Contacts of the helix formed by residues 122 - 138 (chain B) in PDB entry 1E3S
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 LEU 122 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PHE* 4.5 7.4 - - + -
118A ILE* 4.0 23.1 - - + -
122A LEU* 4.3 17.7 - - + -
170A ALA* 4.2 4.9 - - + +
118B ILE* 3.0 20.7 + - + +
121B ASN* 1.3 75.7 - - - +
123B ILE* 1.3 65.4 + - + +
124B GLY 3.3 0.7 - - - -
125B THR* 3.3 3.1 + - - -
126B PHE* 3.1 20.3 + - - +
171B SER* 3.9 18.4 - - - +
174B GLY* 3.7 41.3 - - - +
175B ILE* 3.7 9.9 - - + +
178B MET* 4.1 18.1 - - - +
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 3.8 24.4 - - + +
114A PHE* 4.2 22.7 - - + -
115A GLN* 4.1 34.1 - - + +
118A ILE* 4.4 12.8 - - + -
119A ASN* 5.2 4.9 - - - +
66B THR* 5.8 6.5 - - + +
118B ILE* 3.1 20.8 + - + +
119B ASN* 3.3 37.2 - - + +
122B LEU* 1.3 74.3 - - + +
124B GLY* 1.3 57.3 + - - +
126B PHE* 3.3 2.8 + - - +
127B ASN* 3.0 27.0 + - - +
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Residues in contact with GLY 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 3.6 31.8 - - - +
66B THR* 4.5 2.0 - - - -
119B ASN 2.9 14.0 + - - -
120B VAL 3.6 12.7 + - - -
122B LEU 3.3 0.6 - - - -
123B ILE* 1.3 75.2 - - - +
125B THR* 1.3 61.4 + - - +
127B ASN* 3.5 2.0 + - - +
128B VAL* 3.2 28.8 + - - +
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Residues in contact with THR 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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90B ASN* 3.7 26.6 + - + +
92B ALA 4.8 7.3 + - - -
120B VAL 4.1 1.0 + - - -
121B ASN 3.3 23.2 + - - -
122B LEU 3.3 4.9 + - - -
124B GLY* 1.3 76.2 - - - +
126B PHE* 1.3 61.0 + - - +
128B VAL* 3.4 3.6 + - - +
129B ILE* 3.1 29.6 + - + +
152B ASN* 3.8 26.9 - - + +
153B THR 5.7 0.2 + - - -
175B ILE* 4.5 13.4 - - + +
178B MET* 4.0 11.2 - - + -
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Residues in contact with PHE 126 (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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100A THR* 4.0 23.6 - - + -
109A HIS* 3.8 33.7 - + + -
110A THR 4.7 0.2 - - - -
111A LEU* 5.0 3.6 - - + -
114A PHE* 3.4 67.5 - + + -
166A ALA* 4.2 6.1 - - + -
122B LEU 3.1 7.9 + - - +
123B ILE 3.3 3.8 + - - +
125B THR* 1.3 72.6 - - - +
127B ASN* 1.3 61.5 + - - +
129B ILE* 3.7 5.5 - - + +
130B ARG* 2.9 54.6 + - + +
178B MET* 4.1 6.9 - - + +
182B ILE* 4.0 23.6 - - + -
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Residues in contact with ASN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 3.7 17.8 - - + +
65B VAL 3.2 20.5 + - - +
66B THR* 4.2 2.9 - - - +
67B SER 3.5 25.9 + - - -
68B GLU* 3.8 3.3 - - - +
71B VAL* 3.8 9.5 - - - +
123B ILE* 3.0 17.9 + - + +
124B GLY* 3.7 5.6 - - - +
125B THR 3.4 0.2 - - - -
126B PHE* 1.3 77.4 - - - +
128B VAL* 1.3 63.8 + - - +
130B ARG* 2.9 44.6 + - - +
131B LEU* 3.3 31.6 + - - +
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Residues in contact with VAL 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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14B VAL* 5.8 3.4 - - + -
16B THR* 4.0 14.6 - - + -
40B LEU* 5.2 3.4 - - + -
65B VAL* 3.9 24.5 - - + -
71B VAL* 4.3 24.5 - - + -
75B LEU* 4.9 5.9 - - + +
88B ALA* 5.1 8.5 - - + -
89B VAL 6.3 0.2 - - - -
90B ASN* 3.4 28.7 - - - +
124B GLY 3.2 16.6 + - - +
125B THR 3.9 0.2 - - - +
127B ASN* 1.3 76.0 - - - +
129B ILE* 1.3 62.0 + - - +
131B LEU* 4.0 0.9 - - - +
132B VAL* 2.9 33.7 + - + +
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A THR* 4.2 10.3 - - + -
90B ASN* 3.9 13.0 - - - +
125B THR* 3.1 26.2 + - + +
126B PHE* 3.7 6.5 - - + +
128B VAL* 1.3 75.7 - - - +
130B ARG* 1.3 63.2 + - - +
132B VAL* 3.7 8.2 - - - +
133B ALA* 3.1 24.4 + - - +
150B ILE* 4.0 21.2 - - + +
152B ASN* 3.4 27.8 - - - +
178B MET* 4.1 14.6 - - + -
182B ILE* 4.1 34.8 - - + -
186B LEU* 5.1 1.1 - - + -
193B VAL* 5.4 1.3 - - + -
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Residues in contact with ARG 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A THR* 4.1 17.5 - - + +
101A TYR* 5.1 1.0 - - - +
108A VAL* 3.3 36.4 - - + +
109A HIS 2.9 26.7 + - - +
110A THR* 4.0 3.0 - - - +
111A LEU* 3.7 25.9 - - - +
68B GLU* 2.8 38.2 + - - +
126B PHE* 2.9 46.3 + - + +
127B ASN* 2.9 33.9 + - - +
129B ILE* 1.3 75.7 - - - +
131B LEU* 1.3 81.1 + - - +
133B ALA* 3.8 7.8 + - - +
134B GLY* 4.0 6.4 + - - -
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Residues in contact with LEU 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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108A VAL* 5.0 9.0 - - + -
68B GLU* 4.2 15.5 - - + +
71B VAL* 3.8 24.5 - - + -
72B GLN* 3.8 28.4 + - - +
75B LEU* 3.8 15.6 - - + +
127B ASN* 3.3 33.4 + - - +
128B VAL 4.2 0.4 - - - +
130B ARG* 1.3 102.5 - - + +
132B VAL* 1.3 65.7 + - - +
133B ALA 3.3 1.0 + - - -
134B GLY* 3.6 8.5 + - - -
135B VAL* 3.7 15.6 + - - +
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 5.6 1.3 - - + -
75B LEU* 3.8 16.8 - - + +
85B ILE* 3.9 38.6 - - + -
88B ALA* 4.0 21.3 - - + -
128B VAL* 2.9 25.1 + - + +
129B ILE* 3.7 7.9 - - - +
131B LEU* 1.3 76.0 - - - +
133B ALA* 1.3 66.6 + - - +
135B VAL* 3.1 4.2 + - + +
136B MET* 3.0 31.1 + - + +
150B ILE* 3.9 20.9 - - + -
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Residues in contact with ALA 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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100A THR* 5.0 1.3 - - + -
101A TYR* 4.3 11.4 - - + -
129B ILE 3.1 17.9 + - - +
130B ARG* 4.0 7.6 - - - +
131B LEU 3.3 0.6 - - - -
132B VAL* 1.3 79.9 - - - +
134B GLY* 1.3 57.4 + - - +
136B MET* 3.5 2.4 + - - -
137B GLY* 3.0 25.6 + - - -
150B ILE* 4.9 1.3 - - + -
186B LEU* 4.1 35.0 - - + -
189B ILE* 4.4 3.6 - - - +
191B ILE* 3.9 15.0 - - + +
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Residues in contact with GLY 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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101A TYR* 4.0 31.7 + - - -
130B ARG 4.0 5.0 + - - -
131B LEU 3.6 6.5 + - - -
132B VAL 3.3 0.8 - - - -
133B ALA* 1.3 80.2 - - - +
135B VAL* 1.3 63.2 + - - +
137B GLY* 3.4 8.1 + - - -
138B GLN* 3.6 19.0 + - - +
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Residues in contact with VAL 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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72B GLN* 5.3 6.5 - - - +
75B LEU* 4.7 13.7 - - + +
79B LYS* 4.9 16.4 - - + -
84B ARG* 5.3 1.3 - - - -
85B ILE* 3.8 42.2 + - + +
131B LEU 3.7 14.5 + - - +
132B VAL* 3.1 9.5 + - - +
134B GLY* 1.3 74.5 - - - +
136B MET* 1.3 64.6 + - - +
138B GLN* 3.2 38.0 + - - +
139B ASN* 4.2 4.5 + - - +
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Residues in contact with MET 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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85B ILE* 3.7 16.4 - - + +
86B ASP 3.7 13.9 - - - +
87B VAL 3.8 3.6 - - - +
88B ALA* 3.6 32.5 - - + +
132B VAL* 3.0 27.7 + - + +
133B ALA 3.9 0.2 - - - +
135B VAL* 1.3 76.2 - - - +
137B GLY* 1.3 57.3 + - - +
139B ASN* 3.0 35.0 + - - +
147B ARG* 3.8 18.4 - - - +
148B GLY* 4.0 6.1 - - - -
149B VAL 3.7 12.1 - - - +
150B ILE* 3.9 25.1 - - + -
191B ILE* 3.7 30.5 - - + -
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Residues in contact with GLY 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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101A TYR* 5.3 5.2 - - - -
133B ALA 3.0 16.8 + - - -
134B GLY* 3.8 5.8 - - - -
135B VAL 3.2 1.0 - - - -
136B MET* 1.3 76.1 - - - +
138B GLN* 1.3 58.7 + - - +
139B ASN 3.3 1.1 + - - +
147B ARG* 3.6 25.2 + - - -
189B ILE* 4.3 16.6 - - - +
191B ILE* 4.4 0.6 - - - +
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Residues in contact with GLN 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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79B LYS* 2.6 37.4 + - - +
134B GLY 3.6 16.8 + - - +
135B VAL* 3.4 26.1 - - - +
136B MET 3.1 1.0 + - - -
137B GLY* 1.3 75.7 - - - +
139B ASN* 1.3 61.5 + - - +
140B GLU 3.8 0.9 + - - -
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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
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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