Contacts of the helix formed by residues 151 - 168 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A LEU* 5.5 0.2 - - - -
124A CYS* 4.0 1.3 - - - -
126A PHE* 4.0 4.5 - - - -
127A CYS* 3.6 19.4 - - + +
144A HIS* 3.5 4.5 - - - +
148A PHE* 3.0 16.6 + - - +
149A PRO 3.4 0.6 - - - -
150A SER* 1.3 75.1 + - - +
152A GLN* 1.3 64.8 + - - +
153A PHE* 3.3 22.9 - - - -
154A LEU* 3.2 14.5 + - + +
155A LEU* 3.1 22.2 + - - +
1001A ZN 2.2 37.0 - - - -
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Residues in contact with GLN 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 3.6 34.5 - - + +
76A SER 2.7 24.7 + - - +
77A ARG* 3.6 30.5 + - - +
126A PHE* 3.2 33.2 - - + -
150A SER 3.0 4.9 + - - +
151A CYS* 1.3 73.1 - - - +
153A PHE* 1.3 57.1 + - - +
155A LEU* 3.8 8.8 - - + +
156A ARG* 3.1 46.0 + - - +
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Residues in contact with PHE 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLY 5.8 0.7 - - - -
90A ARG* 4.1 13.9 - - - -
110A ALA 3.8 13.0 - - - -
111A ALA 3.7 2.5 - - - -
112A GLY* 3.4 25.1 - - - -
124A CYS* 4.6 0.7 - - - -
125A PHE* 3.6 28.5 - + + -
126A PHE* 3.7 29.9 - + + -
141A TRP* 3.4 22.4 - + - -
144A HIS* 4.2 6.3 - + - -
151A CYS* 3.1 4.8 - - - -
152A GLN* 1.3 77.6 - - - +
154A LEU* 1.3 65.1 + - - +
156A ARG* 3.5 5.3 + - + +
157A SER* 2.9 46.9 + - - -
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TRP* 3.6 46.0 - - + +
144A HIS* 3.7 14.4 - - + +
145A ALA* 3.5 28.7 - - + +
148A PHE 3.6 20.2 - - - +
149A PRO* 4.2 7.6 - - + +
151A CYS* 3.2 16.0 + - + +
153A PHE* 1.3 78.3 - - - +
155A LEU* 1.3 57.9 + - - +
157A SER* 3.9 0.3 - - - -
158A LYS* 2.8 43.0 + - + +
162A PHE* 4.3 0.9 - - + -
163A VAL* 3.8 21.0 - - + +
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 5.9 0.9 - - + -
149A PRO 3.6 20.6 - - - +
150A SER* 3.7 14.1 - - - +
151A CYS 3.1 17.8 + - - +
152A GLN* 4.0 9.2 - - + +
153A PHE 3.2 0.2 - - - -
154A LEU* 1.3 75.4 - - + +
156A ARG* 1.3 60.8 + - - +
159A GLY* 2.9 30.1 + - - +
160A ARG* 3.5 56.0 + - - +
163A VAL* 3.6 22.7 - - + -
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Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ARG* 3.8 31.6 - - - +
152A GLN* 3.1 34.2 + - - +
153A PHE* 4.0 7.4 - - + +
154A LEU 3.5 0.2 - - - -
155A LEU* 1.3 76.8 - - - +
157A SER* 1.3 61.5 + - - +
159A GLY* 4.7 1.2 + - - -
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Residues in contact with SER 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A TRP* 3.4 26.5 - - - -
153A PHE* 2.9 41.2 + - - -
154A LEU 3.9 0.2 - - - -
156A ARG* 1.3 80.2 - - - +
158A LYS* 1.3 65.0 + - - +
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Residues in contact with LYS 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TRP* 3.7 57.4 - - + +
154A LEU* 2.8 17.1 + - + +
157A SER* 1.3 79.7 - - - +
159A GLY* 1.3 60.7 + - - +
162A PHE* 3.4 63.6 + - + +
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Residues in contact with GLY 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A LEU 3.9 0.2 + - - -
155A LEU* 2.9 25.3 + - - -
156A ARG 4.6 0.8 - - - -
157A SER 3.7 0.8 - - - -
158A LYS* 1.3 81.9 - - - +
160A ARG* 1.3 65.7 + - - -
161A ASP 3.3 2.5 - - - -
162A PHE 3.4 4.9 + - - -
163A VAL* 3.4 17.8 + - - +
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Residues in contact with ARG 160 (chain A).
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 5.0 2.8 + - - -
150A SER* 6.2 0.2 - - - +
155A LEU* 3.5 40.4 + - - +
159A GLY* 1.3 71.9 - - - -
161A ASP* 1.3 66.7 + - - +
163A VAL* 3.5 6.4 + - - +
164A HIS* 3.1 28.6 + - + +
147D TRP* 5.8 6.3 - - - -
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Residues in contact with ASP 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLY* 3.3 0.8 - - - -
160A ARG* 1.3 80.9 + - - +
162A PHE* 1.3 62.7 + - - +
164A HIS* 3.5 5.4 + - - +
165A SER* 3.0 25.0 + - - -
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Residues in contact with PHE 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ASP* 4.8 1.3 - - - -
141A TRP* 3.5 29.4 - - + -
142A THR* 3.9 18.4 - - - -
145A ALA* 3.8 12.6 - - + -
154A LEU* 4.3 2.7 - - + -
158A LYS* 3.4 66.1 + - + +
159A GLY 3.4 3.4 + - - +
160A ARG 3.4 0.2 - - - -
161A ASP* 1.3 77.8 - - - +
163A VAL* 1.3 68.1 + - - +
165A SER* 3.1 10.6 + - - -
166A VAL* 3.1 33.0 + - + +
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Residues in contact with VAL 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ALA* 4.2 9.2 - - - +
149A PRO* 3.5 41.1 - - + +
154A LEU* 3.8 33.0 - - + +
155A LEU* 3.6 20.9 - - + -
159A GLY 3.4 16.0 + - - +
160A ARG* 4.0 8.3 - - - +
161A ASP 3.4 0.2 - - - -
162A PHE* 1.3 79.2 - - + +
164A HIS* 1.3 59.5 + - - +
166A VAL* 3.0 5.4 + - - +
167A GLN* 2.9 29.3 + - + +
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Residues in contact with HIS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ARG* 3.1 19.9 + - + +
161A ASP* 3.7 6.1 - - - +
163A VAL* 1.3 78.3 - - - +
165A SER* 1.3 57.9 + - - +
167A GLN* 3.3 6.4 + - - +
168A GLU* 2.8 59.8 + - + +
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Residues in contact with SER 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ASP 3.0 18.2 + - - -
162A PHE* 3.1 9.6 + - - -
164A HIS* 1.3 74.9 - - - +
166A VAL* 1.3 65.1 + - - +
168A GLU* 3.9 3.3 + - - -
169A THR* 2.9 30.7 + - - +
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Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A THR* 3.6 39.3 - - + +
145A ALA* 3.7 15.0 - - + -
146A LYS* 3.7 21.7 - - + +
162A PHE* 3.1 32.7 + - + +
163A VAL 3.0 7.4 + - - +
165A SER* 1.3 79.3 - - - +
167A GLN* 1.3 65.2 + - - +
169A THR* 3.3 22.5 + - - +
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Residues in contact with GLN 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ALA 3.2 13.3 + - - +
146A LYS* 3.0 29.7 + - - +
149A PRO* 3.9 30.5 - - + +
163A VAL* 2.9 20.1 + - + +
164A HIS* 3.7 7.6 - - - +
166A VAL* 1.3 73.6 - - - +
168A GLU* 1.3 57.0 + - - +
169A THR 3.0 18.7 + - - +
149D PRO* 5.3 2.8 - - - +
167D GLN* 4.4 12.1 - - - +
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Residues in contact with GLU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A HIS* 2.8 50.3 + - + +
165A SER* 3.9 5.6 + - - +
166A VAL 3.5 0.2 - - - -
167A GLN* 1.3 69.7 - - - +
169A THR* 1.3 64.3 + - + +
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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