Contacts of the helix formed by residues 149 - 161 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B ILE* 3.7 17.3 - - + -
122B LEU* 3.7 29.5 - - + +
124B VAL* 3.7 20.2 - - + -
146B ASN* 3.1 12.6 + - - +
148B GLU* 1.3 77.4 - - - +
150B TRP* 1.3 63.8 + - - +
151B PRO 3.4 0.7 - - - -
152B HIS* 3.3 4.6 + - - +
153B ILE* 3.2 25.9 + - - +
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Residues in contact with TRP 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B PRO* 3.8 20.0 - - + -
146B ASN 4.0 1.8 + - - -
147B LYS* 3.0 27.2 + - + +
149B ALA* 1.3 77.4 - - - +
151B PRO* 1.3 60.9 - - + +
153B ILE* 3.9 17.2 - - + +
154B LYS* 2.9 70.6 + - + +
157B PHE* 4.9 0.4 - - + -
158B GLN* 3.5 24.7 - - + -
171B CYS* 3.9 13.5 - - - -
172B ASP* 3.5 38.4 + - - -
173B TRP* 3.9 38.2 - + + +
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Residues in contact with PRO 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B LYS* 3.3 13.2 - - + +
148B GLU* 3.3 14.4 - - - +
149B ALA 3.6 0.2 - - - -
150B TRP* 1.3 96.6 - - + +
152B HIS* 1.3 67.4 + - + +
154B LYS* 4.3 10.7 + - + +
155B THR* 4.3 10.0 + - - -
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Residues in contact with HIS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PRO* 3.4 37.4 - - + +
70B ARG* 3.1 32.2 + - - +
95B GLY 5.9 0.2 - - - -
97B ILE* 3.7 25.2 - - + +
122B LEU* 5.2 5.6 - - + -
148B GLU* 3.7 22.6 + - + -
149B ALA* 3.9 2.2 + - - +
150B TRP 3.1 0.6 - - - -
151B PRO* 1.3 87.2 - - + +
153B ILE* 1.3 63.4 + - - +
154B LYS 3.3 0.8 + - - -
155B THR* 4.0 10.4 + - - -
156B ILE 4.7 0.7 + - - -
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Residues in contact with ILE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 5.9 1.3 - - + -
70B ARG* 4.2 10.3 - - - +
97B ILE* 4.2 17.0 - - + -
99B ILE* 3.6 26.0 - - + -
124B VAL* 4.0 34.8 - - + -
143B PRO* 4.7 6.3 - - + -
149B ALA 3.2 19.9 + - - +
150B TRP* 3.8 23.6 - - + +
152B HIS* 1.3 74.9 - - - +
154B LYS* 1.3 61.3 + - - +
155B THR 3.2 3.3 + - - -
156B ILE* 3.4 4.2 + - - +
157B PHE* 2.9 48.5 + - + +
173B TRP* 4.9 1.1 - - + -
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Residues in contact with LYS 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B TRP* 2.9 55.4 + - + +
151B PRO* 4.4 9.6 - - + +
152B HIS 3.3 0.8 - - - -
153B ILE* 1.3 77.7 - - - +
155B THR* 1.3 63.0 + - - +
158B GLN* 2.6 67.3 + - - +
172B ASP* 5.3 2.0 + - - -
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Residues in contact with THR 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B PHE* 4.3 17.6 - - + -
70B ARG* 5.6 1.6 - - - -
151B PRO 4.3 7.8 + - - -
152B HIS 4.0 10.5 + - - -
153B ILE 3.2 1.0 - - - -
154B LYS* 1.3 80.6 - - - +
156B ILE* 1.3 64.8 + - - +
158B GLN* 4.7 1.5 - - - +
159B GLY* 3.3 18.2 + - - -
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Residues in contact with ILE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ASP* 4.4 6.3 - - + -
6B ILE* 4.0 35.4 - - + -
22B MET* 3.8 33.4 - - + -
27B PHE* 3.9 37.7 - - + -
70B ARG* 3.6 31.4 - - - +
152B HIS 4.9 0.4 - - - +
153B ILE* 3.4 6.5 + - - +
155B THR* 1.3 78.1 - - + +
157B PHE* 1.3 71.0 + - + +
159B GLY* 3.4 0.9 + - - -
160B ILE* 3.2 26.1 + - + +
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Residues in contact with PHE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 5.1 2.5 - - + -
72B ILE* 4.0 20.0 - - + -
99B ILE* 3.7 44.0 - - + -
126B SER* 3.5 25.6 - - - -
141B LEU* 3.4 32.9 - - + +
143B PRO* 4.4 10.5 - - + -
150B TRP* 4.9 1.6 - - + -
153B ILE* 2.9 32.4 + - + +
154B LYS* 4.5 1.6 - - - +
156B ILE* 1.3 85.1 - - + +
158B GLN* 1.3 59.0 + - - +
160B ILE* 3.5 4.8 - - + +
161B ALA* 2.9 30.7 + - - +
171B CYS* 3.5 21.1 - - - -
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Residues in contact with GLN 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B TRP* 3.5 13.2 - - + -
154B LYS* 2.6 63.0 + - + +
155B THR* 4.7 1.0 - - - +
157B PHE* 1.3 76.3 - - - +
159B GLY* 1.3 60.9 + - - +
161B ALA* 3.6 4.3 + - - -
163B LYS* 3.2 18.7 + - - -
169B PRO* 3.4 34.6 - - + +
171B CYS* 3.4 27.1 - - - +
172B ASP* 4.7 2.8 - - - +
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Residues in contact with GLY 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B HIS* 3.0 29.3 + - - -
27B PHE* 5.4 4.5 - - - -
155B THR 3.3 15.2 + - - -
156B ILE* 3.8 3.4 - - - -
157B PHE 3.2 1.2 - - - -
158B GLN* 1.3 78.8 - - - +
160B ILE* 1.3 57.8 + - - +
163B LYS* 3.4 16.8 + - - -
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Residues in contact with ILE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 4.3 26.5 - - + +
21B ASN* 3.4 27.5 + - - +
22B MET* 3.6 45.5 - - + -
25B HIS* 4.0 10.3 - - + -
27B PHE* 4.7 2.0 - - + -
72B ILE* 6.1 2.5 - - + -
137B TYR 4.2 1.2 - - - +
138B GLY* 3.4 5.9 - - - -
139B PRO* 3.2 16.8 - - + +
141B LEU* 4.1 13.9 - - + -
156B ILE* 3.2 21.0 + - + +
157B PHE* 3.5 10.8 - - + +
159B GLY* 1.3 73.7 - - - +
161B ALA* 1.3 70.9 + - - +
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Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B TYR 5.0 0.9 - - - +
138B GLY* 3.9 2.0 - - - -
139B PRO* 3.4 14.6 - - - +
141B LEU* 4.0 6.3 - - + -
157B PHE 2.9 18.0 + - - +
158B GLN* 4.0 7.2 - - - +
159B GLY 3.4 1.4 - - - -
160B ILE* 1.3 81.9 - - - +
162B ALA* 1.3 65.6 + - - +
163B LYS* 2.8 22.9 + - - +
170B CYS 4.1 8.1 - - - +
171B CYS* 3.7 24.2 - - + -
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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