Contacts of the helix formed by residues 151 - 159 (chain C) in PDB entry 3F7G
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 CYS 151 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124C CYS* 4.0 1.3 - - - -
126C PHE* 4.2 1.8 - - - -
127C CYS* 3.7 22.9 - - + +
144C HIS* 3.5 4.7 - - - +
148C PHE* 3.1 17.7 + - + +
149C PRO 3.3 0.8 - - - -
150C SER* 1.3 75.1 + - - +
152C GLN* 1.3 60.4 + - - +
153C PHE* 3.7 11.7 - - - -
154C LEU* 3.5 21.6 - - + +
155C LEU* 2.9 29.5 + - - +
1001C ZN 2.3 36.3 - - - -
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Residues in contact with GLN 152 (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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75C LEU* 3.7 25.0 + - + +
76C SER 2.8 22.6 + - - +
77C ARG* 3.7 33.1 - - - +
126C PHE* 3.6 29.4 - - + -
150C SER 3.2 8.4 + - - +
151C CYS* 1.3 72.2 - - - +
153C PHE* 1.3 60.9 + - - +
155C LEU* 3.9 8.0 - - + +
156C ARG* 2.8 39.1 + - + +
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Residues in contact with PHE 153 (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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90C ARG* 4.3 9.0 - - - -
110C ALA 3.8 15.7 - - - -
111C ALA 3.7 8.7 - - - -
112C GLY* 3.5 30.3 - - - -
124C CYS* 4.8 0.4 - - - -
125C PHE* 3.6 28.7 - + + -
126C PHE* 3.7 30.7 - - + -
141C TRP* 3.7 11.7 - + - -
144C HIS* 4.3 9.2 - + - -
151C CYS* 3.3 3.2 - - - -
152C GLN* 1.3 78.2 - - - +
154C LEU* 1.3 61.1 + - - +
156C ARG* 3.4 5.0 + - + +
157C SER* 2.8 46.8 + - - -
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Residues in contact with LEU 154 (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 TRP* 3.8 40.4 - - + +
144C HIS* 3.6 17.9 - - + +
145C ALA* 3.5 30.3 - - + +
148C PHE 3.6 19.5 - - - +
149C PRO* 4.5 4.0 - - + +
151C CYS* 3.3 16.8 + - + +
152C GLN 3.3 0.2 - - - -
153C PHE* 1.3 83.6 - - - +
155C LEU* 1.3 58.1 + - - +
157C SER* 3.3 0.9 + - - -
158C LYS* 2.8 42.2 + - + +
159C GLY 5.0 0.2 - - - +
162C PHE* 4.6 1.3 - - + -
163C VAL* 3.8 19.1 - - + -
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Residues in contact with LEU 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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147B TRP* 6.5 0.2 - - + -
75C LEU* 5.7 2.2 - - + -
149C PRO 3.6 20.9 - - - +
150C SER* 3.9 15.9 - - - +
151C CYS 2.9 19.4 + - - +
152C GLN* 3.9 9.4 - - + +
154C LEU* 1.3 76.8 - - - +
156C ARG* 1.3 57.5 + - - +
159C GLY* 2.8 31.8 + - - +
160C ARG* 3.8 52.7 - - + +
163C VAL* 3.7 24.7 - - + -
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Residues in contact with ARG 156 (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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77C ARG* 5.8 4.4 - - - +
152C GLN* 2.8 29.0 + - + +
153C PHE* 3.7 6.3 - - + +
155C LEU* 1.3 73.5 - - - +
157C SER* 1.3 61.3 + - - +
159C GLY 4.7 0.5 + - - -
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Residues in contact with SER 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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141C TRP* 3.9 22.4 - - - -
153C PHE* 2.8 42.8 + - - -
154C LEU 3.9 2.0 - - - -
156C ARG* 1.3 78.3 - - - +
158C LYS* 1.3 70.5 + - - +
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Residues in contact with LYS 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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141C TRP* 3.3 67.6 - - + +
154C LEU* 2.8 18.6 + - + +
157C SER* 1.3 81.6 + - - +
159C GLY* 1.3 64.5 + - - +
162C PHE* 3.4 41.9 + - + +
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Residues in contact with GLY 159 (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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154C LEU 3.8 0.2 + - - -
155C LEU* 2.8 30.2 + - - -
156C ARG 4.6 0.6 + - - -
157C SER 3.8 0.6 - - - -
158C LYS* 1.3 77.6 - - - +
160C ARG* 1.3 64.2 + - - -
161C ASP 3.4 2.7 - - - -
162C PHE* 3.6 0.7 + - - +
163C VAL* 3.4 23.2 + - - +
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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