Contacts of the helix formed by residues 140 - 153 (chain A) in PDB entry 5UFL
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 ILE 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ASN* 4.6 9.4 - - + +
104A ALA* 4.3 13.7 - - + -
124A LEU* 6.4 0.2 - - + -
133A ILE* 4.8 7.9 - - + -
134A PHE* 3.9 36.3 - - + +
136A SER* 3.1 16.5 + - - +
137A GLY 3.4 16.6 - - - +
138A ALA 3.7 11.7 - - - +
139A ASN* 1.3 78.6 - - - +
141A ASP* 1.3 65.5 + - - +
142A GLU 3.2 2.5 - - - -
143A LEU* 3.0 23.9 + - + +
144A ILE* 3.1 28.2 + - + +
169A LEU* 4.8 14.1 - - + -
176A VAL* 5.5 4.0 - - + -
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Residues in contact with ASP 141 (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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136A SER* 2.9 29.0 + - - +
139A ASN 3.7 0.4 - - - -
140A ILE* 1.3 76.3 - - - +
142A GLU* 1.3 62.3 + - + +
144A ILE* 3.6 12.1 + - - +
145A THR* 3.5 19.8 + - - +
179A HIS* 3.0 38.3 + - - -
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Residues in contact with GLU 142 (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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108A CYS* 3.6 31.5 - - - +
139A ASN* 4.2 23.3 + - - +
140A ILE 3.2 0.4 - - - +
141A ASP* 1.3 79.3 - - + +
143A LEU* 1.3 59.7 + - - +
145A THR* 3.3 16.7 + - - -
146A PHE* 3.3 13.9 + - - +
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Residues in contact with LEU 143 (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 ALA* 4.3 14.4 - - + +
107A VAL* 3.8 26.9 - - + -
108A CYS* 4.7 3.3 - - - -
121A ILE* 4.5 7.6 - - + -
124A LEU* 3.6 28.7 - - + -
139A ASN 4.2 4.2 + - - +
140A ILE* 3.0 24.2 + - + +
142A GLU* 1.3 78.3 - - - +
144A ILE* 1.3 59.4 + - - +
146A PHE* 3.4 6.9 + - + -
147A LEU* 3.0 58.7 + - + +
165A LEU* 4.4 12.8 - - + -
169A LEU* 4.4 10.3 - - + -
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Residues in contact with ILE 144 (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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136A SER* 6.3 0.4 - - - -
140A ILE* 3.1 23.8 + - + +
141A ASP* 3.9 8.7 - - - +
142A GLU 3.4 0.6 - - - -
143A LEU* 1.3 77.8 - - - +
145A THR* 1.3 57.7 + - + +
147A LEU* 3.4 4.4 + - - +
148A ILE* 3.1 51.3 + - + +
166A LEU* 4.2 10.0 - - + +
169A LEU* 3.7 28.3 - - + -
176A VAL* 3.8 26.0 - - + -
179A HIS* 4.3 19.7 - - + +
180A ILE* 4.0 17.9 - - + -
183A LEU* 4.6 1.8 - - + -
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Residues in contact with THR 145 (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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141A ASP* 3.5 18.2 + - - +
142A GLU* 3.3 15.8 + - - -
144A ILE* 1.3 76.3 - - + +
146A PHE* 1.3 61.6 + - - +
148A ILE* 4.5 6.1 - - + -
149A ASP* 3.1 33.8 + - - +
179A HIS* 5.2 0.2 - - + -
183A LEU* 4.9 22.4 - - + -
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Residues in contact with PHE 146 (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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107A VAL* 4.1 39.7 - - + -
108A CYS* 5.8 5.2 - - - -
117A PHE* 4.2 31.9 - + + -
121A ILE* 4.7 9.6 - - + -
142A GLU 3.3 16.0 + - - +
143A LEU* 3.5 13.0 - - + +
144A ILE 3.3 0.4 - - - -
145A THR* 1.3 81.0 + - - +
147A LEU* 1.3 70.3 + - + +
149A ASP* 3.6 3.4 + - - +
150A HIS* 3.3 57.8 + + - -
158A LEU* 6.4 0.2 - - + -
162A CYS* 6.4 0.7 - - + -
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Residues in contact with LEU 147 (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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121A ILE* 3.8 25.1 - - + -
143A LEU* 3.0 34.9 + - + +
144A ILE* 3.4 3.3 + - - +
146A PHE* 1.3 78.5 - - + +
148A ILE* 1.3 65.1 + - - +
150A HIS* 3.5 6.3 + - - +
151A ILE* 3.2 29.8 + - - +
162A CYS* 3.4 37.3 - - + +
165A LEU* 4.0 11.9 - - + -
166A LEU* 4.2 18.6 - - + +
169A LEU* 3.7 28.7 - - + -
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Residues in contact with ILE 148 (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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144A ILE* 3.1 38.3 + - + +
145A THR* 4.2 6.7 - - + +
146A PHE 3.4 0.2 - - - -
147A LEU* 1.3 76.2 - - - +
149A ASP* 1.3 69.4 + - - +
151A ILE* 3.1 19.7 + - - +
152A GLN* 3.2 19.2 + - + +
166A LEU* 4.1 18.8 - - + -
180A ILE* 4.9 10.3 - - + -
183A LEU* 3.8 22.0 - - + -
189A PHE* 3.9 32.3 - - + -
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Residues in contact with ASP 149 (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 THR* 3.1 23.0 + - - +
146A PHE* 3.6 4.0 + - - +
148A ILE* 1.3 84.1 - - - +
150A HIS* 1.3 61.8 + - + +
152A GLN* 3.4 12.7 + - - +
153A SER* 3.2 23.7 + - - -
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Residues in contact with HIS 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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114A ASP* 5.8 1.8 - - - -
117A PHE* 5.1 11.7 - + - -
146A PHE* 3.3 66.1 + + - +
147A LEU* 3.9 5.6 - - - +
148A ILE 3.3 0.2 - - - -
149A ASP* 1.3 76.0 - - + +
151A ILE* 1.3 64.3 + - - +
152A GLN 3.3 0.2 - - - -
153A SER* 3.3 28.1 + - - -
158A LEU* 3.4 25.5 - - + +
159A LYS* 3.9 9.4 - - - +
162A CYS* 4.1 19.0 - - + -
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Residues in contact with ILE 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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147A LEU 3.2 17.8 + - - +
148A ILE 3.1 8.1 + - - +
150A HIS* 1.3 74.1 - - - +
152A GLN* 1.3 63.8 + - - +
159A LYS* 3.6 23.3 + - - +
162A CYS* 4.1 18.8 - - - +
163A LEU* 3.8 40.6 - - + -
166A LEU* 3.5 30.5 - - + -
189A PHE* 4.0 19.3 - - + -
192A THR* 3.9 19.0 - - + +
193A LEU* 4.8 2.2 - - + -
196A LEU* 4.5 8.7 - - + -
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Residues in contact with GLN 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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148A ILE* 3.2 19.0 + - + +
149A ASP* 3.5 15.0 - - - +
150A HIS 3.3 0.4 - - - -
151A ILE* 1.3 79.4 - - - +
153A SER* 1.3 60.0 + - - +
159A LYS* 5.1 2.8 + - - -
188A SER* 4.4 12.5 + - - +
189A PHE* 3.7 23.9 - - - -
192A THR* 3.2 39.8 + - - +
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Residues in contact with SER 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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149A ASP 3.2 15.1 + - - -
150A HIS* 3.3 29.6 + - - -
151A ILE 4.4 2.5 - - - -
152A GLN* 1.3 81.1 - - - +
159A LYS* 4.3 19.1 + - - +
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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