Contacts of the helix formed by residues 149 - 155 (chain A) in PDB entry 1F16
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 LEU 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A SER* 3.9 26.7 - - - +
19A ILE* 4.2 17.3 - - + -
20A MET* 4.3 11.4 - - - -
144A LEU* 3.9 2.2 - - + +
145A ARG* 3.4 43.3 - - + +
146A GLU 5.2 1.1 - - - +
147A ARG 3.0 3.4 + - - -
148A LEU* 1.3 78.0 - - - +
150A GLY* 1.3 68.3 + - - +
151A TRP 3.2 0.7 - - - -
152A ILE* 3.3 12.2 + - - +
153A GLN* 3.2 33.0 + - - +
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Residues in contact with GLY 150 (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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147A ARG 4.2 3.0 + - - -
149A LEU* 1.3 80.1 - - - +
151A TRP* 1.3 64.7 + - - +
153A GLN* 3.3 26.7 + - - +
154A ASP* 2.5 26.5 - - - +
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Residues in contact with TRP 151 (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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104A ASN* 4.6 19.9 + - + +
105A PHE* 4.0 40.0 - + + +
109A ARG* 5.2 2.5 - - - +
146A GLU 5.6 0.4 - - - -
147A ARG* 3.1 44.9 - - - +
148A LEU* 5.0 7.4 - - + -
149A LEU 3.2 0.8 - - - +
150A GLY* 1.3 83.7 - - - +
152A ILE* 1.3 65.5 + - + +
153A GLN 3.2 0.7 + - - -
154A ASP* 3.3 18.0 + - + +
155A GLN* 3.5 16.1 + - - +
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Residues in contact with ILE 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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19A ILE* 3.8 32.9 - - + +
105A PHE* 6.1 1.8 - - + -
144A LEU* 4.0 5.4 - - + -
148A LEU* 2.6 35.9 - - + +
149A LEU 3.3 6.3 + - - +
151A TRP* 1.3 77.6 - - + +
153A GLN* 1.3 60.2 + - - +
155A GLN* 3.0 37.9 - - - +
156A GLY 4.0 0.2 - - - +
157A GLY* 3.5 16.2 + - - -
158A TRP* 3.5 44.6 - - + +
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Residues in contact with GLN 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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14A THR* 4.7 19.7 + - - +
16A SER* 4.3 13.9 - - - +
19A ILE* 3.6 16.8 - - + -
149A LEU* 3.2 35.8 - - - +
150A GLY* 3.3 17.7 + - - +
151A TRP 3.0 0.6 - - - -
152A ILE* 1.3 79.2 - - - +
154A ASP* 1.3 67.6 + - - +
156A GLY* 3.0 17.8 + - - +
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Residues in contact with ASP 154 (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 GLY 2.5 30.3 - - - +
151A TRP* 3.3 10.8 + - + +
153A GLN* 1.3 78.4 - - - +
155A GLN* 1.3 59.4 + - - +
156A GLY 2.9 5.6 + - - -
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Residues in contact with GLN 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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105A PHE* 3.5 29.5 - - + -
107A TRP* 5.5 3.0 - - + -
151A TRP 3.5 9.2 + - - +
152A ILE* 3.0 35.4 - - - +
154A ASP* 1.3 77.2 - - - +
156A GLY* 1.3 54.1 + - - +
157A GLY 2.9 32.6 + - - +
158A TRP* 4.0 9.3 - - - +
159A ASP* 3.9 10.7 - - - +
160A GLY* 4.7 8.5 + - - -
161A LEU* 4.2 14.5 - - - +
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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