Contacts of the helix formed by residues 184 - 196 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C TYR* 3.6 27.7 - - - +
67C VAL 2.8 27.5 + - - -
68C ASN* 3.3 16.5 - - - +
69C PRO* 3.4 4.0 - - - +
182C GLY 2.6 11.8 + - - +
183C MET* 1.3 80.7 - - - +
185C PRO* 1.3 70.5 - - - +
186C ALA* 2.9 22.6 + - - +
187C ARG* 2.9 27.2 + - + +
188C SER* 3.0 15.2 + - - -
204C TYR 4.4 1.1 - - - -
208C PRO* 4.0 2.0 - - - +
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Residues in contact with PRO 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ASN* 3.4 16.2 - - - +
69C PRO* 4.1 5.4 - - + -
70C ALA* 3.7 24.7 - - + +
184C ASN* 1.3 82.9 - - - +
186C ALA* 1.3 52.6 + - - +
188C SER* 3.0 4.2 + - - -
189C PHE* 2.6 39.0 + - - +
204C TYR 3.5 20.8 - - - +
205C TRP* 3.6 51.1 + - + +
208C PRO* 4.1 5.4 - - + -
209C VAL* 4.6 2.5 - - + -
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Residues in contact with ALA 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C SER* 5.8 1.3 - - - -
24C VAL* 5.7 0.4 - - + -
67C VAL 5.1 1.6 - - - +
69C PRO* 3.4 21.6 - - + +
93C GLN* 3.8 24.5 - - + +
94C LEU* 3.9 17.0 - - + +
97C ALA* 3.3 15.5 - - + +
184C ASN* 2.9 11.8 + - - +
185C PRO* 1.3 78.9 - - - +
187C ARG* 1.3 61.2 + - - +
189C PHE* 3.7 0.6 - - - +
190C ALA 3.1 19.9 + - - -
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Residues in contact with ARG 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C TYR* 3.9 15.7 - - + +
24C VAL* 4.2 12.5 - - + +
28C LEU* 3.5 18.3 - - + +
31C SER* 5.0 1.2 + - - -
48C PHE* 3.8 38.2 - - + -
117C ALA* 2.8 34.3 + - - +
119C ASN* 3.1 38.3 + - - +
172C HIS* 5.3 0.6 + - - -
180C GLY 4.7 5.1 + - - -
181C ALA 4.0 5.5 + - - -
182C GLY 3.9 13.5 - - - -
184C ASN* 2.9 25.7 + - + +
186C ALA* 1.3 76.0 - - - +
188C SER* 1.3 57.1 + - - +
190C ALA* 4.3 0.6 - - - +
191C PRO* 2.8 31.2 - - - +
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Residues in contact with SER 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LEU* 4.4 2.9 - - - +
119C ASN* 2.5 32.3 + - - +
182C GLY* 3.8 3.8 - - - -
184C ASN 3.0 9.6 + - - -
185C PRO* 3.0 8.0 + - - -
187C ARG* 1.3 76.0 - - - +
189C PHE* 1.3 68.2 + - - +
191C PRO* 3.0 13.0 - - - +
192C ALA* 3.3 12.6 + - - +
201C HIS* 3.4 10.4 + - - -
204C TYR* 3.2 33.8 + - - +
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Residues in contact with PHE 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C LEU* 3.8 30.5 - - + -
98C VAL* 3.9 24.9 - - + -
185C PRO 2.6 21.5 + - - +
186C ALA* 3.7 8.1 - - - +
188C SER* 1.3 73.6 - - - +
190C ALA* 1.3 57.3 + - - +
192C ALA* 2.7 22.3 + - - +
193C ILE* 2.8 42.3 + - + +
198C PHE* 4.1 17.7 - + - -
201C HIS* 3.4 25.7 + + + -
205C TRP* 4.3 10.5 - + + -
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Residues in contact with ALA 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C VAL* 4.0 6.5 - - + -
97C ALA* 3.6 33.9 - - + +
98C VAL* 3.7 13.5 - - - +
101C ALA* 3.8 12.3 - - + -
186C ALA 3.1 12.9 + - - +
187C ARG 4.3 0.2 - - - +
189C PHE* 1.3 80.0 - - - +
191C PRO* 1.3 68.2 - - + +
193C ILE* 3.7 1.3 - - - +
194C LEU* 3.4 28.9 + - - +
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Residues in contact with PRO 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C LEU* 3.8 11.9 - - + -
101C ALA* 4.7 0.4 - - + -
115C ASN 4.3 1.1 - - - +
116C LEU* 3.5 32.5 - - + +
118C LEU* 3.6 22.2 - - + -
187C ARG* 2.8 45.1 - - - +
188C SER 3.0 13.9 - - - +
190C ALA* 1.3 83.5 - - + +
192C ALA* 1.3 52.8 + - - +
194C LEU* 4.0 1.5 - - + -
195C THR* 2.7 38.8 + - - +
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Residues in contact with ALA 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LEU* 3.4 11.8 - - + +
188C SER 3.3 11.5 + - - +
189C PHE 2.7 9.7 + - - +
191C PRO* 1.3 80.5 - - - +
193C ILE* 1.3 58.7 + - - +
195C THR 3.3 1.0 + - - -
196C ARG* 3.0 24.6 + - - -
197C ASN 3.1 21.4 + - - +
198C PHE* 3.7 18.0 - - + -
201C HIS* 3.7 21.1 - - + +
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Residues in contact with ILE 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C VAL* 4.1 24.5 - - + -
189C PHE* 2.8 43.5 + - + +
190C ALA 3.7 10.3 - - - +
192C ALA* 1.3 73.3 - - - +
194C LEU* 1.3 73.2 + - + +
196C ARG* 3.9 32.5 + - - +
198C PHE* 3.5 20.1 - - + -
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Residues in contact with LEU 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C VAL* 3.8 17.5 - - + +
101C ALA* 3.5 33.7 - - + +
102C ALA* 3.6 22.2 - - + +
105C TYR* 5.5 5.9 - - + -
116C LEU* 4.4 15.9 - - + +
190C ALA 3.4 12.6 + - - +
191C PRO 4.3 2.2 - - - +
192C ALA 3.2 0.8 - - - -
193C ILE* 1.3 90.5 - - + +
195C THR* 1.3 62.0 + - - +
196C ARG* 3.4 3.5 - - - +
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Residues in contact with THR 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C GLY 5.5 0.4 - - - +
115C ASN* 3.6 35.9 - - - +
116C LEU* 4.4 12.8 - - + -
118C LEU* 4.0 5.6 - - - +
191C PRO 2.7 23.7 + - - +
192C ALA* 3.4 5.4 + - - -
194C LEU* 1.3 81.6 - - - +
196C ARG* 1.3 70.7 + - - +
197C ASN* 3.2 18.5 + - - +
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Residues in contact with ARG 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C ALA 3.0 6.8 + - - -
193C ILE* 3.9 28.8 + - - +
194C LEU 3.4 3.7 - - - +
195C THR* 1.3 82.3 - - - +
197C ASN* 1.3 58.5 + - - +
198C 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