Contacts of the helix formed by residues 235 - 244 (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 THR 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B THR* 3.5 25.8 - - + -
69B ALA 3.5 14.1 - - - +
70B PRO* 3.9 13.4 - - + +
121B ARG* 3.5 17.1 + - - +
125B ARG* 5.1 0.9 - - - +
231B ALA* 2.3 34.4 + - - +
234B ASP* 1.3 76.9 - - - +
236B THR* 1.4 59.8 + - - -
237B ALA 3.5 1.1 - - - -
238B ASP* 3.2 4.4 + - - +
239B GLU* 3.0 36.1 + - - +
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Residues in contact with THR 236 (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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108B LYS* 4.5 9.2 - - - -
110B GLU* 4.7 5.6 - - - +
121B ARG* 2.8 50.9 + - - +
232B HIS* 3.3 23.5 + - - +
235B THR* 1.4 76.6 + - - +
237B ALA* 1.3 67.6 - - - +
239B GLU* 3.2 4.7 + - - +
240B ILE* 3.0 32.6 + - + +
260B THR* 5.7 1.1 - - + -
264B ILE* 4.1 19.3 - - + -
373B ILE* 4.7 4.9 - - + -
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Residues in contact with ALA 237 (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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232B HIS 2.8 20.2 + - - +
233B TYR 3.6 3.8 - - - +
236B THR* 1.3 78.0 - - - +
238B ASP* 1.3 60.5 + - - +
240B ILE* 3.7 6.5 - - - +
241B LEU* 3.4 26.3 + - - +
264B ILE* 3.9 25.1 - - + +
267B LYS* 3.5 31.9 - - + -
268B LEU* 5.3 2.5 - - + +
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Residues in contact with ASP 238 (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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70B PRO* 3.9 16.1 - - + +
234B ASP 3.7 18.5 + - - +
235B THR 3.2 5.9 + - - +
236B THR 3.2 0.8 - - - -
237B ALA* 1.3 77.4 - - - +
239B GLU* 1.3 65.7 + - - +
241B LEU* 3.5 10.8 + - - +
242B GLN* 3.1 22.9 + - - +
267B LYS* 3.1 36.3 - - - +
271B LYS* 3.7 14.8 + - - -
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Residues in contact with GLU 239 (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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70B PRO* 5.0 10.0 - - + +
71B ALA 5.3 2.4 + - - +
72B LYS* 6.5 0.4 - - - -
85B GLY* 3.3 1.6 - - - -
86B ASP* 2.2 42.1 + - - +
87B THR 3.9 0.2 - - - +
108B LYS* 2.8 27.4 + - - +
121B ARG* 2.9 25.7 + - - -
235B THR* 3.0 24.5 + - - +
236B THR* 3.2 5.1 + - - +
238B ASP* 1.3 72.3 - - - +
240B ILE* 1.3 68.8 + - - +
242B GLN* 2.7 17.9 + - - +
243B GLN* 2.7 25.7 + - + +
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Residues in contact with ILE 240 (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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89B MET* 4.0 13.5 - - + -
108B LYS* 3.3 37.0 - - + -
236B THR* 3.0 21.5 + - + +
237B ALA* 3.7 7.2 - - - +
239B GLU* 1.3 81.1 - - - +
241B LEU* 1.3 64.3 + - + +
242B GLN 3.1 0.7 + - - -
243B GLN* 3.2 9.3 + - - +
244B CYS* 3.3 17.7 + - - +
248B LEU* 3.4 28.9 - - + -
251B LEU* 4.3 11.7 - - + -
264B ILE* 3.8 28.5 - - + -
268B LEU* 5.0 4.7 - - + -
371B VAL* 4.3 3.4 - - + -
373B ILE* 4.2 5.2 - - + -
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Residues in contact with LEU 241 (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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237B ALA 3.4 15.2 + - - +
238B ASP* 3.7 14.4 - - - +
239B GLU 3.2 1.0 - - - -
240B ILE* 1.3 78.5 - - + +
242B GLN* 1.3 56.2 + - - +
244B CYS* 4.1 2.2 - - + -
245B ASP* 4.0 0.3 - - - -
246B GLY* 3.0 56.8 + - - +
248B LEU* 4.6 8.3 - - + -
267B LYS* 4.5 7.4 - - + +
268B LEU* 3.8 32.1 - - + -
271B LYS* 3.5 36.6 - - + +
272B CYS* 4.1 10.1 - - + +
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Residues in contact with GLN 242 (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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75A LYS* 3.5 32.4 - - - +
72B LYS* 6.1 6.1 - - + -
238B ASP 3.1 15.8 + - - +
239B GLU* 2.7 12.5 + - - +
241B LEU* 1.3 72.5 - - - +
243B GLN* 1.3 65.7 + - + +
244B CYS 3.1 5.6 + - - -
245B ASP* 3.6 10.1 + - - +
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Residues in contact with GLN 243 (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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74A PRO 5.3 0.8 + - - -
75A LYS* 3.8 36.8 + - + +
76A ILE* 3.3 26.2 - - - +
86B ASP* 4.6 8.1 + - - -
87B THR 3.1 22.5 + - - -
88B PRO* 4.2 1.4 - - - +
89B MET* 3.4 31.8 - - + +
108B LYS* 3.5 25.7 + - - +
239B GLU* 2.7 24.6 + - + +
240B ILE 3.2 4.2 + - - +
242B GLN* 1.3 82.1 - - + +
244B CYS* 1.3 57.6 + - - +
245B ASP* 3.6 3.6 - - - +
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Residues in contact with CYS 244 (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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76A ILE* 4.9 0.9 - - - -
89B MET* 4.0 6.7 - - - -
106B LEU* 4.4 4.5 - - - -
240B ILE 3.3 16.9 + - - +
241B LEU* 4.8 1.6 - - - +
242B GLN 3.1 1.0 - - - +
243B GLN* 1.3 84.2 - - - +
245B ASP* 1.3 73.6 + - - +
246B GLY* 2.9 7.4 + - - +
247B LYS* 3.1 22.0 + - - +
248B LEU* 4.5 8.3 - - + -
369B ARG* 3.6 39.3 + - - +
371B VAL* 3.9 24.9 - - - -
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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