Contacts of the helix formed by residues 121 - 141 (chain B) in PDB entry 1O0W
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 ARG 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B GLU* 2.4 33.3 + - - -
116B THR* 3.2 29.5 + - - -
117B GLY 3.5 6.4 + - - +
118B GLY* 3.1 19.7 + - - +
119B ARG 3.5 0.2 - - - -
120B ASP* 1.3 75.1 - - - +
122B ASP* 1.3 68.6 + - + +
123B SER* 3.4 25.6 - - - +
124B ILE* 3.1 19.2 + - + +
125B LEU* 2.9 24.2 + - - +
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Residues in contact with ASP 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLU* 3.8 20.5 - - + +
92B GLU* 5.0 11.8 - - - +
95B ALA* 3.9 16.9 - - + +
99B ARG* 2.7 43.9 + - - +
120B ASP 3.4 1.3 + - - +
121B ARG* 1.3 72.8 - - - +
123B SER* 1.3 58.0 + - - +
125B LEU* 3.3 2.6 + - - +
126B ALA* 2.9 31.4 + - - +
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLU* 3.2 24.8 + - - -
121B ARG* 3.1 22.1 + - - +
122B ASP* 1.3 79.5 - - - +
124B ILE* 1.3 65.8 + - - +
126B ALA* 3.9 1.0 - - - +
127B ASP* 2.9 37.5 + - - +
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Residues in contact with ILE 124 (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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32B HIS* 3.7 39.9 - - + +
50B ASN* 5.3 1.5 + - - +
107B LEU* 3.9 24.2 - - + -
109B LEU* 4.3 6.5 - - + -
113B GLU* 3.4 14.6 - - + +
118B GLY* 3.3 23.1 - - - +
121B ARG* 3.1 40.4 + - + +
123B SER* 1.3 83.1 + - - +
125B LEU* 1.3 64.8 + - - +
127B ASP* 3.4 6.7 + - - +
128B ALA* 3.0 23.5 + - + +
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Residues in contact with LEU 125 (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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95B ALA* 4.5 3.8 - - + -
98B SER* 3.1 33.2 + - - -
99B ARG* 3.4 49.6 - - + +
103B LEU* 4.3 3.3 - - + +
104B GLY* 3.8 34.5 - - - +
107B LEU* 4.0 9.4 - - + -
119B ARG 3.8 11.2 - - - +
120B ASP* 4.0 9.2 - - - +
121B ARG 2.9 18.8 + - - +
122B ASP* 3.6 4.5 - - - +
124B ILE* 1.3 78.5 - - + +
126B ALA* 1.3 63.1 + - - +
128B ALA* 3.4 5.0 + - - +
129B PHE 3.1 13.3 + - - -
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLU* 3.9 25.6 - - + +
94B LEU* 3.7 31.9 - - + +
95B ALA* 4.3 1.5 - - - +
98B SER* 4.4 2.9 - - - -
122B ASP 2.9 16.8 + - - +
123B SER 3.9 2.2 - - - +
125B LEU* 1.3 76.8 - - - +
127B ASP* 1.3 65.3 + - - +
129B PHE* 3.2 3.8 + - - +
130B GLU* 3.0 29.6 + - - +
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Residues in contact with ASP 127 (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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32B HIS* 6.0 3.2 - - + -
50B ASN* 4.5 9.6 - - - +
54B GLU* 3.3 40.3 - - + +
123B SER* 2.9 28.4 + - - +
124B ILE* 3.7 6.9 - - - +
126B ALA* 1.3 80.0 - - - +
128B ALA* 1.3 58.0 + - - +
130B GLU* 3.3 5.9 + - - +
131B ALA* 2.9 28.1 + - - +
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Residues in contact with ALA 128 (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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29B ALA* 3.8 13.2 - - - +
30B LEU* 5.1 1.4 - - + +
50B ASN* 3.7 15.1 - - - +
103B LEU* 4.2 8.7 - - + +
107B LEU* 3.4 34.1 - - + -
124B ILE* 3.0 15.5 + - + +
125B LEU* 3.9 4.0 - - - +
126B ALA 3.4 0.2 - - - -
127B ASP* 1.3 76.1 - - - +
129B PHE* 1.3 51.3 + - - +
131B ALA* 3.2 2.9 + - - +
132B LEU* 2.7 34.3 + - - +
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Residues in contact with PHE 129 (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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94B LEU* 4.1 22.9 - - + +
97B VAL* 3.5 28.9 - - + -
98B SER* 3.1 25.8 - - - +
101B MET* 3.9 19.3 - - - -
103B LEU* 3.9 8.7 - - + +
125B LEU 3.1 5.3 + - - -
126B ALA* 3.5 8.5 - - - +
127B ASP 3.2 0.2 - - - -
128B ALA* 1.3 74.5 - - - +
130B GLU* 1.3 67.8 + - - +
132B LEU* 3.2 7.5 + - + +
133B LEU* 2.9 56.4 + - + +
149B PHE* 3.8 25.1 - + - -
153B PHE* 4.1 22.9 - + - -
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Residues in contact with GLU 130 (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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54B GLU* 3.7 22.0 - - + +
57B GLY* 3.1 19.9 - - - -
58B ASP* 3.0 43.2 + - - +
61B LEU* 4.5 8.6 - - + +
89B ALA 4.8 2.1 - - - +
94B LEU* 3.3 29.3 - - + +
126B ALA* 3.0 20.3 + - - +
127B ASP* 3.7 9.3 - - - +
129B PHE* 1.3 77.6 - - + +
131B ALA* 1.3 62.9 + - - +
133B LEU* 3.2 11.8 + - - +
134B ALA 3.1 17.2 + - - -
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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
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29B ALA* 3.7 12.3 - - - +
50B ASN* 3.7 39.0 - - + +
53B LEU* 3.9 5.7 - - + +
54B GLU* 3.8 13.4 - - - +
127B ASP 2.9 14.7 + - - +
128B ALA 3.3 8.3 - - - +
130B GLU* 1.3 78.4 - - - +
132B LEU* 1.3 60.7 + - - +
134B ALA* 3.1 5.2 + - - +
135B ALA* 2.9 22.0 + - - +
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Residues in contact with LEU 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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12B PHE* 3.8 26.7 - - + -
18B ILE* 5.0 0.2 - - + -
20B PHE* 4.2 6.5 - - + -
26B LEU* 4.1 16.4 - - + -
29B ALA* 3.8 10.5 - - + +
30B LEU* 5.9 2.7 - - + -
101B MET* 3.6 36.6 - - + -
103B LEU* 4.7 8.1 - - + -
128B ALA 2.7 19.8 + - - +
129B PHE* 3.2 14.6 + - + +
131B ALA* 1.3 73.8 - - - +
133B LEU* 1.3 63.1 + - - +
135B ALA* 3.1 4.4 + - + +
136B ILE* 2.9 47.3 + - + +
149B PHE* 5.0 1.8 - - + -
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Residues in contact with LEU 133 (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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57B GLY 4.5 2.9 - - - +
60B VAL* 4.5 10.0 - - + +
61B LEU* 3.8 37.9 - - + +
64B PHE* 5.9 2.7 - - + -
129B PHE* 2.9 46.2 + - + +
130B GLU* 3.2 11.2 + - - +
132B LEU* 1.3 77.3 - - + +
134B ALA* 1.3 57.4 + - - +
136B ILE* 3.4 0.8 + - - -
137B TYR* 2.9 30.6 + - - +
145B ILE* 3.5 23.7 - - + +
149B PHE* 3.4 39.3 - - + -
153B PHE* 6.1 0.4 - - + -
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Residues in contact with ALA 134 (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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53B LEU* 3.0 42.2 - - + +
56B LEU* 4.0 11.7 - - + -
57B GLY* 3.4 15.1 - - - +
60B VAL* 4.6 3.1 - - - -
130B GLU 3.1 4.9 + - - -
131B ALA 3.1 6.8 + - - +
133B LEU* 1.3 76.2 - - - +
135B ALA* 1.3 57.3 + - - +
137B TYR* 3.2 7.6 + - - +
138B LEU* 2.9 34.1 + - - +
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Residues in contact with ALA 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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20B PHE* 3.5 19.8 - - + -
25B LEU* 3.5 33.3 - - + +
26B LEU 4.4 0.2 - - - +
29B ALA* 4.1 7.9 - - + -
53B LEU* 4.0 9.6 - - + +
131B ALA 2.9 12.3 + - - +
132B LEU* 3.5 8.7 - - + +
134B ALA* 1.3 76.2 - - - +
136B ILE* 1.3 58.5 + - - +
138B LEU* 3.4 1.9 + - - -
139B ASP* 2.8 32.1 + - - +
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Residues in contact with ILE 136 (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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18B ILE* 4.1 13.9 - - + -
20B PHE* 3.6 24.7 - - + -
132B LEU* 2.9 37.4 + - + +
133B LEU* 4.9 0.2 - - - -
135B ALA* 1.3 73.7 - - - +
137B TYR* 1.3 59.0 + - - +
139B ASP* 4.5 1.3 - - - +
140B GLN* 2.7 35.7 + - + +
141B GLY 3.1 5.0 + - - -
144B LYS* 3.9 28.9 - - + -
145B ILE* 3.7 20.0 - - + -
148B LEU* 3.8 21.8 - - + -
149B PHE* 4.2 14.6 - - + -
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Residues in contact with TYR 137 (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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63A LEU* 3.9 25.5 - - + +
67A GLU* 2.5 41.1 + - + -
142A TYR* 3.3 20.5 - + - -
56B LEU* 4.4 6.1 - - + -
60B VAL* 3.8 25.8 - - + -
133B LEU 2.9 18.4 + - - +
134B ALA 3.4 4.3 - - - +
136B ILE* 1.3 77.1 - - - +
138B LEU* 1.3 74.8 + - + +
141B GLY* 3.0 29.6 + - - +
142B TYR* 3.9 37.2 - + + -
145B ILE* 4.2 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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67A GLU* 5.3 0.2 - - - -
70A TYR* 3.5 37.5 - - + +
71A LYS* 3.7 32.3 - - - +
25B LEU* 4.0 18.4 - - + -
53B LEU* 3.9 9.6 - - + -
56B LEU* 3.8 21.8 - - + -
134B ALA 2.9 19.3 + - - +
135B ALA 3.8 2.9 - - - +
137B TYR* 1.3 86.7 - - + +
139B ASP* 1.3 59.9 + - - +
141B GLY 4.9 0.3 + - - -
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Residues in contact with ASP 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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20B PHE* 3.4 27.1 - - + -
21B LYS* 2.8 49.7 + - - +
22B ASN* 2.7 32.9 + - - +
25B LEU* 3.8 7.2 - - + +
135B ALA 2.8 21.3 + - - +
136B ILE* 4.2 1.1 - - - +
138B LEU* 1.3 76.6 - - - +
140B GLN* 1.3 75.1 + - + +
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Residues in contact with GLN 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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18B ILE* 4.2 10.9 - - - +
19B ASN 3.0 25.1 + - - +
20B PHE* 4.9 2.0 - - + -
21B LYS* 4.4 17.3 + - - +
136B ILE* 2.7 18.9 + - + +
139B ASP* 1.3 93.6 - - + +
141B GLY* 1.3 58.5 + - - +
143B GLU* 6.0 0.5 - - - +
144B LYS* 3.8 48.7 + - + +
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Residues in contact with GLY 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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136B ILE 3.1 3.7 + - - +
137B TYR* 3.0 25.6 + - - -
138B LEU 4.9 0.2 + - - -
140B GLN* 1.3 78.3 - - - +
142B TYR* 1.3 65.7 + - - -
143B GLU* 3.3 3.1 - - - -
144B LYS* 3.2 15.0 + - - +
145B ILE* 3.4 12.3 + - - +
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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
------------------------------------------------------------
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