Contacts of the helix formed by residues 215 - 222 (chain B) in PDB entry 1M1J
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 GLU 215 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213B GLY 3.2 0.6 - - - -
214B ARG* 1.3 96.3 + - + +
216B CYS* 1.3 64.7 + - - +
217B GLU* 2.6 38.6 + - - +
218B ASP* 3.1 20.9 + - - +
219B ILE* 3.0 21.3 + - - +
232B ILE* 3.6 19.1 - - + -
255B THR* 3.8 11.5 + - - +
306B LEU* 4.3 13.5 - - + -
309B ILE* 4.3 16.4 - - + +
460B PRO* 3.9 24.0 - - + +
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Residues in contact with CYS 216 (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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215B GLU* 1.3 77.7 - - - +
217B GLU* 1.3 55.7 + - - +
219B ILE* 3.0 5.5 + - - +
220B TYR* 2.7 26.5 + - - +
232B ILE* 4.1 0.2 - - - +
243B VAL* 4.5 4.5 - - - -
244B TYR 3.9 1.8 - - - -
245B CYS* 2.0 53.4 - - + -
247B MET* 3.5 5.6 - - + +
253B GLY* 3.7 18.8 - - - +
254B TRP 3.7 2.0 - - - -
255B THR* 3.0 40.8 + - - +
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Residues in contact with GLU 217 (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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215B GLU* 2.6 18.6 + - - +
216B CYS* 1.3 73.5 - - - +
218B ASP* 1.3 61.6 + - - +
220B TYR* 3.1 7.1 + - - +
221B ARG* 2.8 60.1 + - + +
252B GLY 4.0 1.0 - - - +
253B GLY* 3.3 25.9 + - - +
459B LYS* 3.6 17.8 - - + -
460B PRO* 3.6 28.9 - - + +
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Residues in contact with ASP 218 (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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213B GLY* 3.5 6.9 - - - -
214B ARG* 3.1 52.8 + - - +
215B GLU* 3.1 28.5 + - - +
217B GLU* 1.3 75.8 - - - +
219B ILE* 1.3 64.4 + - - +
221B ARG* 3.2 10.4 + - - +
222B LYS* 3.0 41.9 + - - +
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Residues in contact with ILE 219 (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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211B VAL* 4.1 6.9 - - + +
212B SER* 3.7 18.6 - - - -
213B GLY 3.5 18.4 - - - +
215B GLU 3.0 13.1 + - - +
216B CYS 3.4 7.9 - - - +
218B ASP* 1.3 76.3 - - - +
220B TYR* 1.3 55.1 + - - +
222B LYS* 2.7 29.8 + - - +
223B GLY 3.1 8.7 + - - -
224B GLY* 3.2 11.6 + - - -
230B TYR* 3.5 57.7 - - + -
231B ILE 3.9 0.7 - - - +
232B ILE* 3.8 18.4 - - + -
245B CYS* 4.6 3.4 - - - -
247B MET* 3.7 10.8 - - + -
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Residues in contact with TYR 220 (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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216B CYS 2.7 16.0 + - - +
217B GLU* 3.1 11.4 + - - +
219B ILE* 1.3 73.9 - - - +
221B ARG* 1.3 93.1 + - - +
223B GLY* 3.1 13.9 + - - -
224B GLY 3.5 22.3 + - - -
225B GLU* 4.2 24.0 + - + +
247B MET* 3.6 35.4 + - + +
251B ASN* 3.6 26.8 + - - -
253B GLY* 4.1 11.4 - - - +
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Residues in contact with ARG 221 (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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217B GLU* 2.8 45.3 + - + +
218B ASP* 3.2 13.2 + - - +
220B TYR* 1.3 102.2 - - - +
222B LYS* 1.3 59.1 + - + +
223B GLY 3.3 1.5 + - - -
251B ASN* 4.5 11.1 + - - +
459B LYS* 5.5 2.0 - - - +
209C VAL* 3.8 12.5 - - - +
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Residues in contact with LYS 222 (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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211B VAL* 3.7 13.8 - - + +
212B SER 3.0 30.1 + - - +
213B GLY* 4.2 4.8 - - - -
218B ASP* 3.0 34.9 + - - +
219B ILE 2.7 11.7 + - - +
221B ARG* 1.3 79.9 - - + +
223B GLY* 1.3 56.4 + - - +
224B GLY 3.7 0.2 - - - -
209C VAL* 3.3 22.5 - - - +
210C GLN* 4.4 1.4 - - - -
213C GLU* 3.3 49.1 + - + +
214C GLY 5.4 0.5 - - - +
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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