Contacts of the helix formed by residues 201 - 212 (chain C) in PDB entry 3U8Z
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 ASP 201 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A ARG* 3.3 15.9 - - - -
112C GLU* 2.8 19.9 + - - +
115C GLN* 2.9 20.3 - - - +
147C GLN 4.0 4.7 - - - +
148C ALA* 2.6 42.5 - - - +
152C ASP* 3.4 25.1 + - - +
198C ARG* 4.2 1.3 - - - +
199C ALA 3.3 1.0 + - - -
200C ARG* 1.3 69.0 - - - +
202C GLU* 1.3 60.3 + - - +
203C ALA* 3.3 7.2 + - - +
204C GLU* 3.2 29.5 + - - +
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Residues in contact with GLU 202 (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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115C GLN* 4.8 1.8 - - - +
200C ARG* 2.8 19.6 + - + +
201C ASP* 1.3 71.8 + - - +
203C ALA* 1.4 56.4 + - - +
205C MET* 2.9 28.6 + - + +
206C GLU* 3.1 28.1 + - + +
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Residues in contact with ALA 203 (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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144C TYR* 3.6 37.6 - - + +
147C GLN* 3.9 14.4 - - + +
148C ALA* 3.6 20.9 - - - +
201C ASP* 3.3 3.3 + - - +
202C GLU* 1.4 77.4 - - - +
204C GLU* 1.4 55.1 + - - +
206C GLU* 3.5 6.3 + - - +
207C TYR* 3.0 27.0 + - - +
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Residues in contact with GLU 204 (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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52A ARG* 4.3 2.5 + - - +
112C GLU* 4.6 2.4 - - - +
115C GLN* 3.0 19.7 - - + +
116C HIS* 2.8 46.4 + - - +
119C PHE* 3.5 41.5 - - + -
148C ALA* 3.7 7.3 - - + +
201C ASP* 3.3 36.8 - - - +
202C GLU 3.1 0.6 + - - -
203C ALA* 1.4 73.3 - - - +
205C MET* 1.4 59.3 + - - +
207C TYR* 3.3 3.6 - - - +
208C LEU* 3.0 33.6 + - - +
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Residues in contact with MET 205 (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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105C ALA* 3.7 28.3 - - - +
106C GLU* 3.7 39.7 - - + +
109C LEU* 3.8 21.3 - - + +
115C GLN* 3.4 41.0 - - + +
200C ARG* 4.9 0.7 - - - +
202C GLU* 2.9 15.2 + - + +
204C GLU* 1.4 75.7 - - - +
206C GLU* 1.3 60.2 + - - +
208C LEU* 3.2 4.2 + - + -
209C LYS* 2.9 46.4 + - + +
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Residues in contact with GLU 206 (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 GLU* 4.8 0.9 - - - +
144C TYR* 3.6 39.7 + - + +
202C GLU* 3.1 33.7 + - + +
203C ALA* 3.6 9.4 - - - +
205C MET* 1.3 76.4 - - - +
207C TYR* 1.4 60.2 + - - +
209C LYS* 2.9 36.6 + - - +
210C ILE* 3.4 27.4 + - - +
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Residues in contact with TYR 207 (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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119C PHE* 3.5 28.3 - + + -
122C VAL* 4.4 11.7 - - + -
123C LYS* 3.3 45.8 - - + +
126C ILE* 3.5 23.7 - - + +
127C LEU* 5.2 1.9 - - - +
141C LEU* 3.2 64.3 - - + +
144C TYR* 4.2 6.7 - - + +
145C ALA* 4.1 15.5 - - + -
203C ALA 3.0 14.9 + - - +
204C GLU 3.3 10.5 - - - +
206C GLU* 1.4 73.6 - - - +
208C LEU* 1.3 61.3 + - + +
210C ILE 3.3 3.1 + - - -
211C ALA* 3.0 24.7 + - + +
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Residues in contact with LEU 208 (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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105C ALA* 4.1 12.8 - - + -
109C LEU* 3.9 24.2 - - + -
115C GLN* 3.7 31.6 - - + +
118C PHE* 3.9 4.7 - - + -
119C PHE* 3.9 22.9 - - - +
122C VAL* 3.9 29.6 - - + -
204C GLU 3.0 20.9 + - - +
205C MET* 3.2 8.9 + - - +
207C TYR* 1.3 77.9 - - + +
209C LYS* 1.3 53.0 + - - +
211C ALA* 3.7 3.6 - - - +
212C GLN* 2.8 38.5 + - - +
217C TYR* 4.6 9.4 - - + +
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Residues in contact with LYS 209 (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 GLU* 3.2 37.2 + - + +
205C MET* 2.9 40.8 + - + +
206C GLU* 2.9 34.9 + - - +
207C TYR 3.3 0.2 - - - -
208C LEU* 1.3 72.8 - - - +
210C ILE* 1.4 66.4 + - + +
212C GLN* 3.5 33.6 + - - +
213C ASP* 3.7 13.9 - - - +
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Residues in contact with ILE 210 (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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137C ALA* 4.2 23.1 - - + +
140C LEU* 4.0 24.7 - - + -
141C LEU* 3.8 24.7 - - + -
144C TYR* 3.6 35.9 - - + -
206C GLU 3.4 10.9 + - - +
207C TYR 3.3 7.2 + - - +
209C LYS* 1.4 75.4 - - + +
211C ALA* 1.4 65.7 + - - +
213C ASP* 3.2 21.5 + - - +
214C LEU* 4.0 8.2 + - + +
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Residues in contact with ALA 211 (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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122C VAL* 3.6 31.6 - - + -
126C ILE* 4.7 2.9 - - + -
141C LEU* 4.6 7.4 - - + -
207C TYR* 3.0 19.7 + - + +
208C LEU* 3.3 6.5 + - - +
210C ILE* 1.4 77.0 - - - +
212C GLN* 1.4 55.7 + - - +
214C LEU* 3.0 42.1 + - + +
217C TYR* 3.4 12.5 - - + +
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Residues in contact with GLN 212 (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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102C PRO 5.0 1.0 - - - +
103C GLU 3.8 11.3 - - - +
104C ASN* 3.8 12.6 + - - +
105C ALA* 3.0 34.1 + - - +
106C GLU* 5.2 0.6 - - - +
208C LEU 2.8 22.9 + - - +
209C LYS* 3.5 30.2 + - - +
211C ALA* 1.4 71.2 - - - +
213C ASP* 1.3 66.9 + - - +
214C LEU 3.3 6.9 + - - +
217C TYR* 3.5 35.5 + - + +
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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