Contacts of the helix formed by residues 267 - 280 (chain H) in PDB entry 5LS6
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 267 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264H ARG* 4.0 14.1 + - - -
265H ILE* 3.3 0.4 - - - +
266H ASN* 1.3 83.1 + - - +
268H LYS* 1.3 64.8 + - - +
269H ARG* 3.6 8.3 + - - +
270H MET* 3.0 27.5 + - - +
271H MET* 2.9 22.9 + - - +
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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
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266H ASN 3.8 0.8 + - - -
267H SER* 1.3 72.2 - - - +
269H ARG* 1.3 61.2 + - - +
271H MET* 4.0 4.7 - - - +
272H ASN* 2.8 41.0 + - - +
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Residues in contact with ARG 269 (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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267H SER* 3.2 8.2 + - - +
268H LYS* 1.3 78.0 - - - +
270H MET* 1.3 63.0 + - + +
272H ASN* 3.3 6.2 + - - +
273H ALA* 3.0 26.7 + - - +
292H GLN* 2.5 33.0 + - + +
293H LYS 3.0 29.7 + - - -
294H ILE* 4.1 21.0 - - - +
590I GLU* 3.2 23.0 + - - -
594I GLU* 5.4 10.9 + - - +
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Residues in contact with MET 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217H LEU* 3.8 28.3 - - + -
226H VAL* 4.3 8.3 - - + -
227H ALA* 3.9 17.3 - - + -
229H PHE* 4.2 5.6 - - + -
264H ARG 4.0 11.7 - - - +
265H ILE* 3.7 30.7 - - + +
267H SER* 3.0 15.6 + - - +
269H ARG* 1.3 80.5 - - + +
271H MET* 1.3 65.9 + - - +
273H ALA* 3.4 1.7 + - + -
274H ILE* 3.1 30.0 + - + +
292H GLN* 4.7 6.5 - - - -
294H ILE* 3.7 33.9 - - + -
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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
----------------------------------------------------------
265H ILE 3.7 10.0 + - - +
266H ASN* 3.2 26.7 - - + +
267H SER 2.9 25.2 + - - +
268H LYS* 4.0 5.4 - - - +
270H MET* 1.3 76.0 - - - +
272H ASN* 1.3 59.1 + - - +
274H ILE* 3.0 14.3 + - + +
275H LYS* 2.8 29.1 + - - +
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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
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268H LYS* 2.8 32.4 + - - +
269H ARG* 3.3 5.4 + - - +
271H MET* 1.3 79.5 - - - +
273H ALA* 1.3 56.6 - - - +
275H LYS* 3.9 15.2 + - - +
276H GLU* 3.0 50.8 + - - +
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Residues in contact with ALA 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226H VAL* 3.6 17.7 - - + +
269H ARG 3.0 17.1 + - - +
270H MET* 3.6 10.5 - - + +
271H MET 3.2 0.2 - - - -
272H ASN* 1.3 74.1 - - - +
274H ILE* 1.3 58.9 + - - +
276H GLU* 3.4 5.2 + - - -
277H SER* 2.9 28.1 + - - -
289H PHE* 3.8 8.8 - - + -
292H GLN* 3.6 29.4 - - + -
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Residues in contact with ILE 274 (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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199H HIS* 5.5 2.9 - - - +
202H ASP* 4.7 1.3 - - - +
205H LEU* 3.7 32.5 - - + -
217H LEU* 4.2 18.2 - - + -
226H VAL* 3.8 15.9 - - + -
265H ILE* 4.4 16.2 - - + +
270H MET* 3.1 24.5 + - + +
271H MET* 3.0 16.2 + - + +
273H ALA* 1.3 72.8 - - - +
275H LYS* 1.3 67.8 - - - +
277H SER* 2.4 29.2 + - - +
278H TYR* 3.4 18.6 + - + -
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Residues in contact with LYS 275 (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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271H MET 2.8 19.0 + - - +
272H ASN* 3.9 15.2 + - - +
274H ILE* 1.3 75.3 - - - +
276H GLU* 1.3 75.7 + - - +
278H TYR* 3.3 14.8 + - - +
279H ASP* 3.2 48.6 + - - +
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Residues in contact with GLU 276 (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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272H ASN* 3.0 40.0 + - - +
273H ALA* 3.9 4.9 - - - +
275H LYS* 1.3 91.3 + - - +
277H SER* 1.3 63.7 + - - +
279H ASP* 3.1 12.4 + - + +
280H TYR* 3.0 19.8 + - - +
287H ARG* 5.9 1.2 + - - -
289H PHE* 3.6 15.5 - - + -
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Residues in contact with SER 277 (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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219H ASN* 2.8 23.3 + - - +
222H THR* 2.7 27.1 + - - -
224H THR* 3.4 20.7 + - - -
226H VAL* 3.7 15.7 - - - +
273H ALA 2.9 13.0 + - - -
274H ILE* 2.4 28.3 + - - +
276H GLU* 1.3 75.5 - - - +
278H TYR* 1.3 56.6 + - - +
280H TYR* 3.8 8.7 + - - +
289H PHE* 3.6 14.3 - - - -
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Residues in contact with TYR 278 (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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202H ASP* 2.5 42.3 + - - -
204H ASN* 3.3 13.0 + - - +
205H LEU* 4.3 2.4 - - + +
219H ASN* 3.3 26.9 - - - -
221H GLN* 3.1 37.0 + - + +
222H THR* 3.6 15.7 - - + +
274H ILE* 3.5 31.6 - - + -
275H LYS* 3.3 11.4 + - - +
276H GLU 3.2 0.4 - - - -
277H SER* 1.3 80.4 + - - +
279H ASP* 1.3 67.2 + - - +
280H TYR 3.2 3.2 + - - +
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Residues in contact with ASP 279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H LYS* 3.2 43.1 + - - +
276H GLU* 3.1 15.4 + - + +
278H TYR* 1.3 78.7 - - - +
280H TYR* 1.3 63.1 + - - +
281H ASN* 3.6 4.9 + - - +
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Residues in contact with TYR 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222H THR* 3.9 14.5 - - - +
223H ASP 5.9 0.4 - - - -
224H THR* 3.4 24.7 - - + -
276H GLU 3.0 9.4 + - - +
277H SER 3.9 5.6 - - - +
278H TYR 3.2 8.8 - - - +
279H ASP* 1.3 78.1 - - - +
281H ASN* 1.3 62.9 + - - +
282H PRO* 3.8 31.4 - - + +
285H THR* 4.1 14.6 - - + -
287H ARG* 3.5 26.1 + - + +
288H PRO* 3.6 7.8 - - - +
289H PHE* 3.5 55.8 + + + -
575I ARG* 3.4 25.3 + - - -
578I GLU* 4.8 0.2 + - - -
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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
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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