Contacts of the helix formed by residues 154 - 163 (chain C) in PDB entry 4JCQ
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 SER 154 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ALA* 4.2 0.4 - - - -
152C GLY 4.0 0.6 + - - -
153C GLN* 1.3 79.4 + - - +
155C TYR* 1.3 65.0 + - - +
156C GLU* 3.7 7.5 + - - +
157C GLN* 3.3 21.9 + - - +
158C ILE* 3.2 20.4 + - - +
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Residues in contact with TYR 155 (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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141C GLU* 3.3 35.2 - - + +
144C ASN* 3.5 32.1 + - + -
145C ARG* 3.7 41.3 - - + -
148C ALA* 4.2 12.0 - - + +
153C GLN 3.9 0.4 + - - -
154C SER* 1.3 74.0 - - - +
156C GLU* 1.3 60.3 + - + +
158C ILE* 3.4 2.5 + - - +
159C SER* 2.8 45.8 + - - -
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Residues in contact with GLU 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C SER* 3.2 7.1 - - - +
155C TYR* 1.3 84.4 - - + +
157C GLN* 1.3 60.5 + - - +
159C SER* 3.6 6.2 + - - -
160C LYS* 3.2 23.6 + - - +
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Residues in contact with GLN 157 (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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153C GLN* 3.5 26.0 - - + +
154C SER* 3.3 20.9 + - - +
156C GLU* 1.3 75.5 - - - +
158C ILE* 1.3 64.3 + - - +
160C LYS* 3.4 16.5 + - - +
161C ASP* 2.8 63.8 + - - +
176C TYR* 4.0 9.2 - - + +
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Residues in contact with ILE 158 (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 ILE* 4.1 1.8 - - + -
144C ASN* 3.5 35.7 - - - +
147C ILE* 3.7 26.7 - - + -
148C ALA* 3.7 18.4 - - + -
151C THR* 3.9 2.2 - - - +
153C GLN* 3.6 19.3 - - + -
154C SER 3.2 16.2 + - - +
155C TYR 3.8 3.6 - - - +
157C GLN* 1.3 73.1 - - - +
159C SER* 1.3 60.6 + - - +
161C ASP* 3.1 1.2 + - - +
162C THR* 2.8 44.0 + - + +
176C TYR* 3.4 29.2 - - + +
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Residues in contact with SER 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C ARG* 4.8 1.4 + - - +
144C ASN* 3.5 26.6 + - - +
155C TYR* 2.8 36.9 + - - -
156C GLU* 3.8 7.6 - - - -
158C ILE* 1.3 73.0 - - - +
160C LYS* 1.3 62.2 - - - +
162C THR* 3.4 9.5 + - - -
163C ASP* 3.8 13.2 + - - +
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Residues in contact with LYS 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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156C GLU 3.2 13.6 + - - +
157C GLN* 3.6 19.3 - - - +
159C SER* 1.3 77.1 - - - +
161C ASP* 1.3 70.0 + - - +
163C ASP* 3.3 13.8 + - - +
164C ARG* 3.6 38.3 + - - +
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Residues in contact with ASP 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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115C ILE* 3.5 18.4 - - + +
116C HIS 4.0 1.7 + - - -
157C GLN* 2.8 32.2 + - - +
158C ILE 3.1 2.2 + - - -
160C LYS* 1.3 78.8 - - - +
162C THR* 1.3 59.6 + - - +
163C ASP 3.2 2.0 - - - -
164C ARG* 3.2 43.8 + - - +
166C PHE* 3.5 27.5 - - + -
176C TYR* 2.6 37.3 + - - +
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Residues in contact with THR 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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115C ILE* 3.4 30.1 - - + +
116C HIS* 3.4 9.2 - - - +
117C GLN* 2.9 42.6 + - + +
140C ARG* 3.6 13.1 + - - -
143C ILE* 5.4 0.2 - - + -
144C ASN* 2.7 28.7 + - - +
147C ILE* 4.0 7.4 - - + -
158C ILE* 2.8 29.5 + - + +
159C SER 3.4 6.6 + - - -
161C ASP* 1.3 76.5 - - - +
163C ASP* 1.3 57.6 + - - +
164C ARG 3.4 1.1 - - - -
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Residues in contact with ASP 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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116C HIS* 4.4 5.9 + - - -
119C ALA* 5.6 2.4 - - - +
140C ARG* 2.9 27.4 + - - +
159C SER 3.8 13.2 - - - +
160C LYS* 3.3 7.2 + - - +
161C ASP 3.2 1.2 - - - -
162C THR* 1.3 79.6 + - - +
164C ARG* 1.3 58.6 + - - +
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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