Contacts of the helix formed by residues 267 - 281 (chain B) in PDB entry 3OP5
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 ASP 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B ASN* 3.1 39.7 + - - +
265B LEU 4.5 0.4 - - - -
266B LYS* 1.4 78.5 - - - +
268B PRO* 1.4 67.0 - - - +
269B LYS* 2.7 41.6 + - - +
270B TYR* 3.3 20.0 + - + +
271B VAL* 3.2 17.9 + - - +
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Residues in contact with PRO 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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225B ILE* 3.8 30.5 - - + -
233B HIS* 4.5 6.3 + - - +
265B LEU 4.7 2.5 - - - +
266B LYS 3.5 9.2 - - - +
267B ASP* 1.4 86.5 - - - +
269B LYS* 1.4 58.3 + - + +
271B VAL* 3.1 5.6 + - + +
272B ARG* 2.8 30.4 + - - +
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Residues in contact with LYS 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ASP* 2.7 35.5 + - - +
268B PRO* 1.4 78.7 - - + +
270B TYR* 1.3 60.7 + - + +
272B ARG* 3.6 22.4 + - - +
273B ASP* 3.0 29.3 + - - +
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Residues in contact with TYR 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B PRO 3.8 16.3 + - - -
261B TRP* 3.8 23.4 - - + -
263B ASP* 5.6 1.3 - - - +
264B ASN* 3.6 38.1 - - + -
267B ASP* 3.3 27.5 + - - +
268B PRO 3.2 0.6 - - - -
269B LYS* 1.3 82.2 - - + +
271B VAL* 1.4 63.4 + - + +
273B ASP* 3.3 11.2 + - - +
274B SER* 3.0 46.9 + - - -
277B ARG* 5.7 3.0 + - - -
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Residues in contact with VAL 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B ILE* 3.5 30.1 - - + +
233B HIS* 3.6 16.4 - - + +
261B TRP* 3.8 18.8 - - + +
264B ASN 3.6 15.3 - - - +
265B LEU* 4.1 21.3 - - + -
267B ASP 3.2 15.7 + - - +
268B PRO* 3.1 9.5 + - + +
270B TYR* 1.4 79.5 - - + +
272B ARG* 1.4 61.6 + - - +
274B SER* 3.4 2.6 + - - -
275B LYS* 3.1 33.8 + - - +
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Residues in contact with ARG 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ILE* 4.9 4.0 - - + -
233B HIS* 3.7 48.0 + - + -
234B ASN* 2.8 40.4 + - - +
268B PRO 2.8 18.8 + - - +
269B LYS* 3.8 20.9 + - - +
271B VAL* 1.4 70.7 - - - +
273B ASP* 1.3 57.5 + - - +
275B LYS* 3.2 4.1 + - - +
276B ILE* 2.9 49.7 + - + +
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Residues in contact with ASP 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B LYS 3.0 19.8 + - - +
270B TYR* 3.3 12.4 + - - +
272B ARG* 1.3 75.3 - - - +
274B SER* 1.3 60.7 + - - +
276B ILE* 3.5 9.3 + - - +
277B ARG* 3.1 39.1 + - - +
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Residues in contact with SER 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B PRO 5.6 0.3 - - - -
261B TRP* 3.8 24.5 - - - +
270B TYR* 3.0 41.8 + - - -
271B VAL 3.6 4.9 - - - -
272B ARG 3.3 0.2 - - - -
273B ASP* 1.3 74.2 + - - +
275B LYS* 1.3 60.5 + - - +
277B ARG* 3.4 21.3 + - - +
278B TYR* 2.8 43.4 + - - -
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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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225B ILE 2.9 19.0 + - - -
226B GLU 3.6 15.3 + - - -
228B THR 2.6 34.9 + - - +
230B ILE* 3.6 11.4 - - + +
233B HIS* 2.9 31.5 + - + +
245B GLU* 4.7 1.6 - - - +
249B TYR* 3.5 28.7 + - + +
261B TRP* 3.7 31.2 - - + +
271B VAL* 3.1 16.0 + - - +
272B ARG 3.6 4.7 - - - +
274B SER* 1.3 77.7 - - - +
276B ILE* 1.4 56.7 + - - +
278B TYR* 3.4 3.0 + - - +
279B ARG* 2.9 30.8 + - - +
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Residues in contact with ILE 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ILE* 3.9 30.7 - - + -
234B ASN* 4.9 4.7 - - - +
272B ARG* 2.9 48.6 + - + +
273B ASP* 3.8 7.6 - - - +
275B LYS* 1.4 75.4 - - - +
277B ARG* 1.3 56.6 + - - +
279B ARG* 3.3 5.7 + - - +
280B GLU* 3.0 30.4 + - + +
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Residues in contact with ARG 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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270B TYR* 5.7 2.2 + - - -
273B ASP* 3.1 27.0 + - - +
274B SER* 3.7 19.4 + - - +
276B ILE* 1.3 77.1 - - - +
278B TYR* 1.3 103.8 + - + +
280B GLU* 3.4 8.7 + - - +
281B ASN* 3.0 28.0 + - + +
284B SER* 4.7 4.6 + - - +
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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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249B TYR* 6.3 1.3 - - + -
260B PRO* 3.6 23.8 - - + +
261B TRP* 3.8 17.3 - + + -
274B SER* 2.8 32.2 + - - +
275B LYS* 4.1 4.5 - - - +
277B ARG* 1.3 107.3 + - - +
279B ARG* 1.4 59.7 + - - +
281B ASN 3.1 21.3 - - - +
282B ILE* 3.3 11.8 + - - +
284B SER* 3.6 26.5 - - - -
285B LEU* 3.5 44.5 - - + +
288B LYS* 3.5 26.6 + - + +
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Residues in contact with ARG 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ILE* 3.7 23.8 - - + -
241B ARG* 4.5 3.2 - - - +
245B GLU* 5.7 1.8 - - - -
249B TYR* 5.5 2.0 - - - +
275B LYS 2.9 17.5 + - - +
276B ILE* 3.6 5.6 - - - +
277B ARG 3.3 0.4 - - - -
278B TYR* 1.4 72.4 - - - +
280B GLU* 1.3 69.2 + - - +
281B ASN 3.3 0.7 + - - -
282B ILE* 3.5 13.2 - - + +
306B VAL 5.1 0.4 + - - -
307B LYS* 2.8 84.6 + - + +
309B LEU 4.5 6.9 + - - -
367B EDO 3.0 27.5 + - - -
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Residues in contact with GLU 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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276B ILE* 3.0 18.5 + - + +
277B ARG* 3.6 9.9 - - - +
279B ARG* 1.3 83.2 + - - +
281B ASN* 1.4 56.9 + - + +
282B ILE 4.4 0.2 + - - -
307B LYS* 3.4 23.0 + - - +
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Residues in contact with ASN 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ARG* 3.0 12.6 + - + +
278B TYR 3.1 11.2 - - - +
280B GLU* 1.4 79.6 - - + +
282B ILE* 1.3 62.0 + - - +
283B ALA* 3.7 12.6 + - - +
284B SER* 2.7 53.4 + - - +
285B LEU 3.4 2.8 + - - -
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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
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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