Contacts of the helix formed by residues 267 - 280 (chain B) in PDB entry 5H15
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264B ARG* 3.9 15.0 + - - -
265B ILE 3.2 0.6 - - - -
266B ASN* 1.3 83.8 - - - +
268B LYS* 1.3 59.5 + - - +
269B ARG* 3.8 8.4 + - - +
270B MET* 3.2 26.7 + - - +
271B MET* 2.8 28.2 + - - +
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Residues in contact with LYS 268 (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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266B ASN 3.8 0.6 + - - +
267B SER* 1.3 71.9 - - - +
269B ARG* 1.4 56.4 + - - +
271B MET* 4.0 18.9 - - + +
272B ASN* 2.9 32.1 + - - +
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Residues in contact with ARG 269 (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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267B SER* 4.1 7.8 - - - +
268B LYS* 1.4 77.1 - - - +
270B MET* 1.3 57.9 + - - +
272B ASN* 3.8 5.0 + - - +
273B ALA* 2.9 28.3 + - - +
292B GLN* 2.8 33.5 + - - +
293B LYS 3.1 27.9 + - - +
294B ILE* 3.4 31.6 - - + +
295B HIS 5.5 0.8 - - - +
296B PHE* 6.3 0.8 - - - -
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Residues in contact with MET 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B LEU* 3.8 28.9 - - + -
226B VAL* 4.3 4.3 - - + -
227B ALA* 4.0 21.8 - - + -
229B PHE* 3.9 16.8 - - + -
264B ARG 3.7 17.3 - - - +
265B ILE* 3.4 27.1 - - + +
267B SER* 3.2 12.9 + - - +
269B ARG* 1.3 76.0 - - + +
271B MET* 1.3 60.5 + - - +
273B ALA* 3.3 8.7 + - - +
274B ILE* 2.9 40.1 + - + +
292B GLN* 4.6 1.6 - - - -
294B ILE* 4.0 23.8 - - + -
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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
----------------------------------------------------------
265B ILE 3.8 12.3 - - - +
266B ASN* 3.6 27.4 - - - +
267B SER 2.8 21.6 + - - +
268B LYS* 4.0 20.6 - - + +
270B MET* 1.3 69.7 - - - +
272B ASN* 1.4 57.2 + - - +
274B ILE* 3.3 9.6 + - + +
275B LYS* 3.0 28.3 + - - +
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Residues in contact with ASN 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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268B LYS 2.9 20.2 + - - +
269B ARG* 3.8 5.0 + - - +
271B MET* 1.4 76.4 - - - +
273B ALA* 1.4 56.3 + - - +
275B LYS* 3.1 14.5 + - - +
276B GLU* 2.9 56.8 + - - +
292B GLN* 5.7 3.4 - - - +
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Residues in contact with ALA 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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226B VAL* 3.9 16.2 - - + +
269B ARG 2.9 18.3 + - - +
270B MET* 3.5 9.2 - - - +
272B ASN* 1.4 71.6 - - - +
274B ILE* 1.4 60.4 + - - +
276B GLU* 3.4 12.3 + - - +
277B SER* 3.0 28.1 + - - -
289B PHE* 4.1 5.8 - - + -
292B GLN* 3.5 33.7 - - + +
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Residues in contact with ILE 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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199B HIS* 5.9 0.7 - - + +
202B ASP* 5.0 0.9 - - - +
205B LEU* 4.1 34.8 - - + -
217B LEU* 4.3 16.2 - - + -
226B VAL* 4.0 16.2 - - + -
265B ILE* 4.2 24.5 - - + +
270B MET* 2.9 25.2 + - + +
271B MET* 3.7 8.1 - - + +
272B ASN 3.3 0.2 - - - -
273B ALA* 1.4 75.2 - - - +
275B LYS* 1.4 64.4 + - - +
277B SER* 2.7 24.5 + - - -
278B TYR* 3.3 23.9 + - + -
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Residues in contact with LYS 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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159A SER* 5.9 2.2 + - - -
271B MET 3.0 14.4 + - - +
272B ASN* 3.1 19.7 + - - +
274B ILE* 1.4 77.4 - - - +
276B GLU* 1.3 59.2 + - + +
278B TYR* 3.0 25.0 + - + +
279B ASP* 3.1 44.4 + - - +
62C GLN 4.9 10.3 + - - -
63C ARG* 6.2 0.4 - - - +
64C ARG* 6.1 5.1 - - - +
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Residues in contact with GLU 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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272B ASN* 2.9 44.0 + - - +
273B ALA* 3.8 9.5 - - - +
274B ILE 3.3 0.2 - - - -
275B LYS* 1.3 73.5 - - + +
277B SER* 1.4 65.6 + - - +
279B ASP* 3.2 17.0 + - + +
280B TYR* 3.1 19.1 + - - +
289B PHE* 3.6 19.6 - - + -
292B GLN* 5.1 6.1 + - - -
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Residues in contact with SER 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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205B LEU* 5.0 0.2 - - - +
219B ASN* 2.8 23.8 + - - +
222B THR* 2.7 26.3 + - - +
224B THR* 3.5 19.3 - - - -
226B VAL* 3.8 18.0 - - - +
273B ALA 3.0 13.6 + - - -
274B ILE* 2.7 20.6 + - - +
276B GLU* 1.4 76.1 - - - +
278B TYR* 1.3 57.7 + - - +
280B TYR* 3.6 8.0 - - - +
289B PHE* 3.7 17.9 - - - -
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Residues in contact with TYR 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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202B ASP* 2.7 31.5 + - - -
204B ASN* 2.9 23.7 + - - +
205B LEU* 4.9 2.2 - - + +
219B ASN* 3.7 23.3 - - - +
221B GLN* 3.5 38.3 - - - +
222B THR* 3.9 12.7 - - + +
274B ILE* 3.3 31.4 + - + -
275B LYS* 3.0 12.8 + - + +
277B SER* 1.3 78.6 + - - +
279B ASP* 1.4 61.5 + - - +
280B TYR 3.2 7.4 + - - +
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Residues in contact with ASP 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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157A ASN 4.6 13.4 - - - +
275B LYS* 3.1 44.9 + - - +
276B GLU* 3.2 15.5 + - + +
278B TYR* 1.4 75.7 - - - +
280B TYR* 1.3 62.9 + - - +
281B ASN* 3.5 6.9 + - - +
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Residues in contact with TYR 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B THR* 3.8 25.6 - - - +
224B THR* 3.6 19.7 - - + -
276B GLU 3.1 10.9 + - - +
277B SER 3.6 14.1 - - - +
278B TYR 3.2 3.1 - - - +
279B ASP* 1.3 75.7 - - - +
281B ASN* 1.3 63.8 + - - +
282B PRO* 4.0 35.8 - - + +
285B THR* 4.2 16.4 + - + -
286B ASN 5.5 0.2 - - - -
287B ARG 3.0 27.7 + - - -
288B PRO* 3.6 8.8 - - - +
289B PHE* 3.6 38.3 + + + -
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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