Contacts of the helix formed by residues 155 - 167 (chain B) in PDB entry 5OF4
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 CYS 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B HIS* 3.9 6.7 - - + +
137B LEU* 4.0 20.2 - - + -
138B THR* 3.5 19.1 - - + +
153B PRO 2.8 11.1 + - - +
154B HIS* 1.3 69.8 - - - +
156B ARG* 1.3 61.6 + - - +
157B PHE 3.3 1.3 - - - -
158B TYR* 3.3 30.8 + - + +
159B GLU* 3.8 13.5 + - - +
1000B SF4 2.3 39.3 - - - -
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Residues in contact with ARG 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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118B HIS* 5.7 0.2 - - + -
154B HIS* 3.2 16.0 + - + +
155B CYS* 1.3 75.3 - - - +
157B PHE* 1.3 72.1 + - + +
158B TYR 3.3 0.2 - - - -
159B GLU* 3.1 23.3 + - + +
160B GLU* 3.0 51.1 + - - +
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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
----------------------------------------------------------
117B ILE* 3.7 42.8 - - + -
118B HIS* 3.4 36.1 - + - -
156B ARG* 1.3 88.0 - - + +
158B TYR* 1.3 60.4 + - - +
159B GLU 3.2 0.4 - - - -
160B GLU* 3.5 13.0 - - + +
161B PHE 2.9 19.8 + - - -
184B GLY 5.4 4.3 - - - -
189B TRP* 3.0 45.6 - - + -
190B CYS* 3.6 20.0 - - - -
1000B SF4 3.4 20.6 - - - -
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Residues in contact with TYR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B THR* 4.0 25.5 - - + +
139B ALA* 5.8 2.3 - - - +
155B CYS* 3.3 28.1 + - + +
157B PHE* 1.3 81.2 - - - +
159B GLU* 1.3 61.1 + - + +
161B PHE* 3.2 17.8 + + - +
162B ASP* 2.9 46.6 + - - +
190B CYS* 4.9 4.4 - - - -
193B PHE* 3.5 53.6 - + - -
298B ALA* 4.5 16.8 - - - +
299B ARG* 5.2 3.9 - - + +
1000B SF4 5.0 1.8 - - - -
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Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B VAL* 6.1 0.9 - - - +
153B PRO 5.1 5.2 - - - +
155B CYS* 3.8 18.4 + - - +
156B ARG* 3.1 20.5 + - - +
158B TYR* 1.3 79.7 - - + +
160B GLU* 1.3 58.6 + - - +
162B ASP* 3.2 20.1 + - + +
163B ALA* 3.0 24.6 + - - +
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Residues in contact with GLU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG* 3.0 29.5 + - - +
157B PHE* 3.5 22.2 - - + +
158B TYR 3.3 0.2 - - - -
159B GLU* 1.3 74.2 - - - +
161B PHE* 1.3 58.3 - - - +
163B ALA* 3.3 10.6 + - - +
164B HIS* 3.0 51.8 + - - -
189B TRP* 3.3 33.7 - - + -
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Residues in contact with PHE 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 PHE 2.9 10.6 + - - +
158B TYR* 3.2 22.6 + + - +
160B GLU* 1.3 76.2 - - - +
162B ASP* 1.3 68.5 + - - +
164B HIS 5.5 0.7 - - - -
165B GLY* 2.7 44.2 + - - -
189B TRP* 3.4 24.1 - + - +
193B PHE* 3.2 55.0 - + + -
194B LEU* 4.5 2.0 - - - -
196B ARG* 5.0 7.9 - - + -
197B TYR* 4.1 16.6 - - + -
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Residues in contact with ASP 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 TYR* 2.9 35.2 + - - +
159B GLU* 3.2 27.9 + - + +
161B PHE* 1.3 87.9 - - - +
163B ALA* 1.3 62.5 + - - +
165B GLY* 3.9 0.8 - - - -
166B ARG* 3.0 44.1 + - - +
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Residues in contact with ALA 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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159B GLU 3.0 12.2 + - - +
160B GLU* 3.6 18.2 - - - +
161B PHE 3.2 0.2 - - - -
162B ASP* 1.3 76.5 - - - +
164B HIS* 1.3 66.8 + - + +
166B ARG* 3.2 18.7 + - - +
167B GLU* 3.0 25.7 + - - +
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Residues in contact with HIS 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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160B GLU* 3.0 32.3 + - - +
161B PHE* 3.7 1.6 - - - -
163B ALA* 1.3 76.0 - - + +
165B GLY* 1.3 58.9 + - - +
167B GLU* 2.9 54.6 + - + +
169B PRO* 3.6 27.3 - - + +
187B GLN* 6.5 0.4 - - + -
189B TRP* 3.2 36.4 - + + -
197B TYR* 4.5 5.8 - - - -
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Residues in contact with GLY 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B PHE* 2.7 39.3 + - - -
162B ASP* 3.9 1.6 - - - -
164B HIS* 1.3 71.6 - - - +
166B ARG* 1.3 64.1 + - - +
167B GLU 3.8 4.6 - - - +
197B TYR* 4.9 10.7 - - - -
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Residues in contact with ARG 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ASP* 3.0 44.0 + - - +
163B ALA* 3.4 14.1 - - - +
165B GLY* 1.3 78.4 - - - +
167B GLU* 1.3 60.9 + - + +
168B VAL* 5.0 2.4 - - - +
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Residues in contact with GLU 167 (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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163B ALA 3.0 18.2 + - - +
164B HIS* 2.9 49.9 + - + +
165B GLY 3.3 5.6 - - - +
166B ARG* 1.3 83.3 - - + +
168B VAL* 1.3 71.0 + - - +
169B PRO* 3.9 1.3 - - + +
197B TYR* 4.1 6.4 + - - -
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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