Contacts of the helix formed by residues 149 - 161 (chain A) in PDB entry 5UQ9
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 ALA 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A ILE* 3.6 22.5 - - + +
122A LEU* 3.6 24.6 - - + +
124A VAL* 3.6 28.3 - - + -
146A ASN 3.2 4.1 + - - +
147A LYS 3.0 0.8 - - - -
148A GLU* 1.3 76.0 - - - +
150A TRP* 1.3 63.8 + - - +
151A PRO 3.5 0.9 - - - -
152A HIS* 3.4 4.0 + - - -
153A ILE* 3.2 26.6 + - - +
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Residues in contact with TRP 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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143A PRO* 3.7 22.7 - - + -
146A ASN 4.0 1.2 + - - -
147A LYS* 3.0 33.5 + - + +
149A ALA* 1.3 78.4 - - - +
151A PRO* 1.3 59.4 - - + +
152A HIS 3.0 0.3 + - - -
153A ILE* 3.2 15.8 + - + -
154A LYS* 2.7 92.7 + - + +
157A PHE* 4.6 2.7 - + + -
158A GLN* 4.0 12.1 - - + -
171A CYS* 4.4 7.9 - - - -
172A ASP* 3.9 11.7 + - - -
173A TRP* 3.5 61.3 - + + +
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Residues in contact with PRO 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 LYS* 3.3 13.5 - - + +
148A GLU* 3.6 13.7 - - - +
150A TRP* 1.3 96.8 - - + +
152A HIS* 1.3 67.7 + - + +
154A LYS* 4.0 15.9 + - + +
155A THR* 4.8 6.2 + - - -
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Residues in contact with HIS 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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68A PRO* 3.3 31.4 - - + +
70A ARG* 3.7 21.1 + - - +
95A GLY 5.4 1.1 + - - -
97A ILE* 3.6 24.5 - - + -
122A LEU* 5.2 3.9 - - + +
148A GLU* 3.6 23.5 + - - +
149A ALA* 4.4 0.7 - - - -
150A TRP 3.1 1.2 - - - -
151A PRO* 1.3 85.8 - - + +
153A ILE* 1.3 60.4 + - - +
154A LYS 3.4 0.2 - - - -
155A THR* 4.7 1.6 + - - -
156A ILE* 3.4 21.0 - - - +
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Residues in contact with ILE 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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6A ILE* 5.7 2.0 - - + -
70A ARG* 3.8 12.3 - - + +
97A ILE* 3.7 26.7 - - + -
99A ILE* 4.4 8.7 - - + -
124A VAL* 3.8 35.9 - - + -
143A PRO* 4.5 0.4 - - + -
149A ALA 3.2 19.5 + - - +
150A TRP* 3.6 20.0 - - + +
152A HIS* 1.3 75.1 - - - +
154A LYS* 1.3 65.8 + - - +
155A THR 3.4 2.5 - - - -
156A ILE* 3.5 7.5 + - + +
157A PHE* 3.1 49.1 + - + +
173A TRP* 4.4 2.2 - - + -
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Residues in contact with LYS 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 TRP* 2.7 65.3 + - + +
151A PRO* 4.1 10.8 - - + +
152A HIS 3.4 1.4 - - - -
153A ILE* 1.3 73.4 - - - +
155A THR* 1.3 66.3 + - - +
157A PHE* 4.4 0.2 - - - +
158A GLN* 3.3 55.6 + - - +
172A ASP* 4.6 5.7 + - - -
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Residues in contact with THR 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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27A PHE* 4.4 16.3 - - + -
151A PRO 4.8 6.3 + - - -
152A HIS 4.7 1.7 + - - -
153A ILE 3.4 0.8 - - - -
154A LYS* 1.3 80.7 - - - +
156A ILE* 1.3 69.1 + - + +
158A GLN* 4.6 2.1 - - - +
159A GLY* 3.3 18.9 + - - -
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Residues in contact with ILE 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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5A ASP* 5.5 7.2 - - + -
6A ILE* 5.0 16.8 - - + -
22A MET* 4.2 28.5 - - + -
27A PHE* 3.8 37.0 - - + -
70A ARG* 4.4 17.9 - - - +
152A HIS 3.4 25.4 - - - +
153A ILE* 3.5 6.7 + - + +
154A LYS 3.3 0.2 - - - -
155A THR* 1.3 83.3 - - - +
157A PHE* 1.3 74.3 + - + +
159A GLY* 3.3 8.5 + - - -
160A ILE* 3.4 15.5 + - + +
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Residues in contact with PHE 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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6A ILE* 5.8 1.8 - - + -
72A ILE* 4.0 21.8 - - + -
99A ILE* 3.7 33.0 - - + -
124A VAL* 4.8 0.2 - - + -
126A SER* 4.2 11.2 - - - -
141A LEU* 3.6 24.0 - - + +
143A PRO* 3.5 30.1 - - + -
150A TRP* 4.6 2.5 - + + -
153A ILE* 3.1 43.6 + - + +
154A LYS 4.4 0.9 - - - +
156A ILE* 1.3 88.0 - - + +
158A GLN* 1.3 58.9 + - - +
159A GLY 3.2 0.3 + - - -
160A ILE* 3.4 10.2 + - + +
161A ALA* 3.0 28.2 + - - +
171A CYS* 3.6 15.5 - - - -
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Residues in contact with GLN 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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150A TRP* 4.0 8.6 - - + -
154A LYS* 3.3 51.5 + - - +
155A THR* 4.6 2.1 - - - +
157A PHE* 1.3 77.3 - - - +
159A GLY* 1.3 62.6 + - - +
161A ALA* 3.6 15.4 + - - +
163A LYS* 3.7 12.0 + - - +
169A PRO* 3.6 30.5 - - + +
171A CYS* 2.9 33.1 + - + +
172A ASP* 4.1 7.5 + - - +
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Residues in contact with GLY 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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25A HIS* 3.1 25.6 + - - -
27A PHE* 5.2 7.0 - - - -
155A THR 3.3 13.2 + - - -
156A ILE 3.3 7.4 + - - -
157A PHE 3.1 1.2 - - - -
158A GLN* 1.3 78.9 - - - +
160A ILE* 1.3 59.0 + - - +
163A LYS* 3.5 13.1 + - - -
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Residues in contact with ILE 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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18A LEU* 4.1 24.0 - - + -
21A ASN* 3.4 31.8 + - - +
22A MET* 3.6 49.4 - - + -
25A HIS* 3.9 10.9 + - + -
27A PHE* 5.1 2.7 - - + -
137A TYR 4.1 2.1 - - - +
138A GLY* 3.2 18.4 + - - -
139A PRO* 3.3 4.7 - - + +
141A LEU* 4.1 15.9 - - + -
156A ILE 3.4 10.9 + - - +
157A PHE* 3.4 15.7 - - + +
159A GLY* 1.3 75.2 - - - +
161A ALA* 1.3 67.8 + - - +
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Residues in contact with ALA 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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137A TYR 5.2 0.7 - - - +
138A GLY* 4.4 0.5 - - - -
139A PRO* 3.4 16.8 - - - +
141A LEU* 4.5 4.0 - - + -
157A PHE 3.0 18.3 + - - +
158A GLN* 4.0 6.7 - - - +
159A GLY 3.4 1.2 - - - -
160A ILE* 1.3 82.3 - - - +
162A ALA* 1.3 66.3 + - - +
163A LYS* 2.9 25.8 + - - -
169A PRO* 5.0 0.7 - - + -
170A CYS 4.3 3.8 - - - +
171A CYS* 3.6 26.5 - - + -
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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