14H HIS* 6.2 0.7 - - - -
195H PHE* 4.0 11.7 - + + -
266H MET 2.9 16.7 + - - +
267H GLU* 3.4 15.7 - - - +
269H HIS* 1.3 73.7 - - - +
271H LYS* 1.3 60.3 + - - +
274H MET* 2.8 47.5 + - + +
291H TYR* 3.5 9.4 - - - -
293H GLY* 5.2 0.2 - - - -
308H THR 4.8 2.7 - - - -
309H GLY* 3.7 16.6 - - - -
310H CYS* 3.1 49.1 + - + +
311H THR 4.3 0.9 - - - -
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Residues in contact with LYS 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267H GLU 3.0 16.7 + - - +
268H LYS* 3.4 16.4 + - + +
270H PHE* 1.3 77.9 - - - +
272H ASN* 1.3 65.1 + - - +
274H MET* 3.9 4.9 - - - +
275H ALA* 3.3 22.0 + - - +
383H GLU* 4.1 17.9 + - - +
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Residues in contact with ASN 272 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268H LYS* 2.9 35.7 + - - +
269H HIS 4.3 0.7 - - - +
271H LYS* 1.3 79.6 - - - +
273H GLY* 1.3 59.6 + - - +
275H ALA* 3.3 4.8 + - - +
276H VAL* 2.9 34.0 + - - +
378H VAL* 3.8 15.9 - - + -
379H GLY 3.4 15.3 + - - +
380H LEU 4.2 0.6 - - - -
381H GLU 2.7 29.7 + - - +
383H GLU* 3.5 24.5 - - - +
386H LEU* 3.4 11.6 - - + +
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Residues in contact with GLY 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269H HIS 2.7 25.2 + - - -
270H PHE 3.8 0.4 - - - -
272H ASN* 1.3 72.7 - - - +
274H MET* 1.3 57.1 + - - +
276H VAL* 3.4 0.7 + - - +
277H ALA* 3.0 29.6 + - - +
291H TYR* 3.9 6.7 - - - -
311H THR 4.1 2.5 - - - -
312H GLY* 4.1 14.8 - - - -
314H VAL* 3.6 8.2 - - - +
378H VAL* 4.1 13.0 - - - +
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Residues in contact with MET 274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270H PHE* 2.8 31.4 + - + +
271H LYS* 3.9 5.8 - - - +
273H GLY* 1.3 76.4 - - - +
275H ALA* 1.3 62.5 + - - +
277H ALA* 3.3 2.3 + - - +
278H GLN* 3.0 56.1 + - - +
291H TYR* 3.7 24.5 + - - +
293H GLY* 3.3 30.7 - - - +
294H LEU* 4.5 6.5 - - + -
295H PRO* 5.4 2.5 - - + -
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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
----------------------------------------------------------
271H LYS 3.3 15.8 + - - +
272H ASN 3.3 4.7 + - - +
274H MET* 1.3 79.7 - - - +
276H VAL* 1.3 62.6 + - - +
278H GLN* 3.5 10.6 + - - +
279H PHE* 3.1 23.6 + - - +
383H GLU* 3.6 37.7 - - + +
387H LEU* 3.8 7.6 - - + +
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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
----------------------------------------------------------
272H ASN 2.9 20.3 + - - +
273H GLY 3.6 3.8 - - - +
275H ALA* 1.3 77.0 - - + +
277H ALA* 1.3 62.6 + - - +
279H PHE* 3.3 3.6 + - - +
280H LEU* 3.1 35.6 + - + +
314H VAL* 4.2 6.3 - - + -
335H PHE* 4.9 0.9 - - + -
376H LEU* 4.1 6.7 - - + -
378H VAL* 3.7 35.7 - - + -
383H GLU* 6.4 0.4 - - + -
386H LEU* 4.7 10.3 - - + -
387H LEU* 3.9 14.6 - - + -
390H LEU* 3.7 29.4 - - + -
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Residues in contact with ALA 277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273H GLY 3.0 17.2 + - - +
274H MET 3.7 3.4 - - - +
276H VAL* 1.3 76.6 - - - +
278H GLN* 1.3 62.5 + - - +
280H LEU* 3.4 3.1 + - - +
281H GLU* 3.1 25.6 + - - +
289H VAL* 4.1 3.9 - - + +
291H TYR* 3.6 38.4 - - + -
294H LEU* 3.9 13.3 - - + +
314H VAL* 4.2 14.4 - - + -
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Residues in contact with GLN 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274H MET* 3.0 52.0 + - - +
275H ALA* 3.9 8.5 - - - +
276H VAL 3.3 0.2 - - - -
277H ALA* 1.3 76.7 - - - +
279H PHE* 1.3 60.9 - - - +
281H GLU* 3.6 4.0 + - - +
282H SER* 3.4 25.3 + - - -
294H LEU* 3.7 21.8 - - + +
295H PRO* 6.2 0.4 - - - +
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Residues in contact with PHE 279 (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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275H ALA 3.1 17.2 + - - +
276H VAL 3.6 4.0 - - - +
277H ALA 3.3 0.2 - - - -
278H GLN* 1.3 78.3 - - - +
280H LEU* 1.3 77.6 + - + +
282H SER* 3.3 6.8 + - - -
283H ASN* 3.1 41.8 + - - +
387H LEU* 3.9 31.6 - - + -
390H LEU* 4.2 13.0 - - + -
391H ASP* 3.6 49.1 - - + -
394H LEU* 4.4 0.7 - - + -
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Residues in contact with LEU 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276H VAL* 3.1 28.0 + - + +
277H ALA* 3.4 2.9 + - - +
279H PHE* 1.3 88.1 - - + +
281H GLU* 1.3 63.6 + - - +
283H ASN* 3.1 16.9 + - - +
286H VAL* 3.3 24.6 - - + +
289H VAL* 3.7 13.9 - - + -
314H VAL* 4.2 9.6 - - + -
316H PHE* 3.6 37.2 - - + -
376H LEU* 3.9 15.5 - - + -
390H LEU* 4.5 10.3 - - + -
394H LEU* 3.7 29.2 - - + -
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Residues in contact with GLU 281 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277H ALA 3.1 16.6 + - - +
278H GLN* 4.1 5.5 - - - +
280H LEU* 1.3 78.0 - - - +
282H SER* 1.3 61.1 + - - +
283H ASN 3.2 3.6 + - - +
286H VAL* 5.4 2.2 - - - +
289H VAL* 3.6 20.9 + - + +
294H LEU* 3.4 24.2 - - + +
295H PRO* 5.6 1.4 - - - +
296H SER* 2.4 38.0 + - - -
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Residues in contact with SER 282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278H GLN 3.4 15.4 + - - -
279H PHE* 3.3 6.1 + - - -
280H LEU 3.2 0.4 - - - -
281H GLU* 1.3 77.4 - - - +
283H ASN* 1.3 60.4 + - - +
284H PRO* 3.8 5.9 - - - +
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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