Contacts of the helix formed by residues 155 - 165 (chain B) in PDB entry 5HVO
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 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B TRP* 3.7 12.8 - - + -
125B TYR* 3.8 21.7 + - + +
126B ARG* 3.3 41.1 - - + +
129B ASN* 3.5 15.8 + - + +
153B LEU 3.3 0.6 - - - -
154B MET* 1.3 78.7 - - - +
156B LEU* 1.3 62.7 + - - +
157B PRO 3.5 0.7 - - - -
158B GLU* 3.4 12.9 + - - +
159B LEU* 3.1 29.2 + - + +
196B GLN* 3.7 26.5 - - + +
197B LEU* 4.2 11.2 - - + -
200B GLY* 4.2 5.8 - - - -
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Residues in contact with LEU 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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16B VAL* 3.8 24.9 - - + -
129B ASN* 3.3 20.5 + - - +
132B PHE* 3.8 5.4 - - + -
133B ALA* 3.6 30.5 - - + +
136B ILE* 4.1 6.7 - - + -
148B VAL* 3.5 27.6 - - + -
153B LEU* 3.3 23.3 - - + +
154B MET 3.2 0.2 - - - -
155B LEU* 1.3 75.1 - - - +
157B PRO* 1.3 61.0 - - + +
159B LEU* 3.1 5.2 + - - -
160B LEU* 2.6 54.1 + - + +
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Residues in contact with PRO 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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148B VAL* 4.6 5.4 - - + -
153B LEU 3.5 9.9 - - - +
154B MET* 3.7 11.0 - - - +
156B LEU* 1.3 94.1 - - + +
158B GLU* 1.3 61.9 + - - +
160B LEU* 3.2 8.9 + - + +
161B ARG* 3.0 27.0 + - - +
174B ILE* 4.2 17.1 - - + +
176B PHE* 4.4 11.9 - - + -
200B GLY 3.4 8.7 - - - +
201B VAL* 4.4 1.8 - - - -
203B HIS* 4.0 4.0 - - + +
204B CYS* 3.4 41.7 - - - +
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Residues in contact with GLU 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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155B LEU* 3.4 12.3 + - - +
156B LEU 3.2 0.2 - - - -
157B PRO* 1.3 74.8 - - - +
159B LEU* 1.3 68.3 + - + +
161B ARG* 3.3 4.7 + - - +
162B ALA* 3.3 19.2 + - - +
196B GLN 4.3 3.1 - - - +
199B ARG* 3.6 8.8 + - - +
200B GLY* 3.1 35.4 + - - +
203B HIS* 3.4 42.0 - - + +
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ARG* 4.3 3.8 - - - +
129B ASN* 3.5 19.1 - - + +
130B LEU* 3.5 46.7 - - + +
133B ALA* 3.8 14.6 - - + -
155B LEU* 3.1 20.9 + - + +
156B LEU* 3.1 6.9 + - - +
158B GLU* 1.3 81.1 - - + +
160B LEU* 1.3 63.3 + - - +
162B ALA* 3.3 9.5 + - + +
163B GLU* 3.1 26.3 + - - +
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Residues in contact with LEU 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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133B ALA* 4.1 27.3 - - - +
136B ILE* 4.2 20.0 - - + -
137B VAL* 4.9 2.9 - - + +
146B ILE* 3.8 33.0 - - + -
148B VAL* 4.2 9.0 - - + -
156B LEU* 2.6 42.8 + - + +
157B PRO 3.4 5.4 - - - +
159B LEU* 1.3 73.0 - - - +
161B ARG* 1.3 57.5 + - - +
163B GLU* 3.3 2.9 + - - +
164B LEU* 2.8 41.8 + - + +
174B ILE* 3.8 19.7 - - + -
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Residues in contact with ARG 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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157B PRO 3.0 19.8 + - - +
158B GLU 3.7 6.5 - - - +
159B LEU 3.3 0.4 - - - -
160B LEU* 1.3 74.2 - - - +
162B ALA* 1.3 64.3 + - - +
164B LEU* 3.3 10.5 + - - +
165B ARG* 3.1 31.2 + - + +
172B ASN 3.1 24.2 + - - -
174B ILE* 3.3 26.9 - - - +
203B HIS* 2.8 47.9 + - + -
204B CYS 4.1 0.2 - - - -
205B ASP* 3.1 31.7 + - - +
240B ARG* 3.8 21.5 - - - +
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Residues in contact with ALA 162 (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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158B GLU 3.3 8.9 + - - +
159B LEU* 3.3 14.0 + - + +
161B ARG* 1.3 78.7 - - - +
163B GLU* 1.3 58.6 + - + +
165B ARG* 2.6 32.1 + - - +
166B ALA* 3.9 6.8 - - - +
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Residues in contact with GLU 163 (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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130B LEU* 4.4 13.6 - - + +
133B ALA* 4.0 21.8 - - + +
134B LYS* 4.2 27.2 + - - +
137B VAL* 3.4 31.5 - - + +
159B LEU 3.1 16.5 + - - +
160B LEU* 3.8 4.7 - - - +
162B ALA* 1.3 76.5 - - + +
164B LEU* 1.3 56.2 + - - +
165B ARG 2.8 15.7 - - - +
166B ALA* 4.2 1.5 - - - +
167B ALA* 3.2 17.7 + - - +
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Residues in contact with LEU 164 (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 VAL* 4.1 19.7 - - + -
140B ALA* 4.1 17.0 - - + -
146B ILE* 4.4 12.8 - - + -
160B LEU* 2.8 28.9 + - + +
161B ARG* 3.3 10.5 + - - +
163B GLU* 1.3 72.6 - - - +
165B ARG* 1.3 62.1 + - + +
167B ALA* 3.2 5.6 + - - +
168B GLY 3.0 21.0 + - - -
169B LYS* 3.1 27.1 + - + +
172B ASN* 3.4 44.0 - - + +
174B ILE* 4.4 13.5 - - + -
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Residues in contact with ARG 165 (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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161B ARG* 3.1 16.3 + - - +
162B ALA* 2.6 24.7 + - - +
163B GLU 2.8 10.7 - - - +
164B LEU* 1.3 72.6 - - + +
166B ALA* 1.3 64.5 + - - +
167B ALA 2.9 5.2 - - - -
168B GLY* 4.2 3.6 - - - +
169B LYS 4.7 3.8 - - - +
170B LYS* 4.8 17.2 - - - +
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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