Contacts of the helix formed by residues 190 - 196 (chain C) in PDB entry 4U7D
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 THR 190 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137C ILE* 4.7 0.9 - - - -
138C CYS 3.6 9.2 - - - +
139C PRO 4.8 8.3 - - - +
141C ILE* 4.8 7.0 - - + -
144C MET* 4.4 16.6 - - + -
161C LEU 4.3 7.9 + - - +
162C ASN* 4.7 12.0 - - - +
163C ALA 5.7 1.3 - - - +
189C VAL* 1.3 82.9 - - - +
191C PRO* 1.3 74.6 - - - +
192C GLU* 3.4 22.5 + - - +
193C LYS* 3.1 24.6 + - - +
194C ILE* 4.0 1.9 + - - +
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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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137C ILE* 4.1 15.0 - - + -
138C CYS 3.9 11.0 - - - +
139C PRO* 4.2 7.6 - - + +
190C THR* 1.3 85.6 - - - +
192C GLU* 1.3 64.3 + - + +
193C LYS 3.2 0.2 - - - -
194C ILE* 3.4 13.9 + - + +
195C ALA* 3.5 13.3 + - - +
232C ARG* 5.6 1.3 - - + -
234C ASP* 3.6 35.2 - - + +
235C TYR* 3.9 29.8 - - + +
238C LEU* 4.4 12.5 - - + +
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Residues in contact with GLU 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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190C THR* 3.1 14.1 - - - +
191C PRO* 1.3 79.3 - - + +
193C LYS* 1.3 57.2 + - - +
195C ALA* 3.4 1.7 + - - +
196C LYS* 2.9 44.2 + - + +
234C ASP* 3.1 27.1 - - + +
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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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161C LEU* 4.3 31.9 - - + +
162C ASN* 4.4 18.4 - - - +
165C SER* 5.5 1.1 - - - -
170C VAL* 4.9 11.7 - - - +
174C HIS* 5.3 2.4 - - - -
189C VAL* 4.2 22.7 - - + -
190C THR* 3.1 20.0 + - - +
192C GLU* 1.3 77.4 - - - +
194C ILE* 1.3 65.0 + - - +
196C LYS 5.1 0.2 - - - -
197C SER* 3.3 49.6 + - - +
200C PHE* 4.5 23.4 - - + +
201C MET* 5.1 0.2 - - - +
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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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135C LEU* 4.6 9.0 - - + -
137C ILE* 4.5 8.1 - - + -
189C VAL* 4.5 10.8 - - + -
190C THR 4.5 7.2 - - - +
191C PRO 3.4 7.8 + - - +
192C GLU 3.3 0.6 - - - -
193C LYS* 1.3 79.0 - - - +
195C ALA* 1.3 62.4 + - + +
197C SER 4.5 1.2 + - - +
200C PHE* 4.4 20.2 - - + -
201C MET* 3.8 28.8 - - - +
204C LEU* 4.8 0.4 - - + -
237C ALA* 4.8 3.6 - - + +
238C LEU* 3.8 29.6 - - + -
240C ILE* 3.8 28.3 - - + +
241C LEU* 4.2 20.2 - - + -
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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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191C PRO 3.5 9.3 + - - +
192C GLU 3.4 3.2 + - - +
193C LYS 3.4 0.2 - - - -
194C ILE* 1.3 82.5 - - - +
196C LYS* 1.3 68.7 + - + +
197C SER 3.6 1.3 + - - -
234C ASP* 4.5 13.2 - - - +
237C ALA* 3.9 26.7 - - + -
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Residues in contact with LYS 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 GLU* 2.9 26.9 + - + +
193C LYS* 5.1 0.2 - - - -
195C ALA* 1.3 87.6 - - + +
197C SER* 1.3 59.0 + - - +
234C ASP* 5.6 4.0 - - - +
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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