Contacts of the helix formed by residues 159 - 168 (chain C) in PDB entry 4FJV
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 159 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157C GLU 4.1 1.8 + - - -
158C MET* 1.3 79.7 - - - +
160C ILE* 1.3 81.8 + - - +
161C LYS* 3.4 44.8 + - - +
162C ASP* 3.2 21.9 + - - +
163C PHE* 2.9 19.3 + - - +
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Residues in contact with ILE 160 (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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143C ILE* 3.9 28.9 - - + -
144C ARG* 4.8 5.8 - - + -
147C ALA* 3.9 26.9 - - + +
150C PHE* 3.9 10.3 - - + +
151C ARG* 3.5 32.8 - - + +
154C ILE* 3.6 30.1 - - + -
158C MET 3.7 1.6 + - - -
159C ASP* 1.3 79.3 + - - +
161C LYS* 1.3 64.7 + - + +
163C PHE* 3.0 9.4 + - + +
164C CYS* 2.9 31.4 + - - -
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Residues in contact with LYS 161 (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 ARG* 3.6 28.7 + - + +
159C ASP* 3.3 21.9 + - - +
160C ILE* 1.3 82.2 - - + +
162C ASP* 1.3 64.0 + - - +
164C CYS* 3.4 0.9 + - - -
165C THR* 2.9 34.7 + - - +
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Residues in contact with ASP 162 (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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158C MET* 4.3 13.4 - - + +
159C ASP* 3.2 28.7 + - + +
161C LYS* 1.3 80.7 + - - +
163C PHE* 1.3 60.8 + - - +
165C THR* 4.4 2.9 + - - -
166C HIS* 2.9 53.5 + - + +
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Residues in contact with PHE 163 (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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143C ILE* 4.3 2.7 - - + -
154C ILE* 4.3 22.0 - - + -
158C MET* 3.8 18.7 - - + -
159C ASP 2.9 14.2 + - - +
160C ILE* 3.0 17.7 + - + +
162C ASP* 1.3 76.2 - - - +
164C CYS* 1.3 63.6 + - - +
167C GLU* 2.9 63.7 + - + +
168C VAL* 3.6 20.5 + - + -
176C ASP* 6.0 1.1 - - + -
178C ILE* 4.0 36.8 - - + -
179C GLN* 3.7 26.9 - - - -
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Residues in contact with CYS 164 (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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140C SER* 3.1 27.4 - - - +
143C ILE* 3.6 37.9 - - - -
144C ARG* 3.7 23.3 - - - +
160C ILE* 2.9 20.0 + - - +
161C LYS 3.9 0.2 - - - +
163C PHE* 1.3 80.8 - - - +
165C THR* 1.3 64.0 + - - +
168C VAL* 3.3 10.8 + - - -
169C GLU* 3.0 30.3 + - - +
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Residues in contact with THR 165 (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 ARG* 2.9 14.4 + - - -
161C LYS* 2.9 19.5 + - - +
162C ASP* 3.8 6.2 + - - -
164C CYS* 1.3 78.2 - - - +
166C HIS* 1.3 80.5 + - + +
169C GLU* 3.8 15.1 + - - +
170C PRO* 3.2 21.7 - - - +
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Residues in contact with HIS 166 (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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158C MET* 6.3 3.0 - - + +
162C ASP* 2.9 42.0 + - + +
165C THR* 1.3 99.6 - - + +
167C GLU* 1.3 70.0 + - + +
170C PRO* 3.8 9.8 - - + +
173C THR* 3.7 16.6 - - - +
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Residues in contact with GLU 167 (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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53C TYR* 4.7 0.5 + - - -
136C ARG* 4.7 0.5 + - - -
156C GLU* 5.2 1.4 - - - +
158C MET* 3.8 24.2 - - - +
163C PHE* 2.9 49.2 + - + +
166C HIS* 1.3 85.6 - - + +
168C VAL* 1.3 62.7 + - - +
173C THR* 3.6 19.0 + - - +
174C GLU 3.9 7.8 - - - +
179C GLN* 3.2 19.6 + - - +
74D ARG* 5.3 9.4 + - - +
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Residues in contact with VAL 168 (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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53C TYR* 4.3 7.6 + - - +
136C ARG* 2.8 53.2 + - - +
139C THR* 3.7 17.5 - - + -
140C SER* 3.6 17.7 - - - +
143C ILE* 4.3 7.4 - - + -
163C PHE* 3.8 27.6 - - + -
164C CYS* 3.3 19.4 + - - +
167C GLU* 1.3 84.3 - - - +
169C GLU* 1.3 61.9 + - - +
170C PRO* 3.6 1.3 - - - -
179C GLN* 3.8 9.9 - - + -
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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