Contacts of the helix formed by residues 258 - 272 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255E VAL* 4.2 3.1 - - - -
256E GLY 3.8 0.4 - - - -
257E THR* 1.3 78.8 + - - +
259E GLY* 1.3 56.6 + - - +
260E THR 3.3 2.9 - - - -
261E ILE* 3.6 13.7 - - - -
262E THR* 2.7 42.5 + - - -
315E LEU* 3.6 16.4 - - - -
1510E PLP 3.1 11.7 + - - -
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Residues in contact with GLY 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228E ASN* 3.1 27.9 - - - +
229E PRO* 3.6 16.3 - - - +
232E HIS* 3.0 14.5 - - - +
257E THR* 3.7 4.0 + - - -
258E GLY* 1.3 78.0 - - - +
260E THR* 1.3 54.6 + - - +
263E GLY* 2.8 29.0 + - - -
314E VAL* 4.9 2.0 - - - +
1510E PLP 3.2 3.6 + - - -
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Residues in contact with THR 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E VAL* 3.9 17.0 - - + -
119E LYS* 5.9 0.4 - - - -
232E HIS* 3.0 34.5 - - + +
236E THR* 6.3 0.4 - - + -
253E ALA* 5.1 2.5 - - - -
254E SER 3.3 9.9 + - - -
259E GLY* 1.3 70.1 - - - +
261E ILE* 1.3 68.0 + - - +
264E ILE* 2.8 43.1 + - - +
373E ILE* 5.9 9.9 - - + -
375E PRO* 6.5 0.7 - - + -
1510E PLP 2.8 44.0 + - - +
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Residues in contact with ILE 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E LEU* 5.4 0.4 - - + -
253E ALA* 3.3 32.7 - - + +
254E SER 4.2 0.7 - - - +
255E VAL* 3.8 24.7 - - + -
258E GLY* 3.0 25.4 - - - +
260E THR* 1.3 81.4 + - - +
262E THR* 1.3 64.9 + - - +
264E ILE* 3.8 0.8 - - - +
265E ALA* 2.6 40.7 + - + +
277E ILE* 3.4 30.3 - - + -
278E ILE 3.9 6.7 - - - +
279E GLY* 4.4 3.8 - - - -
315E LEU* 4.2 4.9 - - + -
320E VAL* 3.5 27.8 - - + -
1510E PLP 4.3 1.3 - - - +
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Residues in contact with THR 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E PRO* 4.8 4.5 - - + -
258E GLY 2.7 21.7 + - - -
259E GLY* 4.6 1.3 - - - -
261E ILE* 1.3 70.7 - - - +
263E GLY* 1.3 69.2 + - - +
264E ILE 2.9 1.4 + - - -
265E ALA* 4.6 4.7 - - - -
266E ARG* 3.1 55.6 + - + +
315E LEU* 2.7 40.0 - - - +
316E ASP* 3.2 15.5 + - + -
319E VAL* 4.8 2.7 - - - -
1520E HEM 4.3 10.8 - - + -
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Residues in contact with GLY 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E PRO* 3.1 22.0 - - - +
232E HIS* 3.9 0.4 - - - -
233E TYR* 3.2 39.2 - - - +
259E GLY* 2.8 27.4 + - - -
262E THR* 1.3 76.4 - - - +
264E ILE* 1.3 61.0 + - - +
267E LYS* 3.7 1.2 + - - +
1520E HEM 4.3 2.7 - - - -
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Residues in contact with ILE 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E HIS* 4.5 15.7 - - + +
236E THR* 4.2 15.3 - - + +
237E ALA* 4.8 6.9 - - - +
240E ILE* 3.5 27.8 - - + -
251E LEU* 3.4 40.2 - - + -
253E ALA* 5.8 0.4 - - + -
260E THR* 2.8 30.9 + - - +
261E ILE 3.8 0.7 - - - +
262E THR 2.9 0.6 + - - -
263E GLY* 1.3 73.1 - - - +
265E ALA* 1.3 69.8 + - - +
266E ARG 3.1 1.6 - - - -
267E LYS* 2.7 16.1 + - - +
268E LEU* 2.7 27.5 + - + +
373E ILE* 4.4 12.6 - - + -
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Residues in contact with ALA 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E ILE* 2.6 22.9 + - + +
262E THR 4.1 0.2 - - - +
264E ILE* 1.3 72.8 - - - +
266E ARG* 1.3 55.8 + - - +
268E LEU* 2.8 20.6 + - - +
269E LYS* 2.9 17.8 + - - +
277E ILE* 3.7 39.6 - - + +
319E VAL* 3.4 31.0 - - + -
320E VAL 4.7 0.7 - - - +
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Residues in contact with ARG 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E SER* 5.5 1.6 + - - -
52E CYS* 3.8 11.1 + - - +
54E TRP* 3.1 53.7 + - + +
233E TYR* 4.2 12.3 - - + -
262E THR* 3.1 33.5 + - + +
263E GLY* 5.3 0.2 - - - -
264E ILE 2.9 1.6 + - - -
265E ALA* 1.3 77.8 - - - +
267E LYS* 1.3 61.1 + - - +
268E LEU 3.5 0.2 + - - -
269E LYS* 4.1 1.6 + - - +
270E GLU* 3.6 24.9 + - - +
316E ASP* 2.7 29.4 + - - +
319E VAL* 4.0 15.0 - - + -
1520E HEM 3.0 56.7 + - - +
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Residues in contact with LYS 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E TYR* 2.6 69.6 + - + +
234E ASP* 4.1 6.9 + - - +
237E ALA* 3.6 25.6 - - + -
238E ASP* 3.0 27.9 + - - +
241E LEU* 5.2 4.9 - - + +
263E GLY 3.7 1.3 + - - +
264E ILE 2.7 7.6 + - - +
266E ARG* 1.3 73.3 - - - +
268E LEU* 1.3 65.2 + - + +
269E LYS 3.6 0.2 - - - -
270E GLU* 3.9 12.1 - - + +
271E LYS* 3.5 37.6 + - + +
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Residues in contact with LEU 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E ALA* 5.0 7.9 - - + +
240E ILE* 5.4 2.5 - - + -
241E LEU* 4.7 20.9 - - + -
248E LEU* 4.5 10.1 - - + -
251E LEU* 3.6 29.6 - - + -
264E ILE* 2.7 21.6 + - + +
265E ALA 2.8 9.4 + - - +
267E LYS* 1.3 78.2 - - - +
269E LYS* 1.3 52.6 + - - +
270E GLU 3.0 1.8 - - - -
272E CYS* 2.1 57.8 + - + +
275E CYS* 4.0 16.6 - - + -
277E ILE* 3.3 29.6 - - + -
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Residues in contact with LYS 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E TRP* 6.1 0.2 - - + -
56E LEU* 3.9 36.2 - - + +
265E ALA 2.9 13.6 + - - +
266E ARG 4.7 1.6 - - - +
268E LEU* 1.3 78.2 - - - +
270E GLU* 1.3 60.7 + - - +
272E CYS 3.3 5.6 - - - -
273E PRO* 3.4 38.7 + - + +
275E CYS 4.6 11.4 + - - +
277E ILE* 5.0 4.3 - - + -
318E THR 6.0 0.4 - - - -
319E VAL* 4.6 25.4 - - + +
321E ASP* 3.2 32.1 + - - +
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Residues in contact with GLU 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E TRP* 3.2 27.9 + - + -
55E GLN 5.0 0.8 - - - +
56E LEU* 4.2 16.2 - - + -
57E GLY 5.0 6.3 - - - +
58E ARG 5.2 6.6 - - - +
60E ALA* 4.3 16.7 - - - +
233E TYR* 3.3 26.7 + - - -
266E ARG 3.6 17.4 + - - +
267E LYS* 3.8 13.0 - - + +
268E LEU 3.0 2.2 - - - -
269E LYS* 1.3 81.2 - - - +
271E LYS* 1.3 74.9 + - + +
273E PRO* 4.4 2.9 - - - +
1520E HEM 5.6 0.7 - - - +
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Residues in contact with LYS 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241E LEU* 3.7 31.0 - - + +
267E LYS* 3.5 26.7 + - - +
270E GLU* 1.3 97.6 + - + +
272E CYS* 1.3 59.6 + - - +
273E PRO* 3.4 8.0 - - - +
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Residues in contact with CYS 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241E LEU* 3.7 20.6 - - + -
246E GLY 3.7 17.3 - - - +
247E LYS* 5.4 0.2 - - - -
248E LEU* 3.2 33.2 - - - -
268E LEU* 2.1 35.2 + - + +
269E LYS* 3.3 2.5 - - - -
271E LYS* 1.3 77.4 - - - +
273E PRO* 1.3 63.2 - - - +
274E GLY* 4.7 2.7 - - - -
275E CYS* 3.5 21.1 + - + +
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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
------------------------------------------------------------
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