Contacts of the helix formed by residues 151 - 170 (chain B) in PDB entry 1OXN
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 151 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B CYS* 3.8 1.6 - - - -
126B PHE* 4.0 5.4 - - - -
127B CYS* 3.6 20.3 - - + +
144B HIS* 3.5 1.6 - - - +
148B PHE* 3.1 17.5 + - - +
149B PRO 3.3 0.4 - - - -
150B SER* 1.3 77.0 + - - +
152B GLN* 1.3 59.6 + - - +
153B PHE* 3.5 13.5 - - - -
154B LEU* 3.4 25.1 - - + +
155B LEU* 2.8 28.3 + - - +
1002B ZN 2.2 36.8 - - - -
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Residues in contact with GLN 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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75B LEU* 3.5 29.9 - - + +
76B SER 2.8 24.4 + - - -
77B ARG* 3.7 31.7 + - - +
126B PHE* 3.4 33.2 - - + -
150B SER 3.1 10.0 + - - +
151B CYS* 1.3 70.8 - - - +
153B PHE* 1.3 60.3 + - - +
155B LEU* 3.8 10.3 - - + +
156B ARG* 2.7 32.2 + - - +
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Residues in contact with PHE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLY 5.6 1.8 - - - -
90B ARG* 3.8 15.7 - - - -
110B ALA 3.8 11.9 - - - -
111B ALA 4.2 2.5 - - - -
112B GLY* 3.3 26.9 - - - -
124B CYS* 4.7 0.7 - - - -
125B PHE* 3.5 27.4 - + + -
126B PHE* 3.6 29.2 - - + -
141B TRP* 3.4 20.9 - + - -
144B HIS* 4.4 5.2 - + - -
151B CYS* 3.2 3.2 - - - -
152B GLN* 1.3 75.3 - - - +
154B LEU* 1.3 63.3 + - - +
156B ARG* 3.5 14.1 + - - +
157B SER* 2.8 49.8 + - - -
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Residues in contact with LEU 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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141B TRP* 3.7 33.4 - - + +
144B HIS* 3.8 12.8 - - + +
145B ALA* 3.6 35.9 - - + +
148B PHE 3.3 25.4 - - - +
149B PRO* 4.0 8.1 - - + +
151B CYS* 3.2 18.0 + - + +
153B PHE* 1.3 80.0 - - - +
155B LEU* 1.3 52.5 + - - +
157B SER* 3.1 0.9 + - - -
158B LYS* 2.8 43.6 + - + +
163B VAL* 3.6 24.7 - - + -
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 5.7 2.2 - - + -
149B PRO 3.6 18.6 - - - +
150B SER* 3.8 15.0 - - - +
151B CYS 2.8 19.0 + - - +
152B GLN* 3.8 9.6 - - + +
154B LEU* 1.3 76.4 - - - +
156B ARG* 1.3 59.4 + - - +
159B GLY* 2.8 30.8 + - - +
160B ARG* 3.8 34.7 + - + -
163B VAL* 3.7 26.5 - - + -
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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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77B ARG* 5.6 5.7 - - - +
152B GLN 2.7 22.6 + - - +
153B PHE* 3.8 15.3 - - - +
155B LEU* 1.3 73.8 - - - +
157B SER* 1.3 63.6 + - - +
159B GLY* 4.6 1.2 + - - -
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Residues in contact with SER 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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141B TRP* 3.3 33.3 - - - -
153B PHE* 2.8 40.4 + - - -
154B LEU 3.1 0.4 + - - -
156B ARG* 1.3 80.8 - - - +
158B LYS* 1.3 63.9 + - - +
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Residues in contact with LYS 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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141B TRP* 3.5 56.6 - - + +
154B LEU* 2.8 19.6 + - + +
157B SER* 1.3 78.6 - - - +
159B GLY* 1.3 61.7 + - - +
162B PHE* 3.3 66.5 + - + +
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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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155B LEU* 2.8 22.6 + - - -
156B ARG 4.5 0.6 + - - -
157B SER 3.7 1.0 - - - -
158B LYS* 1.3 82.5 - - - +
160B ARG* 1.3 65.7 + - - -
161B ASP 3.3 3.3 + - - -
162B PHE 3.5 0.3 + - - -
163B VAL* 3.4 21.1 + - - +
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Residues in contact with ARG 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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155B LEU* 3.8 25.7 + - + +
159B GLY* 1.3 70.1 - - - -
161B ASP* 1.3 65.9 + - - +
163B VAL* 3.2 1.7 + - - +
164B HIS* 2.8 34.0 + - + +
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Residues in contact with ASP 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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159B GLY 3.3 1.2 - - - -
160B ARG* 1.3 81.4 - - - +
162B PHE* 1.3 54.5 + - - +
164B HIS* 3.6 5.9 - - - +
165B SER* 2.7 42.6 + - - +
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Residues in contact with PHE 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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139B ASP* 4.9 1.1 - - - -
141B TRP* 3.5 34.3 - - + -
142B THR* 4.0 10.1 - - - -
145B ALA* 3.6 16.8 - - + -
154B LEU* 4.4 0.9 - - + -
158B LYS* 3.3 67.0 + - + +
159B GLY 3.5 3.0 + - - +
160B ARG 3.3 0.2 - - - -
161B ASP* 1.3 78.3 - - - +
163B VAL* 1.3 60.0 + - + +
165B SER* 3.3 6.8 + - - -
166B VAL* 2.8 49.5 + - + +
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ALA* 4.0 11.8 - - + +
149B PRO* 3.5 41.5 - - + +
154B LEU* 3.6 37.5 - - + +
155B LEU* 3.7 15.9 - - + -
159B GLY 3.4 13.9 + - - +
160B ARG 3.2 6.8 + - - +
162B PHE* 1.3 77.6 - - + +
164B HIS* 1.3 58.7 + - - +
166B VAL* 3.3 2.4 + - - +
167B GLN* 2.9 31.2 + - + +
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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 ARG* 2.8 22.4 + - + +
161B ASP* 3.6 6.2 + - - +
163B VAL* 1.3 75.7 - - - +
165B SER* 1.3 62.6 + - - +
167B GLN* 3.2 8.9 + - + +
168B GLU* 2.9 67.4 + - + +
171C SER* 5.0 12.8 + - - -
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Residues in contact with SER 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ASP* 2.7 29.4 + - - +
162B PHE* 3.6 7.1 - - - -
164B HIS* 1.3 74.0 + - - +
166B VAL* 1.3 61.9 + - - +
168B GLU* 3.3 13.5 + - - +
169B THR* 2.9 34.0 + - - +
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Residues in contact with VAL 166 (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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142B THR* 3.5 33.4 - - + +
145B ALA* 3.7 7.9 - - + -
146B LYS* 3.6 21.3 - - + +
162B PHE* 2.8 51.9 + - + +
163B VAL 3.8 0.2 - - - +
165B SER* 1.3 76.1 - - - +
167B GLN* 1.3 57.7 + - - +
169B THR* 3.3 6.0 + - - -
170B HIS* 2.8 43.0 + - + +
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Residues in contact with GLN 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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145B ALA 2.8 23.6 + - - -
146B LYS* 2.9 24.4 + - - +
149B PRO* 3.7 29.5 - - + +
163B VAL* 2.9 22.3 + - + +
164B HIS* 3.6 9.4 - - + +
166B VAL* 1.3 77.7 - - - +
168B GLU* 1.3 61.9 + - + +
169B THR 3.5 0.2 + - - -
170B HIS 3.7 10.0 + - - +
171B SER* 3.8 21.1 + - - -
149C PRO* 5.3 2.4 - - - +
167C GLN* 4.4 11.3 - - - +
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Residues in contact with GLU 168 (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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164B HIS* 2.9 56.1 + - + +
165B SER* 3.8 13.7 + - - +
166B VAL 3.3 0.2 - - - -
167B GLN* 1.3 77.1 - - + +
169B THR* 1.3 64.8 + - + +
171B SER 4.5 7.9 - - - -
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Residues in contact with THR 169 (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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165B SER* 2.9 20.7 + - - +
166B VAL* 3.3 2.3 + - - +
168B GLU* 1.3 82.7 - - + +
170B HIS* 1.3 90.3 + - - +
171B SER 3.6 2.0 + - - -
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Residues in contact with HIS 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B THR* 3.7 28.2 - - + +
146B LYS* 4.2 41.8 - - + +
166B VAL* 2.8 24.5 + - + +
167B GLN* 3.8 7.9 + - - +
168B GLU 3.5 0.2 - - - -
169B THR* 1.3 110.0 + - - +
171B SER* 1.3 70.7 + - - +
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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