Contacts of the helix formed by residues 151 - 165 (chain A) in PDB entry 1F0C
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A PHE 5.3 0.9 - - - -
148A THR 3.4 6.1 + - - +
150A ASP* 1.3 74.3 + - - +
152A ARG* 1.3 58.6 - - - +
153A THR 2.8 7.0 + - - -
154A VAL* 3.0 24.9 + - - +
155A ASP* 3.4 13.6 + - - +
176A PRO* 3.7 39.5 - - - -
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Residues in contact with ARG 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ASP* 3.0 27.3 + - - +
151A CYS* 1.3 76.3 - - - +
153A THR* 1.3 56.6 + - - +
154A VAL 3.3 0.2 - - - -
155A ASP* 2.8 39.8 + - - +
156A ALA* 2.8 29.6 + - - +
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Residues in contact with THR 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A VAL* 4.0 24.7 - - + +
146A ASP* 2.6 28.5 + - - +
147A PHE* 4.3 11.7 - - + -
150A ASP* 3.1 21.3 + - - +
151A CYS 2.8 0.6 - - - -
152A ARG* 1.3 80.3 - - - +
154A VAL* 1.3 61.4 + - + +
156A ALA* 3.2 7.1 + - - +
157A ILE* 3.0 37.5 + - + +
178A LEU* 5.1 3.4 - - + -
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Residues in contact with VAL 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A PHE 5.8 2.0 - - - +
150A ASP 5.5 0.2 - - - +
151A CYS* 3.0 19.9 + - - +
153A THR* 1.3 76.8 - - - +
155A ASP* 1.3 68.8 + - - +
157A ILE* 3.2 3.0 + - - +
158A ASN* 3.0 40.2 + - - +
173A LEU* 3.9 26.9 - - + +
174A ASP 6.0 0.2 - - - -
175A GLU 4.4 5.2 - - - +
176A PRO* 4.4 8.1 - - + -
178A LEU* 3.8 43.5 - - + +
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Residues in contact with ASP 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A CYS* 3.8 9.4 - - - +
152A ARG* 2.8 47.5 + - - +
153A THR 3.2 0.4 - - - -
154A VAL* 1.3 83.7 - - - +
156A ALA* 1.3 62.2 + - - +
158A ASN* 3.9 8.0 + - - +
159A LYS* 2.9 25.8 + - - +
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Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ARG 2.8 20.8 + - - +
153A THR* 3.2 7.2 + - - +
155A ASP* 1.3 73.6 - - - +
157A ILE* 1.3 64.1 + - + +
159A LYS* 3.4 5.7 + - - +
160A CYS* 3.1 22.5 + - - +
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Residues in contact with ILE 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A TYR* 3.8 46.8 + - + +
145A VAL* 6.1 0.4 - - + -
147A PHE* 4.9 1.6 - - + -
153A THR* 3.0 30.6 + - + +
154A VAL 3.7 6.1 - - - +
156A ALA* 1.3 76.8 - - + +
158A ASN* 1.3 64.1 + - - +
160A CYS* 3.1 6.2 + - - +
161A VAL* 3.0 25.4 + - + +
172A LEU* 5.3 0.2 - - + -
173A LEU* 3.7 15.9 - - + -
178A LEU* 4.9 0.9 - - + -
183A LEU* 3.8 24.2 - - + -
185A ILE* 3.5 30.7 - - + -
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Residues in contact with ASN 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A VAL* 3.0 30.2 + - - +
155A ASP* 4.0 7.6 + - - +
157A ILE* 1.3 72.0 - - - +
159A LYS* 1.3 56.9 + - - +
161A VAL* 3.2 6.5 + - - +
162A ASP* 2.7 38.5 + - - +
169A ILE 4.8 0.9 - - - +
170A ASN* 4.6 5.0 - - - +
171A PRO* 3.2 31.6 - - + +
172A LEU* 3.1 7.9 + - - +
173A LEU* 2.9 42.5 + - - +
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Residues in contact with LYS 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ASP 2.9 18.9 + - - +
156A ALA* 3.7 6.3 - - - +
158A ASN* 1.3 76.2 - - - +
160A CYS* 1.3 59.5 + - - +
162A ASP* 3.3 22.4 + - - +
163A ILE* 2.9 47.3 + - + +
170A ASN* 5.6 2.4 - - - +
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Residues in contact with CYS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A MET* 4.2 16.2 - - + -
117A LYS* 3.6 27.4 - - - -
119A TYR* 4.4 9.2 - - - +
156A ALA 3.1 13.2 + - - +
157A ILE 3.3 9.2 - - - +
159A LYS* 1.3 78.9 - - - +
161A VAL* 1.3 64.4 + - + +
163A ILE* 3.7 14.6 - - - +
164A PHE* 3.1 24.9 + - - +
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Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A MET* 4.2 15.9 - - + -
119A TYR* 6.0 0.4 - - - +
157A ILE* 3.0 20.2 + - + +
158A ASN 3.9 5.6 - - - +
160A CYS* 1.3 75.7 - - + +
162A ASP* 1.3 61.5 + - - +
164A PHE* 3.5 1.1 + - - +
165A THR* 2.8 34.1 + - + +
169A ILE* 3.9 21.3 - - + +
172A LEU* 4.1 16.4 - - + +
185A ILE* 4.0 28.0 - - + -
187A ALA* 4.4 3.6 - - + -
350A ALA* 3.8 26.0 - - + -
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Residues in contact with ASP 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ASN 2.7 23.2 + - - +
159A LYS* 3.3 34.0 + - - +
161A VAL* 1.3 74.4 - - - +
163A ILE* 1.3 66.2 + - - +
165A THR* 3.4 1.0 + - - -
166A GLU 3.3 2.3 + - - -
167A GLY* 2.8 51.1 + - - -
169A ILE 3.5 14.7 + - - +
170A ASN* 3.5 28.8 + - + +
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Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LYS* 5.0 0.3 + - - -
159A LYS* 2.9 48.8 + - + +
160A CYS* 3.4 17.2 + - - +
162A ASP* 1.3 78.4 - - - +
164A PHE* 1.3 67.6 + - + +
166A GLU* 3.2 22.1 + - - +
167A GLY 4.8 1.1 - - - +
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Residues in contact with PHE 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LYS* 3.1 61.6 + - + +
114A SER* 3.6 20.4 - - - -
115A MET* 3.5 41.7 - - + -
160A CYS* 3.1 18.4 + - - +
161A VAL 3.8 3.4 - - - +
163A ILE* 1.3 81.7 - - + +
165A THR* 1.3 59.0 + - + +
166A GLU* 3.3 1.8 + - - +
187A ALA* 3.5 35.9 - - + -
188A VAL* 4.1 3.8 - - - -
189A TYR* 3.8 2.3 - - - +
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Residues in contact with THR 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A VAL* 2.8 28.6 + - + +
162A ASP 3.4 5.2 + - - -
164A PHE* 1.3 83.6 - - + +
166A GLU* 1.3 70.4 + - - +
168A LYS* 2.9 18.9 + - - +
169A ILE* 3.2 43.4 + - + -
187A ALA* 4.4 5.2 - - + -
188A VAL 4.0 17.7 - - - +
189A TYR* 3.7 10.7 - - - -
348A ALA* 4.0 7.2 - - + -
349A ALA 4.6 0.9 - - - +
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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