Contacts of the helix formed by residues 276 - 284 (chain B) in PDB entry 4M5X
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 276 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216B LEU* 4.0 15.7 - - + -
217B LYS 5.2 2.5 + - - +
219B GLN* 2.8 20.1 + - - +
222B THR* 5.3 0.5 - - - +
225B MET* 3.3 26.1 - - + +
226B ASN* 4.2 4.8 + - - +
229B LEU* 3.7 28.9 - - + -
263B VAL* 4.5 7.2 - - + -
274B VAL 4.5 1.6 - - - +
275B GLY* 1.3 79.3 - - - +
277B LYS* 1.3 61.0 + - - +
278B LYS 3.2 3.1 - - - -
279B LEU* 2.8 27.9 + - - +
280B THR* 3.0 15.7 + - - +
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Residues in contact with LYS 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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219B GLN* 3.6 36.9 - - + +
276B THR* 1.3 77.1 + - - +
278B LYS* 1.3 63.5 + - + +
280B THR* 3.4 8.9 + - - +
281B LYS* 3.2 25.9 + - - +
601B BR 3.5 14.5 - - + +
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Residues in contact with LYS 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B SER* 4.7 12.8 + - - +
253B SER* 5.3 1.2 - - - +
259B ALA* 4.0 3.4 - - - +
262B ARG* 3.3 51.1 - - - +
276B THR 3.2 1.0 - - - -
277B LYS* 1.3 79.1 - - + +
279B LEU* 1.3 57.6 + - - +
281B LYS* 3.7 10.0 + - + +
282B SER* 3.1 28.4 + - - -
547B GLU* 4.3 7.6 - - - -
551B GLU* 3.6 25.5 + - - +
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Residues in contact with LEU 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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225B MET* 4.6 7.0 - - - -
229B LEU* 3.6 42.6 - - + -
256B VAL* 4.6 4.7 - - + +
259B ALA* 3.7 29.3 - - + +
260B LEU* 4.3 9.4 - - + +
263B VAL* 4.3 16.5 - - + +
276B THR* 2.8 17.4 + - - +
278B LYS* 1.3 77.3 - - - +
280B THR* 1.3 65.3 + - - +
282B SER* 2.7 23.7 + - - +
283B PHE* 3.4 31.1 + - + -
303B LEU* 4.4 11.2 - - + -
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Residues in contact with THR 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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222B THR* 4.5 4.5 - - + -
225B MET* 3.5 37.9 - - + -
276B THR* 3.0 13.2 + - - +
277B LYS* 3.4 13.7 + - - +
279B LEU* 1.3 74.4 - - - +
281B LYS* 1.3 63.9 + - - +
283B PHE* 3.6 9.1 + - + -
284B GLY 3.1 3.5 + - - -
285B TRP 3.1 40.6 + - - -
286B GLU* 3.8 6.4 - - - +
291B PHE* 3.6 15.7 - - + -
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Residues in contact with LYS 281 (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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253B SER* 3.7 33.5 - - - +
277B LYS 3.2 16.4 + - - +
278B LYS* 3.7 10.0 - - + +
279B LEU 3.2 0.2 - - - -
280B THR* 1.3 82.6 + - - +
282B SER* 1.3 63.2 + - - +
284B GLY* 3.1 12.5 + - - -
286B GLU* 3.4 34.2 + - - +
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Residues in contact with SER 282 (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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252B SER 5.7 0.9 - - - -
253B SER 4.0 13.2 - - - -
254B LYS* 3.7 17.1 - - - +
255B SER 3.8 9.2 - - - -
256B VAL* 3.5 39.7 - - - +
259B ALA* 3.6 5.5 - - - +
278B LYS 3.1 14.8 + - - -
279B LEU* 2.7 23.1 + - - +
281B LYS* 1.3 77.2 - - - +
283B PHE* 1.3 57.8 + - - +
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Residues in contact with PHE 283 (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 MET* 4.6 3.6 - - + -
256B VAL* 3.7 15.3 - - + -
279B LEU* 3.4 44.7 + - + -
280B THR* 4.1 8.1 - - + -
282B SER* 1.3 79.7 + - - +
284B GLY* 1.3 60.4 + - - +
285B TRP* 3.4 57.9 + + + -
291B PHE* 3.9 15.3 - + - -
299B LEU* 3.6 16.6 - - + -
302B VAL* 4.0 19.1 - - + -
303B LEU* 3.9 24.0 - - + -
306B ASN* 5.2 0.7 - - - +
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Residues in contact with GLY 284 (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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280B THR 3.1 3.3 + - - -
281B LYS 3.1 14.7 + - - -
282B SER 3.4 0.6 + - - -
283B PHE* 1.3 79.1 - - - +
285B TRP* 1.3 65.3 + - - +
286B GLU* 3.5 13.2 + - - +
287B THR* 6.0 0.7 - - - +
290B SER* 5.4 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