Contacts of the helix formed by residues 258 - 272 (chain B) in PDB entry 1M54
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 GLY 258 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B VAL* 3.6 21.8 - - - -
256B GLY 2.8 4.0 - - - -
257B THR* 1.3 79.4 + - - +
259B GLY* 1.3 61.6 + - - +
260B THR 3.0 4.0 + - - -
261B ILE* 3.5 2.9 - - - +
262B THR* 2.5 32.5 + - - -
314B VAL* 4.1 2.0 - - - -
315B LEU* 3.5 16.6 - - - -
1210B PLP 3.2 5.2 + - - -
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Residues in contact with GLY 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ASN* 2.9 27.6 - - - -
229B PRO* 3.2 24.9 - - - +
232B HIS* 3.6 4.3 - - - -
257B THR* 3.0 10.0 + - - -
258B GLY* 1.3 80.3 - - - +
260B THR* 1.3 55.5 + - - +
262B THR* 4.3 0.4 - - - -
263B GLY* 3.1 20.5 + - - -
314B VAL* 3.5 5.9 - - - +
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Residues in contact with THR 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL* 4.5 7.9 - - + +
232B HIS* 3.1 30.0 + - + +
236B THR* 5.7 1.3 - - + -
253B ALA* 5.6 3.1 - - + -
254B SER 5.2 4.0 - - - +
258B GLY 3.0 2.4 + - - -
259B GLY* 1.3 74.2 - - - +
261B ILE* 1.3 68.2 + - - +
262B THR 3.0 1.1 + - - -
263B GLY* 3.9 0.2 - - - -
264B ILE* 3.0 45.7 + - + +
373B ILE* 4.6 22.9 - - + -
1210B PLP 2.3 36.9 + - - -
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Residues in contact with ILE 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LEU* 4.8 3.8 - - + +
253B ALA* 4.0 19.4 - - + +
254B SER 5.1 0.9 + - - +
255B VAL* 4.1 21.5 - - + -
258B GLY 3.5 9.4 - - - +
260B THR* 1.3 78.3 - - - +
262B THR* 1.3 59.7 + - - +
264B ILE* 3.5 5.5 - - - +
265B ALA* 2.5 39.8 + - + +
277B ILE* 3.7 22.4 - - + -
278B ILE 3.9 3.1 - - - +
279B GLY* 3.5 21.1 - - - +
315B LEU* 4.1 12.3 - - + -
320B VAL* 3.5 38.8 - - + -
1210B PLP 4.7 1.0 + - - +
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Residues in contact with THR 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PRO* 4.5 5.2 - - + -
258B GLY 2.5 22.6 + - - -
259B GLY* 4.0 2.2 - - - -
260B THR 3.0 0.4 - - - -
261B ILE* 1.3 75.8 - - - +
263B GLY* 1.3 70.7 + - - +
265B ALA* 2.8 17.0 + - - +
266B ARG* 2.9 31.0 + - + +
314B VAL 3.4 18.8 - - - +
315B LEU* 3.2 9.9 - - - +
316B ASP* 3.1 42.6 + - + +
319B VAL* 5.5 0.4 - - + -
1220B HEM 4.9 0.4 - - + -
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Residues in contact with GLY 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PRO* 3.2 28.0 - - - +
232B HIS 4.3 0.2 - - - -
233B TYR* 3.2 39.2 - - - -
259B GLY 3.1 11.3 + - - -
260B THR 3.9 0.4 - - - -
262B THR* 1.3 80.8 - - - +
264B ILE* 1.3 59.7 + - - +
267B LYS* 3.2 4.7 + - - +
1220B HEM 4.1 6.3 - - - -
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Residues in contact with ILE 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B HIS* 4.1 9.0 - - + +
236B THR* 4.1 10.1 - - + -
237B ALA* 3.9 24.5 - - + +
240B ILE* 3.8 25.6 - - + -
251B LEU* 3.4 31.2 - - + -
260B THR* 3.0 37.3 + - + +
261B ILE 3.8 2.5 - - - +
263B GLY* 1.3 74.1 - - - +
265B ALA* 1.3 54.4 + - - +
267B LYS* 3.1 1.7 + - - +
268B LEU* 2.5 55.5 + - + +
373B ILE* 4.1 11.2 - - + -
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Residues in contact with ALA 265 (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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261B ILE* 2.5 27.1 + - + +
262B THR* 2.8 7.1 + - - +
264B ILE* 1.3 72.2 - - - +
266B ARG* 1.3 56.8 + - - +
269B LYS* 2.8 35.9 + - - +
277B ILE* 4.0 25.4 - - + -
319B VAL* 3.1 35.2 - - + -
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Residues in contact with ARG 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B SER* 5.3 4.0 + - - -
52B CYS* 4.7 9.5 + - - +
54B TRP* 3.2 70.2 + - + +
233B TYR* 3.7 18.8 - - + -
262B THR* 2.9 22.4 + - + +
263B GLY 4.8 0.2 - - - -
265B ALA* 1.3 73.1 - - - +
267B LYS* 1.3 61.1 + - - +
269B LYS 4.3 0.2 - - - -
270B GLU* 3.1 29.5 + - - +
314B VAL 5.3 1.2 + - - -
316B ASP* 2.3 41.2 + - - +
319B VAL* 4.6 8.3 - - + -
1220B HEM 3.6 44.7 - - - +
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Residues in contact with LYS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B TYR* 2.8 64.5 + - + -
234B ASP* 4.4 5.7 + - - +
237B ALA* 3.5 29.2 - - + +
238B ASP* 3.1 31.4 + - - +
241B LEU* 4.6 3.8 - - + -
263B GLY 3.2 15.6 + - - +
264B ILE 3.1 1.2 + - - -
266B ARG* 1.3 78.3 - - - +
268B LEU* 1.3 57.9 + - - +
270B GLU* 3.3 5.8 + - - +
271B LYS* 3.0 51.8 + - + +
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Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ALA* 5.3 2.9 - - + +
240B ILE* 5.0 3.1 - - + -
241B LEU* 3.8 35.4 - - + -
248B LEU* 4.2 11.2 - - + -
251B LEU* 4.0 17.9 - - + -
264B ILE* 2.5 34.7 + - + +
265B ALA 3.9 2.2 - - - +
267B LYS* 1.3 71.8 - - - +
269B LYS* 1.3 53.4 + - - +
272B CYS* 2.2 43.5 + - + +
275B CYS* 3.2 37.0 - - + -
277B ILE* 3.5 21.5 - - + -
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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
----------------------------------------------------------
54B TRP* 5.2 5.4 - - + -
56B LEU* 3.8 33.4 - - + +
265B ALA 2.8 29.3 + - - +
266B ARG* 4.4 3.1 - - - +
268B LEU* 1.3 72.6 - - - +
270B GLU* 1.3 61.3 + - - +
272B CYS 3.7 4.3 - - - -
273B PRO* 3.5 26.8 - - - +
275B CYS 4.6 11.7 - - - +
277B ILE* 4.5 8.7 - - + -
319B VAL* 3.3 31.8 + - + +
321B ASP* 3.1 29.4 + - - +
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Residues in contact with GLU 270 (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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54B TRP* 2.6 41.1 + - + -
56B LEU* 4.0 13.7 - - + +
57B GLY 5.2 4.2 + - - +
58B ARG 4.9 11.1 - - - +
60B ALA* 5.9 4.5 - - - +
233B TYR* 2.5 28.9 + - - -
266B ARG 3.1 17.2 + - - +
267B LYS* 3.4 9.2 - - - +
268B LEU 3.1 0.2 - - - -
269B LYS* 1.3 80.1 - - - +
271B LYS* 1.3 68.7 + - + +
273B PRO* 4.7 3.6 - - - +
1220B HEM 5.5 0.3 - - - +
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Residues in contact with LYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ASP* 3.7 24.0 + - - -
241B LEU* 3.5 22.4 - - + +
267B LYS* 3.0 29.5 + - + +
270B GLU* 1.3 80.9 - - + +
272B CYS* 1.3 61.1 + - - +
273B PRO* 3.0 10.9 - - - +
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Residues in contact with CYS 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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241B LEU* 4.1 14.4 - - + -
246B GLY 2.9 29.4 - - - -
247B LYS* 4.5 0.7 - - - -
248B LEU* 3.7 30.5 - - - -
268B LEU* 2.2 32.5 + - + +
269B LYS* 3.7 2.1 - - - -
271B LYS* 1.3 76.5 - - - +
273B PRO* 1.3 70.4 - - - +
274B GLY* 3.5 1.3 - - - -
275B CYS* 3.4 18.6 - - + +
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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