Contacts of the helix formed by residues 126 - 147 (chain B) in PDB entry 4OBP
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 LYS 126 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B THR 4.3 0.2 + - - -
125B LEU* 1.4 73.7 - - - +
127B GLU* 1.3 65.0 + - - +
128B ASP* 2.8 42.1 + - - +
129B TRP* 2.9 36.2 + - + +
130B ILE* 3.2 5.0 + - - +
258B TRP* 5.5 0.2 - - - -
301B GLN* 3.6 28.8 + - - +
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Residues in contact with GLU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU 3.6 2.6 + - - -
126B LYS* 1.3 70.5 - - - +
128B ASP* 1.3 56.9 + - - +
130B ILE* 3.1 12.8 + - - +
131B ALA* 3.0 23.6 + - - +
258B TRP* 3.4 22.3 - - + -
259B SER* 2.5 51.8 + - - -
262B PHE* 3.6 24.1 - - + +
288B PHE* 3.6 22.0 - - + -
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Residues in contact with ASP 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LYS* 2.8 32.3 + - - +
127B GLU* 1.3 74.5 - - - +
129B TRP* 1.3 63.7 + - - +
131B ALA* 3.7 9.3 - - + +
132B TYR* 3.2 25.8 + - - +
292B GLN* 4.2 3.8 - - + +
294B ASN* 3.6 27.4 + - + +
298B VAL* 3.4 27.4 - - + +
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Residues in contact with TRP 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 4.3 9.0 - - + -
120B THR* 4.9 3.8 - - + -
125B LEU* 3.9 32.5 - - + -
126B LYS* 2.9 30.1 + - + +
128B ASP* 1.3 89.7 + - - +
130B ILE* 1.4 60.1 + - - +
132B TYR* 3.2 2.4 + - - +
133B ILE* 2.9 41.6 + - + +
298B VAL* 3.6 20.3 - - + +
301B GLN* 2.9 48.1 + - + +
302B LEU* 3.7 26.5 - - + -
305B HIS* 3.9 38.4 - + + -
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Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 3.5 27.1 - - + +
126B LYS 3.6 8.3 - - - +
127B GLU* 3.1 8.4 + - - +
129B TRP* 1.4 75.3 - - - +
131B ALA* 1.4 52.2 + - - +
133B ILE* 4.1 0.3 - - - +
134B SER* 2.7 50.8 + - - +
223B ALA* 4.0 7.2 - - + +
226B MET* 3.8 30.1 - - + -
227B ALA* 3.8 31.9 - - + +
258B TRP* 4.1 5.8 - - + -
262B PHE* 3.7 36.6 - - + -
288B PHE* 4.2 2.9 - - + -
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLU 3.0 9.6 + - - +
128B ASP* 3.7 12.3 - - + +
129B TRP 3.3 0.2 - - - -
130B ILE* 1.4 76.0 - - - +
132B TYR* 1.4 60.7 + - - +
135B ARG* 3.2 16.1 + - - +
288B PHE* 3.5 46.2 - - + +
289B ILE* 4.0 3.3 - - - +
292B GLN* 2.9 28.4 + - + -
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Residues in contact with TYR 132 (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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80B ARG* 4.9 2.3 + - - -
128B ASP 3.2 13.5 + - - +
129B TRP 3.2 3.8 + - - +
131B ALA* 1.4 75.4 - - - +
133B ILE* 1.3 70.6 + - + +
135B ARG* 3.4 31.9 + - - +
136B GLU* 3.2 45.6 + - + +
165B ALA 3.7 9.5 + - - -
166B GLU* 4.8 3.5 - - - -
167B VAL* 4.0 18.2 + - + +
292B GLN* 3.1 18.0 + - - +
295B GLU* 4.4 16.4 - - + -
298B VAL* 3.8 13.9 - - + -
299B ARG* 3.4 40.6 + - + -
302B LEU* 3.7 28.7 - - + -
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Residues in contact with ILE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 3.8 36.3 - - + -
116B LEU* 4.0 8.1 - - + -
125B LEU* 3.9 25.4 - - + -
129B TRP* 2.9 22.3 + - + +
132B TYR* 1.3 85.0 - - + +
134B SER* 1.4 58.6 + - - +
136B GLU* 3.2 8.1 + - - +
137B ILE* 2.9 42.9 + - + +
167B VAL* 4.3 13.9 - - + -
226B MET* 3.6 24.9 - - + -
302B LEU* 4.4 12.1 - - + -
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Residues in contact with SER 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ILE* 2.7 35.6 + - - +
133B ILE* 1.4 71.8 - - - +
135B ARG* 1.4 57.8 + - - +
137B ILE* 3.4 13.9 + - - +
138B LEU* 2.9 33.6 + - - +
219B CYS* 4.3 6.4 + - - -
223B ALA* 4.0 8.8 - - - +
226B MET* 3.5 14.7 - - - +
265B PHE* 4.1 14.2 - - - -
288B PHE* 4.8 0.2 - - - -
289B ILE* 3.7 19.1 - - - -
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Residues in contact with ARG 135 (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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131B ALA 3.2 19.4 + - - +
132B TYR* 3.4 18.4 + - - +
133B ILE 3.3 0.2 - - - -
134B SER* 1.4 71.5 - - - +
136B GLU* 1.3 76.9 + - - +
138B LEU* 3.1 5.1 + - - +
139B ARG* 2.8 72.7 + - - +
284B LEU* 4.1 5.4 - - + -
289B ILE* 3.6 35.2 + - + +
290B ARG* 5.7 2.0 + - - +
292B GLN* 3.6 23.4 - - - +
295B GLU* 3.1 47.4 + - - +
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ARG* 3.1 19.2 + - - -
81B ASN* 2.8 42.3 + - - +
132B TYR* 3.2 35.3 + - + +
133B ILE 3.2 7.2 + - - +
135B ARG* 1.3 111.0 + - - +
137B ILE* 1.4 61.2 + - - +
139B ARG* 3.2 11.1 + - - -
140B GLY* 3.0 18.9 + - - -
167B VAL* 3.6 31.4 + - + +
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Residues in contact with ILE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ILE* 2.9 37.2 + - + +
134B SER* 3.5 11.7 - - - +
136B GLU* 1.4 72.0 - - - +
138B LEU* 1.3 58.1 + - - +
140B GLY* 3.3 3.5 + - - -
141B LEU* 2.9 45.5 + - + +
154B ILE* 4.1 13.0 - - + -
159B VAL* 3.8 34.8 - - + -
167B VAL* 4.7 1.1 - - + +
169B LEU* 3.9 20.6 - - + +
219B CYS* 4.0 16.4 - - - +
222B THR* 4.1 20.6 - - + -
226B MET* 4.4 3.1 - - + -
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Residues in contact with LEU 138 (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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134B SER 2.9 20.0 + - - +
135B ARG 3.1 6.5 + - - +
137B ILE* 1.3 75.7 - - - +
139B ARG* 1.3 52.1 + - - +
141B LEU* 3.3 3.8 + - + -
142B ALA* 2.8 31.4 + - - +
216B LEU* 3.7 29.6 - - + -
219B CYS* 4.1 16.6 - - - -
265B PHE* 4.1 14.4 - - + -
280B THR* 3.2 17.1 - - + +
283B LEU* 4.3 22.7 - - + +
284B LEU* 3.7 15.0 - - + -
289B ILE* 3.8 35.2 - - + -
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Residues in contact with ARG 139 (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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79B HIS* 3.8 13.2 + - + +
80B ARG* 5.0 7.4 - - - +
81B ASN* 3.3 20.0 - - - +
135B ARG* 2.8 62.7 + - - +
136B GLU* 3.2 23.6 + - - +
138B LEU* 1.3 68.9 - - - +
140B GLY* 1.3 63.5 + - - +
142B ALA* 3.4 9.0 + - - +
143B HIS* 3.2 22.0 + - - +
284B LEU* 3.9 16.6 - - + +
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Residues in contact with GLY 140 (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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79B HIS* 4.3 2.5 - - - -
81B ASN* 3.8 19.2 - - - +
82B ILE* 3.4 21.9 - - - +
136B GLU 3.0 10.5 + - - -
137B ILE 3.7 3.4 - - - -
139B ARG* 1.3 75.9 - - - +
141B LEU* 1.4 59.4 + - - +
143B HIS* 3.4 2.6 + - - +
144B LEU* 3.2 18.0 + - - +
169B LEU* 3.8 15.0 - - - -
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Residues in contact with LEU 141 (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 ILE* 2.9 35.3 + - + +
138B LEU* 3.6 6.5 - - + +
140B GLY* 1.4 72.5 - - - +
142B ALA* 1.4 55.9 + - - +
144B LEU* 3.1 5.5 + - + +
145B HIS* 2.7 51.1 + - + +
151B HIS* 3.9 9.2 - - + -
154B ILE* 3.7 24.2 - - + -
169B LEU* 3.8 6.5 - - + +
215B ASP* 3.7 47.1 - - + +
216B LEU* 4.3 13.5 - - + -
219B CYS* 4.5 4.5 - - + -
280B THR* 4.0 3.6 - - + -
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Residues in contact with ALA 142 (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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138B LEU 2.8 21.3 + - - +
139B ARG* 3.7 6.5 - - - +
140B GLY 3.4 0.2 - - - -
141B LEU* 1.4 70.5 - - - +
143B HIS* 1.3 57.5 + - - +
145B HIS* 3.8 2.4 - - - +
146B ILE* 2.9 35.0 + - - +
280B THR* 3.6 18.3 - - + +
281B GLU* 5.5 8.1 - - + +
284B LEU* 4.0 15.9 - - + -
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Residues in contact with HIS 143 (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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76B TYR* 3.9 13.0 - + - +
77B SER* 3.0 45.0 + - - -
78B HIS 4.1 6.1 - - - -
79B HIS* 3.6 32.1 - + + +
82B ILE* 3.6 21.3 - - + -
139B ARG 3.2 5.0 + - - +
140B GLY 3.4 9.2 - - - +
141B LEU 3.2 0.4 - - - -
142B ALA* 1.3 78.9 - - - +
144B LEU* 1.3 60.0 + - - +
146B ILE* 3.4 9.5 - - - +
147B HIS* 2.7 52.5 + + - -
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Residues in contact with LEU 144 (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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76B TYR* 3.6 41.1 - - + +
82B ILE* 3.9 16.4 - - + -
140B GLY 3.2 12.7 + - - +
141B LEU* 3.1 10.6 + - + +
143B HIS* 1.3 78.1 - - - +
145B HIS* 1.4 62.4 + - + +
147B HIS* 3.1 11.8 + - - -
148B HIS 3.3 0.2 + - - -
149B VAL* 2.9 46.1 + - + +
151B HIS* 4.0 37.7 - - + +
169B LEU* 4.5 8.5 - - + -
171B ASP* 4.8 2.0 - - + +
174B VAL* 4.2 8.7 - - + -
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Residues in contact with HIS 145 (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 LEU* 2.7 36.7 + - + +
142B ALA* 4.0 3.6 - - - +
144B LEU* 1.4 70.4 - - + +
146B ILE* 1.3 64.2 + - - +
148B HIS* 3.1 16.7 + - - +
149B VAL 3.2 20.2 - - - +
212B TYR* 3.1 51.8 + + + +
215B ASP* 2.8 31.1 + - + -
216B LEU* 4.4 4.0 - - + -
280B THR* 2.7 29.8 + - - +
281B GLU* 5.3 5.4 - - - +
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Residues in contact with ILE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ALA 2.9 17.1 + - - +
143B HIS* 3.4 20.9 - - - +
145B HIS* 1.3 76.1 - - - +
147B HIS* 1.4 73.4 + - + +
148B HIS* 3.3 22.2 + - - -
281B GLU* 6.4 1.6 - - + -
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Residues in contact with HIS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LYS* 3.7 9.9 - - - +
75B LYS 3.9 17.6 - - - +
76B TYR* 3.5 31.6 - - + +
77B SER* 4.8 3.7 + - - -
143B HIS* 2.7 48.5 + + - +
144B LEU 3.1 7.8 + - - +
146B ILE* 1.4 86.3 - - + +
148B HIS* 1.4 76.8 + - - +
149B VAL* 3.3 10.8 + - + +
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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
------------------------------------------------------------
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