Contacts of the helix formed by residues 184 - 196 (chain B) in PDB entry 3J41
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 ASN 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B TYR* 3.6 27.7 - - - +
67B VAL 2.8 27.5 + - - -
68B ASN* 3.3 16.6 - - - +
69B PRO* 3.4 4.0 - - - +
182B GLY 2.6 11.6 + - - +
183B MET* 1.3 78.7 - - - +
185B PRO* 1.3 71.2 - - - +
186B ALA* 2.9 22.8 + - - +
187B ARG* 2.9 26.8 + - + +
188B SER* 3.0 14.8 + - - -
204B TYR 4.4 1.1 + - - -
208B PRO* 4.0 2.0 - - - +
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Residues in contact with PRO 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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68B ASN* 3.4 15.7 - - - +
69B PRO* 4.1 5.2 - - + -
70B ALA* 3.7 24.7 - - + +
184B ASN* 1.3 82.2 - - - +
186B ALA* 1.3 53.2 + - - +
188B SER* 3.0 3.8 + - - -
189B PHE* 2.6 39.4 + - - +
204B TYR 3.5 19.5 - - - +
205B TRP* 3.6 50.2 + - + +
208B PRO* 4.1 5.2 - - + -
209B VAL* 4.6 2.5 - - + -
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Residues in contact with ALA 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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20B SER* 5.8 1.3 - - - -
24B VAL* 5.7 0.7 - - + -
67B VAL 5.1 2.2 - - - +
69B PRO* 3.4 21.7 - - + +
93B GLN* 3.8 24.9 - - + +
94B LEU* 3.9 16.4 - - + -
97B ALA* 3.3 15.5 - - + +
184B ASN* 2.9 12.6 + - - +
185B PRO* 1.3 78.5 - - - +
187B ARG* 1.3 62.3 + - - +
189B PHE* 3.7 0.5 - - - +
190B ALA 3.1 20.4 + - - -
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Residues in contact with ARG 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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23B TYR* 3.9 14.6 - - + -
24B VAL* 4.2 11.9 - - + +
28B LEU* 3.5 17.8 - - + +
31B SER* 5.0 1.4 + - - -
48B PHE* 3.8 36.9 - - + -
117B ALA* 2.8 34.4 + - - +
119B ASN* 3.1 37.8 + - - +
172B HIS* 5.3 0.6 + - - -
180B GLY 4.7 5.7 + - - -
181B ALA 4.0 5.3 + - - -
182B GLY 3.9 13.7 - - - -
184B ASN* 2.9 25.5 + - + +
186B ALA* 1.3 77.3 - - - +
188B SER* 1.3 58.1 + - - +
190B ALA* 4.3 0.2 - - - +
191B PRO* 2.8 32.0 - - - +
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Residues in contact with SER 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 4.4 2.9 - - - +
119B ASN* 2.5 31.6 + - - +
182B GLY* 3.8 4.5 - - - -
184B ASN 3.0 9.9 + - - -
185B PRO* 3.0 7.7 + - - -
187B ARG* 1.3 75.3 - - - +
189B PHE* 1.3 67.8 + - - +
191B PRO* 3.0 12.5 - - - +
192B ALA* 3.3 13.2 + - - +
201B HIS* 3.4 9.5 + - - -
204B TYR* 3.2 34.6 + - - +
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Residues in contact with PHE 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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94B LEU* 3.8 31.4 - - + -
98B VAL* 3.9 26.0 - - + -
185B PRO 2.6 21.5 + - - +
186B ALA* 3.7 8.3 - - - +
188B SER* 1.3 72.7 - - - +
190B ALA* 1.3 56.7 + - - +
192B ALA* 2.7 22.5 + - - +
193B ILE* 2.8 43.2 + - + +
198B PHE* 4.1 17.3 - + - -
201B HIS* 3.4 24.7 + + + -
205B TRP* 4.3 10.5 - + + -
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Residues in contact with ALA 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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24B VAL* 4.0 6.7 - - + -
97B ALA* 3.6 34.1 - - + +
98B VAL* 3.7 13.2 - - - +
101B ALA* 3.8 12.3 - - + -
186B ALA 3.1 13.5 + - - +
189B PHE* 1.3 78.8 - - - +
191B PRO* 1.3 69.2 - - + +
193B ILE* 3.7 1.1 - - - +
194B LEU* 3.4 28.1 + - - +
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Residues in contact with PRO 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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28B LEU* 3.8 12.1 - - + -
115B ASN 4.3 0.9 - - - +
116B LEU* 3.5 32.5 - - + +
118B LEU* 3.6 22.7 - - + -
187B ARG* 2.8 44.0 - - - +
188B SER 3.0 14.4 - - - +
190B ALA* 1.3 84.4 - - + +
192B ALA* 1.3 52.7 + - - +
194B LEU* 3.6 2.4 + - + -
195B THR* 2.7 39.0 + - - +
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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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118B LEU* 3.4 11.6 - - + +
188B SER 3.3 12.0 + - - +
189B PHE 2.7 10.6 + - - +
191B PRO* 1.3 80.5 - - - +
193B ILE* 1.3 58.0 + - - +
195B THR 3.3 0.5 + - - -
196B ARG* 3.0 24.9 + - - -
197B ASN 3.1 21.3 + - - +
198B PHE* 3.7 17.2 - - + -
201B HIS* 3.7 21.1 - - + +
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Residues in contact with ILE 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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98B VAL* 4.1 24.7 - - + -
189B PHE* 2.8 41.7 + - + +
190B ALA 3.7 9.9 - - - +
192B ALA* 1.3 72.6 - - - +
194B LEU* 1.3 74.2 + - + +
196B ARG* 3.9 32.3 + - - +
198B PHE* 3.5 20.4 - - + -
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Residues in contact with LEU 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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98B VAL* 3.8 17.0 - - + +
101B ALA* 3.5 34.5 - - + +
102B ALA* 3.6 22.0 - - + +
105B TYR* 5.5 5.0 - - + -
116B LEU* 4.4 14.9 - - + +
190B ALA 3.4 13.1 + - - +
191B PRO 4.3 2.2 - - - +
192B ALA 3.2 1.0 - - - -
193B ILE* 1.3 90.5 - - + +
195B THR* 1.3 61.6 + - - +
196B ARG* 3.4 4.6 - - - +
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Residues in contact with THR 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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114B GLY 5.5 0.9 - - - +
115B ASN* 3.6 35.9 - - - +
116B LEU* 4.4 13.0 - - + -
118B LEU* 4.0 5.4 - - - +
191B PRO 2.7 23.6 + - - +
192B ALA* 3.4 5.7 + - - -
194B LEU* 1.3 79.5 - - - +
196B ARG* 1.3 71.2 + - - +
197B ASN* 3.2 18.2 + - - +
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Residues in contact with ARG 196 (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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192B ALA 3.0 7.0 + - - -
193B ILE* 3.9 29.3 + - - +
194B LEU 3.4 4.0 - - - +
195B THR* 1.3 81.2 - - - +
197B ASN* 1.3 57.5 + - - +
198B PHE* 4.2 15.5 - - - -
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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