Contacts of the helix formed by residues 183 - 195 (chain B) in PDB entry 3M2K
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 ALA 183 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B GLY* 3.6 32.1 - - - +
46B ILE 4.3 0.9 - - - -
47B PHE* 3.1 23.1 - - + +
61B ARG 5.3 0.4 - - - +
62B PRO* 3.7 6.4 + - + +
64B GLU 4.2 4.8 + - - -
66B PHE* 5.8 0.7 - - + -
181B SER 3.9 0.2 + - - -
182B THR* 1.3 72.9 - - - +
184B ARG* 1.3 59.3 + - - +
186B LEU* 4.8 1.3 - - - -
187B VAL* 3.5 6.2 + - - +
262B ALA* 3.5 23.4 - - + +
264B LEU* 3.6 26.1 - - + +
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Residues in contact with ARG 184 (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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47B PHE* 3.6 44.2 - - + +
62B PRO* 3.0 28.2 + - - +
63B ASP* 2.8 38.9 + - - +
182B THR* 2.8 10.3 + - - +
183B ALA* 1.3 73.7 - - - +
185B ALA* 1.3 64.4 + - - +
187B VAL* 3.4 3.5 + - - +
188B THR* 3.2 32.8 + - - +
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Residues in contact with ALA 185 (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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157B ASP* 3.5 6.2 - - - +
159B VAL* 3.0 41.5 - - + -
181B SER* 3.3 17.0 - - - +
182B THR* 2.8 7.4 + - - +
184B ARG* 1.3 79.8 - - - +
186B LEU* 1.4 53.8 + - - +
188B THR* 3.5 8.8 + - - +
189B SER* 3.0 37.9 + - - -
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Residues in contact with LEU 186 (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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68B PHE* 4.2 20.0 - - + -
71B THR* 4.4 8.7 - - - +
72B ILE* 5.6 1.6 - - + -
75B LEU* 4.3 20.8 - - + +
160B THR* 4.1 9.2 - - + +
181B SER* 3.6 30.5 - - - +
182B THR 3.7 5.2 - - - +
183B ALA 4.4 3.1 - - - +
185B ALA* 1.4 70.8 - - - +
187B VAL* 1.4 71.4 + - - +
188B THR 2.9 1.2 + - - -
189B SER* 3.1 8.8 + - - -
190B LEU* 3.2 14.3 + - - +
247B ILE* 4.3 25.2 - - + +
262B ALA* 4.7 2.7 - - + -
264B LEU* 4.0 33.2 - - + -
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Residues in contact with VAL 187 (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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47B PHE* 2.9 56.1 - - + +
49B LEU* 4.7 10.8 - - + -
183B ALA 3.5 13.2 + - - +
184B ARG 3.4 4.3 + - - +
186B LEU* 1.4 77.6 - - - +
188B THR* 1.3 61.5 + - - +
190B LEU* 3.3 3.5 + - - +
191B ARG* 2.6 37.0 + - + +
247B ILE* 6.1 1.3 - - - -
260B VAL* 3.6 33.0 - - + +
261B LEU 4.2 0.4 - - - +
262B ALA* 3.6 14.1 - - - +
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Residues in contact with THR 188 (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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47B PHE* 5.2 1.6 - - - -
155B ILE* 6.1 1.3 - - + +
156B GLY 5.6 6.7 - - - +
157B ASP* 5.9 3.8 - - + -
184B ARG* 3.2 24.7 + - - +
185B ALA* 3.6 8.7 - - - +
186B LEU 3.0 0.6 - - - -
187B VAL* 1.3 86.8 - - - +
189B SER* 1.4 64.1 - - - +
191B ARG* 3.6 8.9 + - - +
192B ALA* 3.4 22.7 + - + +
196B GLU* 4.4 1.9 - - - +
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Residues in contact with SER 189 (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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75B LEU* 3.4 26.7 - - - -
152B LEU* 5.4 1.6 - - - +
155B ILE* 4.4 13.2 - - - +
157B ASP* 2.8 36.4 + - - +
185B ALA 3.0 10.2 + - - -
186B LEU 3.1 2.0 + - - -
188B THR* 1.4 75.7 - - - +
190B LEU* 1.3 60.9 - - - +
192B ALA* 2.9 20.5 + - - +
193B PHE* 3.0 19.2 + - - -
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Residues in contact with LEU 190 (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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74B ALA* 4.0 19.1 - - + -
75B LEU* 3.5 11.6 - - + +
186B LEU 3.2 10.1 + - - +
187B VAL* 3.5 7.9 - - - +
189B SER* 1.3 71.7 - - - +
191B ARG* 1.3 70.5 + - - +
192B ALA 2.6 2.8 + - - -
193B PHE* 3.4 3.3 + - + +
194B ALA* 2.8 29.0 + - + +
207B LEU* 5.5 4.9 - - + -
211B MET* 3.9 29.8 - - + -
247B ILE* 3.8 15.3 - - + -
248B ALA 4.3 17.0 - - - +
249B ILE* 3.4 38.1 - - + -
260B VAL* 4.6 4.5 - - + -
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Residues in contact with ARG 191 (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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49B LEU* 3.2 34.3 - - - +
51B THR* 4.1 24.9 + - - +
54B ASN* 3.9 18.4 - - - +
187B VAL* 2.6 22.3 + - + +
188B THR* 3.8 7.6 - - - +
189B SER 3.5 0.2 - - - -
190B LEU* 1.3 74.6 - - - +
192B ALA* 1.3 58.0 + - - +
194B ALA* 3.7 0.4 - - - -
195B LEU* 3.0 34.8 + - + +
196B GLU* 2.8 55.8 + - + +
249B ILE* 5.7 0.2 - - - -
260B VAL* 4.4 15.3 - - + +
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Residues in contact with ALA 192 (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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155B ILE* 4.6 15.7 - - + +
188B THR* 3.4 12.1 - - + +
189B SER* 2.9 10.3 + - - +
190B LEU 2.6 6.3 + - - -
191B ARG* 1.3 74.3 - - - +
193B PHE* 1.4 65.9 + - - +
196B GLU* 3.2 49.3 + - + +
198B LYS* 3.6 20.8 - - + +
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Residues in contact with PHE 193 (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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74B ALA 5.8 0.4 - - - +
75B LEU* 4.3 24.2 - - + -
78B GLY* 3.5 25.4 - - - -
79B VAL* 3.9 22.0 - - + -
82B GLN* 4.5 8.5 - - - -
152B LEU* 4.4 10.8 - - + -
155B ILE* 3.8 32.5 - - + -
189B SER 3.0 21.9 + - - +
190B LEU* 4.2 4.5 - - + +
192B ALA* 1.4 79.8 - - - +
194B ALA* 1.3 63.0 + - - +
195B LEU 3.5 0.3 + - - -
196B GLU 4.4 1.4 - - - +
198B LYS* 4.2 15.0 - - + +
199B LEU* 3.1 31.9 - - + +
204B ARG* 3.8 14.7 - - - +
207B LEU* 4.0 18.0 - - + +
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Residues in contact with ALA 194 (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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190B LEU* 2.8 27.5 + - + +
193B PHE* 1.3 73.8 - - - +
195B LEU* 1.3 63.4 + - + +
204B ARG* 3.2 24.6 - - - +
207B LEU* 4.3 17.5 - - + -
208B ILE* 3.8 18.3 - - + +
211B MET* 6.2 1.1 - - - -
249B ILE* 4.0 24.9 - - + -
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Residues in contact with LEU 195 (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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51B THR* 4.9 5.2 - - + +
191B ARG* 3.0 26.2 - - + +
194B ALA* 1.3 85.9 - - + +
196B GLU* 1.3 71.0 + - + +
197B ASP* 5.1 0.9 - - - +
204B ARG* 4.3 6.8 + - - +
208B ILE* 4.4 11.9 - - + -
249B ILE* 3.8 32.5 - - + -
251B TRP* 4.9 5.2 - - + +
258B PRO* 4.3 15.7 - - + -
260B VAL* 4.2 19.1 - - + -
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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
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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