Contacts of the helix formed by residues 181 - 193 (chain C) in PDB entry 3DC5
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 181 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C PRO* 6.2 1.2 - - - +
79C THR* 3.0 17.0 + - - +
80C ASN 2.7 28.7 + - - +
81C LEU 3.7 7.0 + - - -
82C ALA* 3.6 19.0 - - + +
84C ASP 4.9 0.5 - - - +
85C GLY* 3.6 12.9 - - - +
179C ILE 3.2 1.2 + - - -
180C ALA* 1.3 67.8 - - - +
182C TRP* 1.3 57.0 + - - +
183C LYS* 3.4 21.1 + - - +
184C ASN* 3.0 13.4 + - - +
185C ILE* 2.9 30.8 + - - +
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Residues in contact with TRP 182 (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 GLY 3.4 6.1 + - - +
86C GLY 3.6 15.9 - - - -
87C GLU* 3.4 24.2 - - - +
88C PRO* 3.6 28.1 - - + +
92C LEU* 4.0 15.0 - - + -
96C ILE* 4.0 10.5 - - + -
103C LEU* 3.8 35.9 - - + +
106C LEU* 4.9 4.5 - - + -
107C GLN* 4.6 2.7 - - - +
125C LEU* 4.9 5.4 - - + -
152C PHE* 5.8 0.2 - + - -
177C TRP* 3.9 33.1 + + - -
180C ALA* 3.1 25.7 + - + +
181C ASN* 1.3 68.4 - - - +
183C LYS* 1.3 57.8 + - - +
185C ILE* 3.8 33.7 - - + -
186C SER* 2.7 37.3 + - - -
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Residues in contact with LYS 183 (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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84C ASP 5.9 0.4 - - - +
85C GLY 3.0 14.4 + - - +
87C GLU 4.9 1.8 + - - -
181C ASN* 3.2 12.3 - - - +
182C TRP* 1.3 77.2 - - - +
184C ASN* 1.3 57.7 + - - +
186C SER* 3.8 4.3 - - - -
187C GLU* 2.8 61.9 + - + +
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Residues in contact with ASN 184 (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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79C THR* 3.1 39.3 + - - +
80C ASN* 2.9 28.8 + - - -
181C ASN* 3.0 16.8 + - - +
183C LYS* 1.3 77.0 - - - +
185C ILE* 1.3 59.3 + - - +
187C GLU* 3.1 17.8 + - - +
188C ARG* 2.9 49.2 + - - +
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Residues in contact with ILE 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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80C ASN* 4.2 6.3 - - - +
92C LEU* 3.8 17.3 - - + -
125C LEU* 4.5 4.3 - - + -
151C LEU* 3.6 40.2 - - + +
152C PHE* 3.5 35.7 - - + -
180C ALA* 4.1 4.3 - - + -
181C ASN 2.9 32.7 + - - +
182C TRP* 3.8 29.8 - - + +
184C ASN* 1.3 73.7 - - - +
186C SER* 1.3 56.9 + - - +
188C ARG* 3.4 4.1 + - - +
189C PHE* 2.9 27.4 + - - +
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Residues in contact with SER 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C GLU 4.2 1.0 + - - -
88C PRO* 3.6 2.4 - - - +
89C SER* 3.0 45.1 + - - -
91C GLU* 4.8 0.5 - - - +
92C LEU* 3.5 15.7 - - - +
182C TRP 2.7 22.9 + - - -
183C LYS* 3.8 4.9 - - - -
185C ILE* 1.3 74.5 - - - +
187C GLU* 1.3 60.9 + - - +
189C PHE* 3.3 5.0 + - - +
190C ALA* 2.9 28.8 + - - +
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Residues in contact with GLU 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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183C LYS* 2.8 54.0 + - + +
184C ASN* 3.1 21.3 + - - +
186C SER* 1.3 77.4 - - - +
188C ARG* 1.3 58.2 + - + +
190C ALA* 3.3 6.7 + - - +
191C ASN* 2.9 40.8 + - - +
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Residues in contact with ARG 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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75C SER 5.1 0.2 - - - -
76C ILE* 3.8 34.2 - - - +
79C THR* 2.9 29.3 + - - +
80C ASN* 3.8 3.2 - - - +
149C VAL* 4.7 3.8 - - + +
150C PRO* 3.7 15.9 + - - +
151C LEU* 3.5 32.5 - - + +
184C ASN* 2.9 39.1 + - - +
185C ILE 3.5 9.0 - - - +
187C GLU* 1.3 75.3 - - + +
189C PHE* 1.3 57.5 + - - +
191C ASN* 3.3 11.2 + - - +
192C ALA* 2.9 30.5 + - - +
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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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89C SER* 4.7 0.2 - - - -
91C GLU* 3.6 15.5 - - + -
92C LEU* 3.6 45.5 - - + -
95C THR* 3.2 29.2 - - + -
127C TYR* 3.9 13.5 - + - -
134C LEU* 3.8 26.0 - - + -
151C LEU* 3.6 13.8 - - + +
185C ILE 2.9 14.7 + - - +
186C SER* 3.4 9.2 - - - +
188C ARG* 1.3 73.4 - - - +
190C ALA* 1.3 67.0 + - - +
192C ALA* 3.1 13.0 + - - +
193C ARG* 3.1 58.0 + - - +
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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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91C GLU* 3.6 22.9 - - - +
186C SER 2.9 13.7 + - - +
187C GLU* 3.6 10.3 - - - +
189C PHE* 1.3 76.7 - - - +
191C ASN* 1.3 63.0 - - - +
193C ARG* 3.3 11.7 + - - +
194C GLN* 3.2 21.5 + - - +
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Residues in contact with ASN 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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129C LYS* 5.4 2.8 + - - -
187C GLU* 2.9 29.2 + - - +
188C ARG* 3.5 11.6 - - - +
190C ALA* 1.3 78.8 - - - +
192C ALA* 1.3 60.7 + - - +
194C GLN* 3.2 44.3 + - - +
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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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127C TYR* 3.6 26.1 - - + -
129C LYS* 3.4 32.2 - - - +
149C VAL* 3.7 33.6 - - + +
151C LEU* 4.5 0.7 - - + -
188C ARG 2.9 17.1 + - - +
189C PHE* 3.1 7.1 + - - +
191C ASN* 1.3 76.3 - - - +
193C ARG* 1.3 59.0 + - - +
194C GLN 3.3 1.3 - - - -
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Residues in contact with ARG 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C GLU* 3.3 29.8 + - - +
95C THR* 3.9 8.9 + - - -
98C ARG* 4.4 17.7 - - - +
127C TYR* 3.6 35.5 + - + +
132C LYS* 6.3 0.4 - - - +
189C PHE* 3.1 54.8 + - + +
190C ALA* 3.3 6.9 + - - +
191C ASN 3.2 0.8 - - - -
192C ALA* 1.3 76.0 - - - +
194C GLN* 1.3 61.2 + - - +
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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