Contacts of the strand formed by residues 145 - 150 (chain C) in PDB entry 3HUU
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 ILE 145 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134C THR* 4.1 24.9 - - + +
137C LEU* 4.4 11.4 - - + -
138C TYR* 4.9 2.2 - - + +
142C HIS* 4.2 26.2 - - + +
143C ARG 3.5 9.5 + - - +
144C HIS* 1.3 76.1 - - - +
146C LEU* 1.3 61.9 + - - +
164C PHE* 3.6 35.5 - - + -
168C CYS* 5.6 0.9 - - - -
173C ILE* 5.1 9.4 - - + -
174C SER 3.9 14.1 + - - +
176C ASP* 4.0 8.5 + - - +
201C PRO* 4.6 1.1 - - - -
203C VAL* 3.6 26.0 - - + +
205C ILE* 3.7 21.3 - - + -
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Residues in contact with LEU 146 (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 HIS 4.1 0.8 + - - -
145C ILE* 1.3 74.0 - - - +
147C PHE* 1.3 62.7 + - - +
148C LEU* 3.6 23.3 - - + -
176C ASP* 3.8 23.8 - - + +
178C VAL* 3.8 12.8 - - + -
189C PHE* 3.6 33.2 - - + -
190C ILE* 5.7 2.5 - - + -
192C GLN* 4.4 7.2 - - - +
201C PRO* 4.0 22.7 - - + -
203C VAL 3.3 5.7 + - - -
204C ILE* 3.4 26.0 - - + +
205C ILE* 2.9 26.2 + - - +
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Residues in contact with PHE 147 (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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130C ALA* 5.2 0.9 - - + -
134C THR* 5.8 0.4 - - - -
145C ILE 4.1 0.8 + - - -
146C LEU* 1.3 73.1 - - - +
148C LEU* 1.3 71.7 + - - +
149C GLN* 3.8 8.9 + - + -
160C ARG* 3.9 28.5 - - + -
161C SER* 3.7 19.1 - - - -
164C PHE* 3.5 47.6 - + + -
176C ASP 3.1 9.4 + - - +
177C CYS* 3.5 20.0 - - - -
178C VAL* 3.0 27.9 + - - +
205C ILE* 3.5 35.0 - - + -
207C SER* 4.2 15.7 - - - -
235C PHE* 4.2 8.1 - + - -
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Residues in contact with LEU 148 (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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146C LEU* 3.6 19.7 - - + -
147C PHE* 1.3 74.5 - - - +
149C GLN* 1.3 59.0 + - - +
178C VAL* 3.3 28.3 - - + -
180C ILE* 4.3 9.2 - - + -
186C LEU* 3.7 24.7 - - + -
189C PHE* 4.2 8.1 - - + -
190C ILE* 4.8 2.5 - - + -
204C ILE* 3.7 26.7 - - + -
205C ILE 2.7 12.9 + - - +
206C THR* 3.5 14.0 - - + -
207C SER* 3.0 27.7 + - - -
211C LEU* 3.7 14.7 - - + +
215C LEU* 4.1 11.4 - - + -
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Residues in contact with GLN 149 (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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147C PHE* 3.8 16.1 + - + -
148C LEU* 1.3 73.9 - - - +
150C GLU* 1.3 60.5 + - - +
152C GLY 5.2 4.0 + - - -
157C THR* 3.3 30.2 + - + +
158C GLU* 3.3 25.7 + - - -
161C SER* 3.7 14.0 + - - -
165C LYS* 4.7 2.1 + - - -
177C CYS* 3.6 19.9 - - - +
178C VAL 2.7 16.8 + - - +
179C VAL* 3.3 24.3 - - + +
180C ILE* 2.7 33.6 + - - +
207C SER* 3.9 2.7 - - - -
211C LEU* 3.8 2.9 - - - -
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Residues in contact with GLU 150 (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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28C LYS* 5.6 5.4 + - - -
149C GLN* 1.3 76.6 + - - +
151C SER* 1.3 71.9 + - - +
152C GLY 4.0 3.1 - - - +
154C TYR* 6.5 0.2 - - + -
156C VAL* 5.0 4.4 - - - +
157C THR* 3.0 36.4 + - - +
160C ARG* 5.2 1.7 + - - -
179C VAL* 4.1 3.9 - - - +
180C ILE 4.3 3.1 - - - -
207C SER* 3.2 23.8 + - - +
208C ASP* 3.5 27.9 - - - +
211C LEU* 3.7 18.1 - - + +
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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