Contacts of the helix formed by residues 151 - 162 (chain F) in PDB entry 3FFC
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 ARG 151 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147F TRP 3.0 5.4 + - - -
148F GLU* 3.2 14.2 + - - +
149F ALA 4.0 7.4 - - - +
150F ALA* 1.3 80.8 - - - +
152F VAL* 1.3 63.8 + - - +
153F ALA* 3.4 2.7 - - - -
154F GLU* 2.9 56.4 + - + +
155F GLN* 3.3 13.8 - - - +
108J PHE* 3.7 35.6 - - + -
116J THR* 4.8 5.0 - - + +
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Residues in contact with VAL 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F TRP* 4.1 7.9 - - + -
147F TRP* 3.1 58.8 + - + +
148F GLU* 5.2 0.2 - - - +
150F ALA* 4.0 11.9 - - + +
151F ARG* 1.3 73.3 - - - +
153F ALA* 1.3 67.1 + - - +
155F GLN* 2.8 27.7 + - - +
156F ASP* 2.9 30.0 + - - +
3H ARG* 6.2 0.7 - - - +
7H TYR* 4.0 20.0 - - + +
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Residues in contact with ALA 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F LEU* 4.0 21.7 - - + +
130F LEU 3.7 4.7 - - - +
131F ARG* 4.0 24.2 - - - +
133F TRP* 3.6 24.1 - - - +
147F TRP 4.7 0.4 + - - -
151F ARG* 3.4 1.1 - - - -
152F VAL* 1.3 77.4 - - - +
154F GLU* 1.3 52.3 + - + +
156F ASP* 3.2 2.9 + - - +
157F ARG* 2.7 40.0 + - - +
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Residues in contact with GLU 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F ARG* 2.9 58.5 + - + +
152F VAL 3.1 0.8 - - - -
153F ALA* 1.3 77.3 - - + +
155F GLN* 1.3 58.4 - - - +
157F ARG* 3.6 33.6 + - - +
158F ALA* 3.0 29.5 + - - +
115J ALA* 5.7 3.6 - - - +
116J THR* 4.1 14.7 + - + +
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Residues in contact with GLN 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F ALA 2.7 29.9 + - - -
151F ARG* 3.3 9.4 + - - +
152F VAL* 2.8 20.6 + - - +
154F GLU* 1.3 76.7 - - - +
156F ASP* 1.3 64.9 + - - +
158F ALA* 3.6 0.6 - - - +
159F TYR* 3.4 17.0 + - - +
3H ARG* 5.7 0.2 - - - +
6H ALA* 4.6 1.7 + - - +
7H TYR* 3.4 27.7 + - - -
108J PHE* 3.8 10.9 - - - +
109J THR* 3.3 28.2 - - + +
112J SER* 3.6 14.9 - - - -
116J THR* 3.6 28.3 - - + +
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Residues in contact with ASP 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F ASN* 2.8 28.2 + - - +
126F LEU* 4.0 15.5 - - + -
133F TRP* 3.3 16.6 - - - -
147F TRP* 5.6 0.2 - - - -
152F VAL* 2.9 23.4 + - - +
153F ALA* 3.7 4.3 - - - +
155F GLN* 1.3 78.6 - - - +
157F ARG* 1.3 60.4 + - - +
158F ALA 3.2 1.3 - - - -
159F TYR* 3.1 5.8 + - - +
160F LEU* 2.9 39.2 + - + +
3H ARG* 2.9 27.5 + - - +
4H GLY 5.1 3.5 - - - +
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Residues in contact with ARG 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F LEU* 4.9 0.8 - - - +
130F LEU* 3.1 34.6 + - + +
131F ARG* 3.4 56.6 + - - +
153F ALA* 2.7 18.8 + - - +
154F GLU* 3.6 43.9 + - - +
156F ASP* 1.3 70.7 - - - +
158F ALA* 1.3 54.3 + - - +
160F LEU* 3.2 4.8 + - - +
161F GLU* 2.8 68.4 + - + +
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Residues in contact with ALA 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F GLU 3.0 17.7 + - - +
155F GLN* 3.6 7.4 - - - +
157F ARG* 1.3 77.3 - - - +
159F TYR* 1.3 61.1 + - - +
161F GLU* 5.2 1.6 - - - -
162F GLY* 3.0 24.0 + - - +
163F THR 3.8 1.6 + - - -
59I TYR* 3.7 8.4 + - - +
112J SER* 3.7 9.0 - - - +
114J GLY* 3.6 33.9 - - - +
115J ALA 5.0 0.7 - - - +
116J THR* 5.1 1.1 - - - +
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Residues in contact with TYR 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F MET* 4.0 8.3 - - - +
7F TYR* 3.5 17.8 - - - -
99F TYR* 3.6 24.0 - + - -
100F GLY* 4.8 0.2 - - - -
155F GLN 3.4 9.1 + - - +
156F ASP 3.1 7.4 + - - +
158F ALA* 1.3 79.3 - - - +
160F LEU* 1.3 77.3 + - + +
163F THR* 3.3 26.1 + - + +
164F CYS* 2.8 50.8 + - + -
1H PHE 2.6 29.6 + - - -
2H LEU 3.3 13.9 - - - -
3H ARG* 3.6 32.1 - - + -
111J THR 5.0 3.8 - - - -
112J SER* 3.5 15.7 + - - +
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Residues in contact with LEU 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F TYR* 5.1 1.8 - - + -
100F GLY* 3.4 35.0 - - - +
101F CYS* 3.9 0.8 - - + +
109F LEU* 3.7 8.0 - - + +
112F GLY* 4.5 8.3 - - - -
113F HIS 3.5 23.1 - - - +
114F ASN* 4.6 3.1 - - + -
126F LEU* 3.7 25.8 - - + -
130F LEU* 3.9 20.9 - - + -
156F ASP* 2.9 22.7 + - + +
157F ARG* 3.9 3.1 - - - +
159F TYR* 1.3 97.4 - - + +
161F GLU* 1.3 57.8 + - - +
164F CYS* 3.6 7.8 - - - +
165F VAL* 3.3 21.0 - - - +
3H ARG* 5.6 1.6 - - - -
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Residues in contact with GLU 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F LEU* 3.8 22.9 - - + +
130F LEU* 4.2 10.7 - - + +
131F ARG* 5.2 5.9 + - - -
157F ARG* 2.8 49.3 + - + +
158F ALA* 4.7 1.3 - - - +
160F LEU* 1.3 72.4 - - - +
162F GLY* 1.3 61.2 + - - +
165F VAL* 3.7 18.2 - - - +
166F GLU* 4.5 3.3 - - - +
59I TYR* 4.3 12.2 - - + -
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Residues in contact with GLY 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F ALA 3.0 14.1 + - - -
161F GLU* 1.3 79.8 - - - +
163F THR* 1.3 59.4 + - - +
164F CYS 3.4 0.8 + - - -
165F VAL 3.5 1.0 + - - -
166F GLU* 2.9 37.3 + - - +
31I SER* 4.6 0.2 - - - -
59I TYR* 3.5 31.6 - - - -
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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