Contacts of the helix formed by residues 158 - 171 (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 LEU 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ASP* 6.1 0.2 - - - +
117A PHE* 5.0 11.7 - - + -
118A LEU* 4.3 29.6 - - + +
121A ILE* 5.7 5.8 - - + -
146A PHE* 6.4 0.2 - - + -
150A HIS* 3.4 40.6 - - + +
157A GLU* 1.3 76.9 - - - +
159A LYS* 1.3 60.5 + - + +
160A MET 3.4 0.2 - - - -
161A PRO* 3.3 20.2 - - + +
162A CYS* 3.1 28.0 - - + -
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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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150A HIS 3.9 17.7 - - - +
151A ILE* 3.6 23.0 + - - +
152A GLN 5.1 2.6 + - - -
153A SER 4.3 17.6 + - - +
157A GLU* 3.2 6.0 - - - +
158A LEU* 1.3 79.1 - - + +
160A MET* 1.3 58.7 + - - +
162A CYS* 3.3 10.5 - - - -
163A LEU* 3.0 39.8 + - + +
192A THR* 5.6 0.4 - - - +
196A LEU* 3.9 34.5 - - + +
199A HIS* 5.6 7.2 - - - +
204A VAL* 6.0 2.9 - - + -
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Residues in contact with MET 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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157A GLU* 3.5 34.3 + - - +
159A LYS* 1.3 78.1 - - - +
161A PRO* 1.4 70.1 - - + +
163A LEU* 3.4 4.5 + - - +
164A GLY 3.1 17.3 + - - -
201A SER* 3.3 30.1 - - - +
203A THR* 3.8 18.2 - - + -
204A VAL* 3.8 24.1 - - + +
207A PHE* 3.4 23.5 - - + -
249A LEU* 6.2 0.2 - - - -
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Residues in contact with PRO 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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118A LEU* 3.8 29.4 - - + -
121A ILE* 3.5 22.5 - - + +
122A GLN* 4.5 10.8 - - + +
125A GLN* 3.6 19.8 + - - +
157A GLU 3.5 9.9 - - - +
158A LEU* 3.3 22.7 - - + +
160A MET* 1.4 97.1 - - + +
162A CYS* 1.3 54.6 + - - +
164A GLY 3.3 1.4 + - - -
165A LEU 3.0 22.0 + - - -
207A PHE* 5.4 0.2 - - + -
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Residues in contact with CYS 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 3.8 10.7 - - + +
146A PHE* 6.4 0.2 - - + -
147A LEU* 3.4 35.3 - - + +
150A HIS* 4.1 24.0 - - + -
151A ILE* 4.1 12.6 - - - +
158A LEU* 3.1 31.4 - - + -
159A LYS* 3.3 17.5 - - - -
161A PRO* 1.3 75.7 - - - +
163A LEU* 1.3 58.9 + - - +
165A LEU* 4.0 0.7 - - - -
166A LEU* 3.1 28.1 + - - +
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Residues in contact with LEU 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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151A ILE* 3.8 24.7 - - + -
159A LYS* 3.0 27.5 + - + +
160A MET* 3.5 6.7 - - - +
162A CYS* 1.3 77.6 - - - +
164A GLY* 1.3 57.9 + - - +
166A LEU* 3.4 0.9 + - - -
167A ALA* 3.0 29.8 + - - +
193A LEU* 3.9 15.9 - - + -
196A LEU* 3.4 27.6 - - + -
204A VAL* 3.7 22.9 - - + +
207A PHE* 3.8 10.9 - - + +
208A ALA* 4.3 7.4 - - - -
211A ILE* 3.6 30.2 - - + +
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Residues in contact with GLY 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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125A GLN* 3.5 22.4 - - - -
160A MET 3.1 7.9 + - - -
161A PRO 3.3 2.9 + - - -
163A LEU* 1.3 76.4 - - - +
165A LEU* 1.3 62.4 + - - +
167A ALA* 3.6 2.8 + - - +
168A ASN* 3.4 27.5 + - - +
207A PHE* 3.5 23.5 - - - -
253A TYR* 3.6 2.6 + - - -
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Residues in contact with LEU 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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121A ILE* 3.6 36.6 - - + +
124A LEU* 3.4 36.1 - - + -
125A GLN* 4.1 11.6 - - + +
128A THR* 4.0 12.3 - - + +
143A LEU* 4.4 7.2 - - + -
147A LEU* 4.0 9.6 - - + -
161A PRO 3.0 15.8 + - - +
162A CYS* 4.1 4.7 - - - +
163A LEU 3.3 0.2 - - - -
164A GLY* 1.3 75.2 - - - +
166A LEU* 1.3 63.2 + - - +
168A ASN* 3.1 19.9 + - - +
169A LEU* 3.2 37.3 + - + +
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Residues in contact with LEU 166 (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* 4.2 29.2 - - + -
147A LEU* 4.2 12.8 - - + +
148A ILE* 4.1 12.3 - - + -
151A ILE* 3.5 26.7 - - + -
162A CYS 3.1 16.9 + - - +
163A LEU 3.4 4.0 + - - +
165A LEU* 1.3 78.7 - - - +
167A ALA* 1.3 60.9 + - - +
169A LEU* 3.3 10.3 + - + -
170A CYS* 3.1 45.7 + - - -
180A ILE* 4.5 5.6 - - + -
189A PHE* 3.6 24.0 - - + -
211A ILE* 4.3 8.1 - - + -
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Residues in contact with ALA 167 (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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163A LEU 3.0 18.0 + - - +
164A GLY* 3.7 8.3 - - - +
165A LEU 3.2 0.2 - - - -
166A LEU* 1.3 74.3 - - - +
168A ASN* 1.3 64.6 + - - +
170A CYS* 4.2 2.7 - - - +
171A ARG* 3.2 25.8 + - - +
207A PHE* 4.0 12.3 - - - +
210A SER* 4.2 16.5 - - - +
211A ILE* 3.7 19.7 - - + +
214A SER* 5.0 1.2 + - - -
253A TYR* 4.4 12.3 - - + -
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Residues in contact with ASN 168 (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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125A GLN* 3.1 30.5 + - - +
128A THR* 3.4 27.8 + - - +
129A TYR* 3.5 19.7 - - - +
133A ILE* 3.3 16.3 - - - +
164A GLY 3.4 8.1 + - - -
165A LEU 3.1 8.1 + - - +
167A ALA* 1.3 75.3 - - - +
169A LEU* 1.3 62.6 + - - +
171A ARG* 3.5 18.9 + - - +
253A TYR* 2.7 37.0 + - - -
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Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR* 4.5 7.6 - - + -
133A ILE* 3.6 34.8 - - + -
140A ILE* 4.8 9.9 - - + -
143A LEU* 4.4 11.2 - - + -
144A ILE* 3.7 29.8 - - + -
147A LEU* 3.7 20.4 - - + -
165A LEU* 3.2 36.4 + - + +
166A LEU* 3.3 8.5 + - + +
168A ASN* 1.3 77.9 - - - +
170A CYS* 1.3 57.2 + - - +
173A ASN* 3.2 28.1 + - - +
176A VAL* 3.4 11.9 - - + +
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Residues in contact with CYS 170 (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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166A LEU* 3.1 31.4 + - - +
167A ALA* 4.2 4.0 - - - +
168A ASN 3.4 0.2 - - - -
169A LEU* 1.3 75.4 - - - +
171A ARG* 1.3 57.9 + - - +
172A HIS 3.3 0.5 + - - -
173A ASN 3.6 3.0 + - - -
176A VAL* 4.4 4.7 - - - -
177A GLN* 2.8 37.3 + - - +
180A ILE* 3.4 30.5 - - - -
211A ILE* 4.3 16.2 - - - -
214A SER* 3.3 20.4 - - - +
215A LEU* 4.4 10.8 - - + -
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Residues in contact with ARG 171 (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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129A TYR* 4.8 4.8 - - - -
130A ASN* 3.7 38.8 + - - +
131A VAL 5.3 1.0 - - - +
133A ILE* 4.8 1.0 - - - +
167A ALA 3.2 16.9 + - - +
168A ASN* 3.5 12.0 - - - +
169A LEU 3.4 0.4 - - - -
170A CYS* 1.3 76.2 - - - +
172A HIS* 1.3 90.8 + - + +
173A ASN* 3.1 15.6 + - - -
210A SER* 6.1 5.4 - - - -
214A SER* 4.2 13.7 + - - -
253A TYR* 6.6 0.4 - - - -
256A ASP* 3.6 39.5 + - - +
257A LEU* 5.9 1.1 - - - +
260A ASP* 3.0 29.8 + - - +
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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