Contacts of the helix formed by residues 183 - 196 (chain C) in PDB entry 2D11
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 LEU 183 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181C GLY 3.6 7.4 + - - +
182C MET* 1.3 73.6 - - - +
184C ARG* 1.3 67.1 + - - +
185C GLU* 3.4 16.8 - - - +
186C ASP* 3.1 26.8 + - - +
187C SER* 2.9 23.6 + - - -
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Residues in contact with ARG 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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36B THR 4.5 14.0 + - - +
37B VAL 5.7 4.4 + - - -
96C GLU* 3.5 24.2 + - - -
100C ARG* 4.5 11.9 - - - +
131C GLN 5.2 1.1 + - - +
132C ALA* 3.1 39.9 - - - +
182C MET 3.9 0.4 + - - -
183C LEU* 1.3 72.2 - - - +
185C GLU* 1.3 80.5 + - - +
187C SER* 3.0 8.5 + - - -
188C MET* 2.9 47.6 + - - +
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Residues in contact with GLU 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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96C GLU* 3.8 27.4 - - + +
99C GLN* 4.3 12.5 + - - +
183C LEU* 3.8 24.1 - - - +
184C ARG* 1.3 99.0 + - - +
186C ASP* 1.3 64.4 + - - +
188C MET* 3.6 14.4 + - + +
189C MET* 3.1 29.1 + - - +
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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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181C GLY 5.4 0.3 - - - +
182C MET* 3.6 17.9 - - + +
183C LEU* 3.3 39.1 + - - +
185C GLU* 1.3 79.8 - - - +
187C SER* 1.3 55.7 + - - +
189C MET* 3.4 6.7 + - - +
190C GLU* 3.0 37.0 + - + +
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Residues in contact with SER 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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128C TYR* 3.7 31.3 - - - +
131C GLN* 3.1 26.3 - - - +
132C ALA* 4.1 8.7 + - - -
182C MET* 3.6 15.4 - - - +
183C LEU 2.9 12.9 + - - -
184C ARG 3.4 8.1 - - - -
186C ASP* 1.3 72.7 - - - +
188C MET* 1.3 61.2 - - - +
190C GLU* 3.4 4.6 + - - +
191C TYR* 3.0 27.4 + - - +
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Residues in contact with MET 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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96C GLU* 3.5 26.2 - - + +
99C GLN* 5.0 8.1 - - + +
100C ARG* 3.8 26.7 - - + +
103C PHE* 3.7 50.2 - - + -
132C ALA* 4.2 10.1 - - + -
184C ARG* 2.9 33.8 + - - +
185C GLU* 3.8 22.0 - - + +
187C SER* 1.3 77.2 - - - +
189C MET* 1.3 62.1 + - + +
191C TYR* 3.2 5.0 - - - +
192C LEU* 3.1 27.4 + - - +
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Residues in contact with MET 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 VAL* 3.6 37.2 - - + +
90C SER* 3.6 27.1 - - - +
93C LEU* 5.0 1.6 - - - +
99C GLN* 3.8 39.7 - - + +
185C GLU 3.1 21.0 + - - +
186C ASP* 3.7 6.5 - - - +
188C MET* 1.3 73.9 - - - +
190C GLU* 1.3 56.7 + - - +
192C LEU* 3.1 13.7 + - - +
193C LYS* 2.8 46.2 + - + +
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Residues in contact with GLU 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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128C TYR* 4.1 26.6 + - + +
182C MET* 4.2 22.9 - - + -
186C ASP* 3.0 23.7 + - + +
187C SER 3.7 4.7 - - - +
188C MET 3.4 0.2 - - - -
189C MET* 1.3 74.0 - - - +
191C TYR* 1.3 65.4 + - - +
193C LYS* 2.7 40.2 + - - +
194C ILE* 3.1 32.7 + - + +
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Residues in contact with TYR 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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103C PHE* 3.7 28.9 - + + -
106C VAL* 4.2 14.8 - - + -
107C LYS* 3.4 45.0 - - + +
110C ILE* 3.8 18.9 - - + +
111C LEU* 5.6 0.3 - - - +
125C LEU* 3.3 64.7 - - + +
126C ALA* 5.3 0.2 - - - -
128C TYR* 4.3 8.0 - - + -
129C ALA* 4.3 4.5 - - + -
187C SER 3.0 13.2 + - - +
188C MET 3.2 10.3 - - - +
190C GLU* 1.3 76.4 - - - +
192C LEU* 1.3 58.5 + - + +
194C ILE 3.1 2.8 + - - -
195C ALA* 2.7 39.4 + - + +
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Residues in contact with LEU 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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89C VAL* 4.0 19.1 - - + -
93C LEU* 4.0 25.1 - - + -
99C GLN* 3.9 11.0 - - - +
102C PHE* 4.0 4.9 - - + +
103C PHE* 3.9 34.3 - - + +
106C VAL* 4.0 31.6 - - + -
188C MET 3.1 15.2 + - - +
189C MET* 3.6 15.7 - - - +
191C TYR* 1.3 81.7 - - + +
193C LYS* 1.3 60.2 + - - +
195C ALA* 3.7 3.3 - - + +
196C GLN* 2.8 35.0 + - - +
201C TYR* 5.2 3.3 - - + +
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Residues in contact with LYS 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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89C VAL* 4.0 3.1 - - + +
90C SER* 3.4 26.4 + - - +
189C MET* 2.8 33.9 + - + +
190C GLU* 2.7 40.2 + - - +
192C LEU* 1.3 73.3 - - - +
194C ILE* 1.3 59.9 + - + +
196C GLN* 3.5 24.2 + - - +
197C ASP* 3.0 22.7 - - - +
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Residues in contact with ILE 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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121C THR* 3.7 28.9 - - + +
124C LEU* 3.7 22.9 - - + -
125C LEU* 3.8 13.9 - - + -
128C TYR* 3.6 31.4 - - + -
190C GLU* 3.1 17.2 + - + +
191C TYR 3.6 4.9 - - - +
193C LYS* 1.3 77.0 - - + +
195C ALA* 1.3 66.3 + - - +
197C ASP* 3.4 16.7 + - - +
198C LEU* 4.0 7.6 + - - +
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Residues in contact with ALA 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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106C VAL* 3.8 29.8 - - + -
110C ILE* 5.2 0.7 - - + -
125C LEU* 4.3 5.6 - - + +
191C TYR* 2.7 28.7 + - + +
192C LEU* 3.2 10.1 + - + +
194C ILE* 1.3 73.8 - - - +
196C GLN* 1.3 57.8 + - - +
197C ASP 3.0 6.2 + - - -
198C LEU* 3.1 34.6 + - + +
201C TYR* 3.4 12.2 - - + +
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Residues in contact with GLN 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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86C PRO 4.9 0.3 - - - +
87C GLU 3.6 17.3 + - - +
88C ASP* 3.6 20.0 + - - -
89C VAL* 3.1 42.4 + - + +
192C LEU 2.8 14.1 + - - +
193C LYS* 3.5 23.0 + - - +
195C ALA* 1.3 75.6 - - - +
197C ASP* 1.3 67.5 + - - +
198C LEU 3.4 2.7 - - - +
201C TYR* 3.5 41.3 + - + +
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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