Contacts of the helix formed by residues 151 - 169 (chain D) in PDB entry 1OXQ
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PHE* 3.9 6.1 - - - -
127D CYS* 3.6 21.3 - - + +
144D HIS* 3.5 1.8 - - - +
148D PHE* 3.1 17.2 + - - +
149D PRO 3.3 0.8 - - - -
150D SER* 1.3 74.6 + - - +
152D GLN* 1.3 61.2 + - - +
153D PHE* 3.4 12.8 - - - -
154D LEU* 3.4 24.9 - - + +
155D LEU* 2.8 29.3 + - - +
1004D ZN 2.4 35.2 - - - -
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Residues in contact with GLN 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D LEU* 3.8 25.6 - - + +
76D SER 2.7 28.8 + - - -
77D ARG* 3.7 32.0 + - - +
126D PHE* 3.5 28.9 - - + -
150D SER 3.1 7.6 + - - +
151D CYS* 1.3 71.8 - - - +
153D PHE* 1.3 61.7 + - - +
155D LEU* 3.8 10.8 - - + +
156D ARG* 2.9 42.7 + - + +
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Residues in contact with PHE 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D GLY 5.9 0.4 - - - -
90D ARG* 4.2 9.0 - - - -
110D ALA 4.0 8.5 - - - -
111D ALA 3.7 4.0 - - - -
112D GLY* 3.4 26.5 - - - -
124D CYS* 4.6 0.9 - - - -
125D PHE* 3.6 30.7 - + - -
126D PHE* 3.6 30.1 - - + -
141D TRP* 3.4 24.7 - + - -
144D HIS* 4.3 7.0 - + - -
151D CYS* 3.2 2.5 - - - -
152D GLN* 1.3 75.7 - - - +
154D LEU* 1.3 64.3 + - - +
156D ARG* 3.4 20.6 + - - +
157D SER* 2.6 46.7 + - - -
160E ARG* 5.4 3.8 - - - -
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Residues in contact with LEU 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D TRP* 3.9 44.9 - - + +
144D HIS* 3.7 14.6 - - + +
145D ALA* 3.6 24.2 - - + +
148D PHE 3.2 26.9 - - - +
149D PRO 4.2 6.1 - - - +
151D CYS* 3.3 16.3 + - + +
153D PHE* 1.3 79.6 - - - +
155D LEU* 1.3 54.6 + - - +
157D SER* 3.2 0.5 + - - -
158D LYS* 2.7 46.5 + - + +
162D PHE* 4.5 0.7 - - + -
163D VAL* 3.7 24.5 - - + -
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Residues in contact with LEU 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A TRP* 6.6 0.2 - - + -
75D LEU* 6.0 1.1 - - + -
149D PRO 3.8 18.6 - - - +
150D SER* 4.0 13.5 - - - +
151D CYS 2.8 18.7 + - - +
152D GLN* 3.8 9.9 - - + +
154D LEU* 1.3 76.6 - - + +
156D ARG* 1.3 58.5 + - + +
159D GLY* 2.7 31.7 + - - +
160D ARG* 3.9 27.8 + - + +
163D VAL* 3.6 28.7 - - + -
155E LEU 4.8 0.5 - - - +
156E ARG* 4.4 5.0 - - - +
159E GLY* 4.2 1.0 - - - -
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Residues in contact with ARG 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D ARG* 5.9 4.0 - - - +
125D PHE* 5.4 2.2 - - - -
126D PHE* 3.2 39.6 - - - -
152D GLN* 2.9 29.2 + - + +
153D PHE* 3.9 22.7 - - - +
155D LEU* 1.3 74.0 - - + +
157D SER* 1.3 57.2 + - - +
155E LEU 4.5 3.2 - - - +
156E ARG* 6.3 1.1 - - - +
159E GLY* 3.4 2.6 - - - -
160E ARG* 2.9 70.7 + - + +
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Residues in contact with SER 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D TRP* 3.5 27.2 - - - -
153D PHE* 2.6 43.5 + - - -
154D LEU 3.9 0.2 - - - -
156D ARG* 1.3 78.1 - - - +
158D LYS* 1.3 60.5 + - - +
158E LYS 4.5 0.5 - - - +
159E GLY* 3.5 1.6 - - - -
160E ARG* 3.4 16.4 + - - +
161E ASP* 3.3 41.3 + - - +
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Residues in contact with LYS 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D TRP* 3.4 59.5 - - + +
154D LEU* 2.7 19.4 + - + +
157D SER* 1.3 78.1 - - - +
159D GLY* 1.3 61.5 + - - +
162D PHE* 3.3 47.9 + - + +
158E LYS* 3.3 15.3 - - - +
161E ASP* 2.9 37.5 + - - +
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Residues in contact with GLY 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D LEU* 2.7 29.1 + - - -
158D LYS* 1.3 77.2 - - - +
160D ARG* 1.3 64.6 + - - -
161D ASP 3.2 3.4 + - - -
163D VAL* 3.4 21.8 + - - +
156E ARG 3.5 3.8 - - - -
157E SER 3.4 5.6 - - - -
159E GLY* 3.3 20.1 - - - -
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Residues in contact with ARG 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D LEU* 3.9 20.7 - - + +
159D GLY* 1.3 69.8 - - - -
161D ASP* 1.3 65.6 + - - +
163D VAL* 3.3 1.8 + - + +
164D HIS* 2.8 39.3 + - + +
153E PHE* 4.7 15.0 - - - -
156E ARG* 3.0 53.2 + - - +
157E SER* 3.3 18.5 + - - -
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Residues in contact with ASP 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ARG* 1.3 82.7 + - - +
162D PHE* 1.3 58.0 + - - +
164D HIS* 3.3 6.0 + - - +
165D SER* 2.8 31.4 + - - -
110E ALA* 6.1 0.3 - - - +
141E TRP* 3.3 32.4 + - - -
157E SER* 3.0 28.2 + - - +
158E LYS* 4.0 13.1 + - + +
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Residues in contact with PHE 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D ASP* 4.8 1.6 - - - -
141D TRP* 3.7 26.0 - - + -
142D THR* 3.8 26.9 - - - -
145D ALA* 3.8 14.6 - - + -
154D LEU* 4.5 1.1 - - + -
158D LYS* 3.3 51.9 + - + +
159D GLY 3.5 1.9 + - - +
161D ASP* 1.3 77.5 - - - +
163D VAL* 1.3 61.5 + - + +
165D SER* 3.2 10.0 + - - -
166D VAL* 2.9 41.6 + - + +
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Residues in contact with VAL 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D ALA* 4.1 16.4 - - + +
149D PRO* 3.6 41.7 - - + +
154D LEU* 3.7 30.1 - - + +
155D LEU* 3.6 20.2 - - + -
158D LYS* 5.1 0.2 - - + -
159D GLY 3.4 14.6 + - - +
160D ARG* 3.3 6.4 + - + +
161D ASP 3.3 0.4 - - - -
162D PHE* 1.3 78.5 - - + +
164D HIS* 1.3 58.3 + - - +
166D VAL* 3.3 2.3 + - - +
167D GLN* 2.8 31.2 + - + +
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Residues in contact with HIS 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ARG* 2.8 28.4 + - + +
161D ASP* 3.7 6.1 - - - +
163D VAL* 1.3 73.6 - - - +
165D SER* 1.3 57.8 + - - +
167D GLN* 3.2 9.4 + - + +
168D GLU* 2.9 60.1 + - + +
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Residues in contact with SER 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D ASP 2.8 21.7 + - - -
162D PHE* 3.3 11.1 + - - -
164D HIS* 1.3 75.8 + - - +
166D VAL* 1.3 65.6 + - - +
168D GLU* 3.4 10.2 + - - +
169D THR* 3.3 28.4 + - - +
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Residues in contact with VAL 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D THR* 3.6 39.3 - - + +
145D ALA* 3.9 3.8 - - + -
146D LYS* 3.6 25.1 - - + +
162D PHE* 2.9 49.2 + - + +
163D VAL 3.8 3.4 - - - +
165D SER* 1.3 77.6 + - - +
167D GLN* 1.3 65.1 + - - +
169D THR* 3.2 27.4 + - - +
170D HIS 4.6 3.3 - - - +
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Residues in contact with GLN 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PRO* 5.2 2.8 - - - +
167A GLN* 4.4 11.5 - - - +
145D ALA 2.8 24.4 + - - +
146D LYS* 2.9 24.7 + - - +
149D PRO* 3.8 30.1 - - + +
163D VAL* 2.8 25.7 + - + +
164D HIS* 3.6 10.1 - - + +
166D VAL* 1.3 72.9 - - - +
168D GLU* 1.3 61.2 + - - +
169D THR 3.7 0.2 + - - -
170D HIS* 3.8 13.4 + - - +
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Residues in contact with GLU 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D HIS* 2.9 43.2 + - + +
165D SER* 3.7 9.5 - - - +
166D VAL 3.2 0.2 - - - -
167D GLN* 1.3 73.7 - - - +
169D THR* 1.3 58.3 + - + +
170D HIS* 2.8 22.3 + - - +
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Residues in contact with THR 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LYS* 6.0 0.2 - - - +
165D SER 3.3 14.0 + - - +
166D VAL* 3.2 19.8 + - - +
168D GLU* 1.3 73.3 - - + +
170D HIS* 1.3 72.9 + - - +
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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
------------------------------------------------------------
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