Contacts of the helix formed by residues 185 - 199 (chain C) in PDB entry 4JDL
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 VAL 185 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148C TYR* 3.8 23.1 - - + +
168C TYR* 3.5 41.9 - - + +
170C VAL* 5.4 4.9 - - + -
181C THR* 2.4 37.4 + - + +
182C LEU* 4.2 0.9 - - - -
184C PHE* 1.3 87.5 - - + +
186C ASP* 1.3 59.3 + - - +
188C ILE* 4.3 11.9 - - + +
189C VAL* 4.0 17.7 + - - +
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Residues in contact with ASP 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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94B ARG* 5.6 10.3 - - - +
60C SER* 4.2 19.1 + - - -
61C SER 4.5 6.9 - - - +
168C TYR* 5.0 4.5 + - - -
182C LEU 2.7 27.0 + - - +
183C SER* 3.6 8.7 - - - -
184C PHE 3.4 0.2 - - - -
185C VAL* 1.3 76.6 - - - +
187C THR* 1.3 66.9 + - - +
188C ILE 3.1 1.8 - - - -
189C VAL* 2.8 30.5 + - - +
190C ARG* 3.1 29.3 + - - +
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Residues in contact with THR 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LYS* 5.7 2.6 + - - -
88A ASN* 3.7 29.2 - - + +
89A PHE* 3.6 37.1 + - + +
183C SER* 3.6 18.6 + - - -
184C PHE 4.4 1.2 - - - -
186C ASP* 1.3 82.3 + - - +
188C ILE* 1.3 50.6 + - - +
190C ARG* 2.9 24.0 - - + +
191C CYS* 2.4 28.4 - - - -
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Residues in contact with ILE 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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89A PHE* 3.6 18.6 - - + -
184C PHE* 3.1 37.2 - - + +
185C VAL* 4.3 12.1 - - + +
186C ASP 3.1 0.6 - - - -
187C THR* 1.3 76.4 - - - +
189C VAL* 1.3 57.3 + - + +
191C CYS* 2.7 30.4 + - + -
192C ASN* 2.9 35.3 - - - +
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Residues in contact with VAL 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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61C SER 5.5 2.2 - - - +
62C VAL* 5.1 11.4 - - + -
148C TYR* 4.4 15.3 - - - +
166C GLU* 4.4 28.0 - - + +
168C TYR* 5.3 10.3 - - + -
185C VAL 4.0 12.7 + - - +
186C ASP* 2.8 30.9 + - - +
188C ILE* 1.3 75.0 - - + +
190C ARG* 1.3 65.2 + - - +
192C ASN* 2.7 13.6 + - + +
193C LEU* 2.7 37.5 + - + +
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Residues in contact with ARG 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASN* 5.0 3.1 - - - +
198A ARG* 4.9 15.1 - - - +
95B ILE* 5.5 8.3 - - - +
61C SER 5.1 5.3 + - - -
62C VAL* 4.7 8.0 - - - +
63C VAL* 4.3 24.5 + - - +
64C GLN* 6.3 1.1 - - - -
186C ASP* 3.1 32.8 + - - -
187C THR* 2.9 37.5 - - + +
189C VAL* 1.3 86.6 - - - +
191C CYS* 1.3 56.6 + - - +
193C LEU* 5.1 3.6 - - - -
194C GLN* 2.8 58.0 + - - +
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Residues in contact with CYS 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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88A ASN* 4.7 4.0 - - - -
89A PHE* 3.3 31.6 - - - -
191A CYS* 3.3 32.5 - - + -
194A GLN* 4.5 3.9 + - - +
85C VAL* 4.5 1.7 - - - +
187C THR* 2.4 34.8 - - - -
188C ILE* 2.7 15.3 + - + +
190C ARG* 1.3 71.8 - - - +
192C ASN* 1.3 61.7 + - - +
194C GLN* 3.9 12.1 + - - +
195C SER* 2.7 22.4 + - - -
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Residues in contact with ASN 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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85C VAL* 3.3 29.6 - - + +
188C ILE* 2.9 35.9 - - - +
189C VAL* 2.7 21.7 + - + +
191C CYS* 1.3 80.0 - - - +
193C LEU* 1.3 64.7 + - + +
194C GLN 3.2 4.0 - - - -
195C SER* 3.4 18.4 - - - -
196C LEU* 3.6 16.3 - - - +
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Residues in contact with LEU 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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62C VAL* 5.1 5.2 - - + -
64C GLN* 3.0 35.1 - - + +
66C ILE* 4.7 1.1 - - + +
77C VAL* 5.9 0.9 - - + -
152C THR* 5.0 6.5 - - + -
164C VAL* 3.5 36.8 - - + +
165C VAL 3.8 0.2 - - - +
166C GLU* 3.4 39.3 - - + +
189C VAL* 2.7 22.3 + - + +
190C ARG* 3.7 3.1 - - - +
192C ASN* 1.3 78.8 - - + +
194C GLN* 1.3 59.4 + - - +
196C LEU* 3.9 27.1 + - + +
197C ALA 3.8 9.2 + - - -
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Residues in contact with GLN 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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88A ASN* 5.3 0.2 - - - +
191A CYS 4.7 0.9 - - - +
194A GLN* 3.1 40.4 + - + +
195A SER* 3.9 14.4 + - - -
198A ARG* 3.2 38.6 - - + +
64C GLN* 4.1 20.2 + - + +
190C ARG* 2.8 45.6 + - - +
191C CYS* 3.9 5.9 + - - +
193C LEU* 1.3 77.3 - - - +
195C SER* 1.3 63.2 + - - +
196C LEU 3.1 2.7 + - - -
197C ALA* 3.3 13.5 + - - +
198C ARG 3.5 7.3 + - - -
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Residues in contact with SER 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ARG* 5.7 1.2 + - - -
194A GLN* 3.5 6.0 + - - +
85C VAL* 3.9 20.0 - - - +
191C CYS 2.7 28.9 + - - -
192C ASN* 3.4 10.5 + - - -
194C GLN* 1.3 75.4 - - - +
196C LEU* 1.3 56.1 + - - -
198C ARG* 2.8 58.4 + - - +
199C SER* 3.4 6.8 + - - -
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Residues in contact with LEU 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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66C ILE* 4.4 8.5 - - + +
73C VAL* 4.6 9.3 - - + +
76C LEU* 4.8 21.9 - - + +
77C VAL* 3.7 37.5 - - + -
85C VAL 4.3 16.8 - - - +
164C VAL* 5.2 6.5 - - + -
192C ASN 3.6 14.5 + - - +
193C LEU* 3.9 30.5 - - + +
194C GLN 3.1 0.8 - - - -
195C SER* 1.3 79.2 - - - +
197C ALA* 1.3 58.8 + - - +
199C SER* 3.4 10.7 + - - -
200C THR* 2.7 27.3 + - - -
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Residues in contact with ALA 197 (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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64C GLN* 3.4 29.4 - - - +
65C MET 4.9 0.4 - - - +
66C ILE* 3.5 20.3 - - + +
193C LEU 3.8 3.2 + - - +
194C GLN* 3.3 9.0 + - - +
196C LEU* 1.3 76.8 - - - +
198C ARG* 1.3 66.7 + - - +
200C THR 2.9 24.5 + - - +
201C ASN* 3.4 3.8 + - - -
202C ARG 5.0 2.4 + - - -
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Residues in contact with ARG 198 (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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190A ARG* 3.5 48.9 - - - +
194A GLN* 3.6 19.7 + - - +
85C VAL* 5.3 1.8 + - - +
194C GLN 3.5 6.2 + - - +
195C SER* 2.8 53.8 + - - +
197C ALA* 1.3 77.7 - - - +
199C SER* 1.3 69.5 + - - +
200C THR 3.2 2.4 + - - -
201C ASN* 2.7 28.5 + - - +
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Residues in contact with SER 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C LEU* 3.9 27.8 - - - +
195C SER 3.4 13.2 + - - -
196C LEU* 3.4 10.7 + - - -
197C ALA 3.1 1.0 - - - -
198C ARG* 1.3 86.3 + - - +
200C THR* 1.3 65.3 + - - +
201C ASN 4.0 0.4 - - - -
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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