Contacts of the helix formed by residues 122 - 138 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114C PHE* 4.5 7.4 - - + -
118C ILE* 4.0 24.0 - - + -
122C LEU* 4.3 17.5 - - + -
170C ALA* 4.3 4.7 - - + +
118D ILE* 3.0 21.3 + - + +
121D ASN* 1.3 76.1 - - - +
123D ILE* 1.3 66.1 + - + +
124D GLY 3.3 1.1 - - - -
125D THR* 3.3 2.1 + - - -
126D PHE* 3.2 21.0 + - - +
171D SER* 3.9 18.4 - - - +
174D GLY* 3.6 41.1 - - - +
175D ILE* 3.7 11.2 - - + +
178D MET* 4.2 16.3 - - + +
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Residues in contact with ILE 123 (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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111C LEU* 3.8 27.2 - - + +
114C PHE* 4.1 25.1 - - + -
115C GLN* 3.1 52.5 - - + +
118C ILE* 4.4 9.6 - - + -
66D THR* 5.9 6.3 - - + +
118D ILE* 3.1 19.1 + - + +
119D ASN* 3.3 26.5 - - + +
122D LEU* 1.3 74.5 - - + +
124D GLY* 1.3 55.7 + - - +
126D PHE* 3.4 3.5 + - - +
127D ASN* 3.0 26.8 + - + +
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Residues in contact with GLY 124 (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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65D VAL* 3.6 31.3 - - - +
66D THR* 4.6 2.0 - - - -
119D ASN 2.9 14.1 + - - -
120D VAL 3.5 13.8 + - - -
122D LEU 3.3 0.6 - - - -
123D ILE* 1.3 72.4 - - - +
125D THR* 1.4 63.0 + - - +
127D ASN* 3.4 2.9 + - - +
128D VAL* 3.2 28.3 + - - +
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Residues in contact with THR 125 (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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90D ASN* 3.7 26.9 + - + +
92D ALA 4.8 7.3 + - - -
120D VAL 4.1 0.9 + - - -
121D ASN 3.2 23.1 + - - -
122D LEU 3.3 5.3 + - - -
124D GLY* 1.4 75.7 - - - +
126D PHE* 1.3 63.1 + - - +
128D VAL* 3.4 4.2 + - - +
129D ILE* 3.1 28.9 + - + +
152D ASN* 3.7 27.6 - - + +
153D THR 5.9 0.2 + - - -
175D ILE* 4.6 12.0 - - + +
178D MET* 4.0 11.7 - - + -
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Residues in contact with PHE 126 (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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100C THR* 4.0 24.5 - - + -
109C HIS* 3.9 32.3 - + + -
110C THR 4.8 0.2 - - - -
111C LEU* 5.0 3.4 - - + -
114C PHE* 3.4 65.5 - + + -
166C ALA* 4.2 5.6 - - + -
122D LEU 3.2 9.0 + - - +
123D ILE 3.8 6.1 - - - +
125D THR* 1.3 76.3 - - - +
127D ASN* 1.3 59.3 + - - +
129D ILE* 3.3 5.0 + - + +
130D ARG* 2.9 55.0 + - + +
178D MET* 4.2 7.6 - - + +
182D ILE* 4.0 22.7 - - + -
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Residues in contact with ASN 127 (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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111C LEU* 3.7 18.5 - - + +
65D VAL 3.2 21.3 + - - +
66D THR* 4.1 2.6 - - - -
67D SER 3.6 5.3 + - - -
68D GLU* 3.6 25.7 - - - +
71D VAL* 4.0 7.9 - - - +
123D ILE* 3.0 18.0 + - + +
124D GLY* 3.6 6.3 - - - +
125D THR 3.3 0.2 - - - -
126D PHE* 1.3 76.7 - - - +
128D VAL* 1.3 61.6 + - - +
130D ARG* 2.8 46.0 + - - +
131D LEU* 3.3 29.3 + - - +
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Residues in contact with VAL 128 (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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14D VAL* 5.8 3.8 - - + -
16D THR* 4.0 23.8 - - + -
40D LEU* 5.4 2.2 - - + -
65D VAL* 4.0 15.3 - - + +
71D VAL* 4.3 23.8 - - + -
75D LEU* 4.9 6.4 - - + +
88D ALA* 5.1 8.3 - - + -
89D VAL 6.3 0.2 - - - -
90D ASN* 3.4 29.2 - - - +
124D GLY 3.2 14.4 + - - +
125D THR 3.8 2.0 - - - +
126D PHE 3.3 0.2 - - - -
127D ASN* 1.3 77.0 - - - +
129D ILE* 1.3 61.8 + - - +
131D LEU* 4.1 0.5 - - - +
132D VAL* 3.0 32.8 + - + +
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Residues in contact with ILE 129 (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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100C THR* 4.1 11.4 - - + -
90D ASN* 4.0 13.2 - - - +
125D THR* 3.1 25.9 + - + +
126D PHE* 3.7 5.4 - - + +
128D VAL* 1.3 75.8 - - - +
130D ARG* 1.3 62.0 + - - +
132D VAL* 3.8 8.3 - - - +
133D ALA* 3.1 23.9 + - - +
150D ILE* 4.0 22.6 - - + +
152D ASN* 3.5 25.8 - - - +
178D MET* 4.2 15.9 - - + -
182D ILE* 4.1 35.7 - - + -
186D LEU* 5.0 1.3 - - + -
193D VAL* 5.4 1.1 - - + -
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Residues in contact with ARG 130 (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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100C THR* 4.2 17.1 - - + +
101C TYR* 5.1 1.6 - - - +
108C VAL* 3.6 33.7 + - + +
109C HIS 3.0 25.8 + - - +
110C THR* 4.0 2.6 - - - +
111C LEU* 3.7 25.5 - - - +
68D GLU* 2.6 40.0 + - - +
126D PHE* 2.9 49.1 + - + +
127D ASN* 2.8 34.5 + - - +
129D ILE* 1.3 72.7 - - - +
131D LEU* 1.3 78.8 + - + +
133D ALA* 3.7 10.2 + - - +
134D GLY 4.0 3.6 + - - -
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Residues in contact with LEU 131 (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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108C VAL* 4.6 9.0 - - + -
68D GLU* 4.0 21.1 - - + +
71D VAL* 3.7 21.8 - - + -
72D GLN* 3.9 29.6 - - - +
75D LEU* 3.8 16.9 - - + +
127D ASN* 3.3 31.8 + - - +
128D VAL 4.3 0.7 - - - +
130D ARG* 1.3 103.9 - - + +
132D VAL* 1.3 61.4 + - - +
133D ALA 3.5 0.3 + - - -
134D GLY* 3.7 5.9 + - - -
135D VAL* 3.7 17.0 + - - +
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Residues in contact with VAL 132 (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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14D VAL* 5.7 1.1 - - + -
75D LEU* 3.8 23.7 - - + +
85D ILE* 4.0 31.4 - - + -
88D ALA* 4.0 20.6 - - + -
128D VAL* 3.0 24.5 + - + +
129D ILE* 3.8 7.4 - - - +
131D LEU* 1.3 74.1 - - - +
133D ALA* 1.3 67.0 + - - +
135D VAL* 3.1 5.0 + - - +
136D MET* 3.0 31.7 + - + +
150D ILE* 3.9 21.5 - - + -
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Residues in contact with ALA 133 (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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100C THR* 5.1 1.1 - - + -
101C TYR* 4.3 12.8 - - + -
129D ILE 3.1 18.6 + - - +
130D ARG* 4.0 6.7 - - - +
131D LEU 3.3 0.6 - - - -
132D VAL* 1.3 80.3 - - - +
134D GLY* 1.3 57.0 + - - +
136D MET* 3.5 1.9 + - - -
137D GLY* 3.0 25.6 + - - -
150D ILE* 5.0 1.1 - - + -
186D LEU* 4.2 33.4 - - + -
189D ILE* 4.3 3.1 - - - +
191D ILE* 3.7 16.0 - - + +
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Residues in contact with GLY 134 (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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101C TYR* 4.0 32.7 + - - -
108C VAL* 5.6 3.4 - - - -
130D ARG 4.0 4.6 + - - -
131D LEU 3.7 6.3 + - - -
132D VAL 3.3 0.4 - - - -
133D ALA* 1.3 78.2 - - - +
135D VAL* 1.3 62.3 + - - +
137D GLY* 3.5 8.1 + - - -
138D GLN* 3.6 19.7 + - - +
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Residues in contact with VAL 135 (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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72D GLN* 5.4 5.2 - - - +
75D LEU* 4.8 17.0 - - + +
79D LYS* 4.3 24.6 - - + -
84D ARG* 5.3 0.7 - - - -
85D ILE* 3.8 36.4 + - + +
131D LEU 3.7 15.7 + - - +
132D VAL* 3.1 9.5 + - + +
134D GLY* 1.3 75.1 - - - +
136D MET* 1.3 64.8 + - - +
138D GLN* 3.2 30.5 + - - +
139D ASN* 4.1 5.0 + - - +
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Residues in contact with MET 136 (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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85D ILE* 3.8 16.2 - - + +
86D ASP 3.9 8.7 - - - +
87D VAL 3.8 7.0 - - - +
88D ALA* 3.6 33.9 - - + +
132D VAL* 3.0 27.3 + - + +
135D VAL* 1.3 76.1 - - - +
137D GLY* 1.3 62.8 + - - +
139D ASN* 3.0 30.5 + - - +
147D ARG* 3.7 18.2 - - - +
148D GLY* 4.0 12.8 - - - -
149D VAL 3.7 10.8 - - - +
150D ILE* 3.9 26.0 - - + -
191D ILE* 3.7 23.1 - - + -
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Residues in contact with GLY 137 (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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101C TYR* 5.4 4.3 - - - -
103C GLU* 5.0 5.2 - - - +
133D ALA 3.0 16.6 + - - -
134D GLY* 3.5 5.4 + - - -
135D VAL 3.2 1.0 - - - -
136D MET* 1.3 76.3 - - - +
138D GLN* 1.3 58.2 + - - +
147D ARG* 3.5 26.4 + - - -
189D ILE* 4.3 16.3 - - - +
191D ILE* 4.4 0.6 - - - +
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Residues in contact with GLN 138 (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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79D LYS* 2.6 44.7 + - - +
134D GLY 3.6 16.5 + - - +
135D VAL* 3.2 24.7 + - - +
136D MET 3.1 0.8 + - - -
137D GLY* 1.3 75.1 - - - +
139D ASN* 1.3 63.9 + - - +
140D 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