Contacts of the helix formed by residues 122 - 138 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ILE* 3.1 20.2 + - + +
121A ASN* 1.3 76.5 - - - +
123A ILE* 1.3 66.6 + - + +
124A GLY 3.4 0.9 - - - -
125A THR* 3.4 2.8 + - - -
126A PHE* 3.1 20.8 + - - +
171A SER* 3.9 19.1 - - - +
174A GLY* 3.7 40.6 - - - +
175A ILE* 3.8 6.3 - - + +
178A MET* 4.1 20.2 - - + -
114B PHE* 4.5 7.9 - - + -
118B ILE* 4.1 22.4 - - + -
122B LEU* 4.3 18.2 - - + -
170B ALA* 4.3 5.4 - - + +
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A THR* 5.8 6.3 - - + +
118A ILE* 3.1 22.8 + - + +
119A ASN* 3.3 39.0 - - + +
122A LEU* 1.3 70.2 - - + +
124A GLY* 1.3 57.1 + - - +
126A PHE* 3.3 2.9 + - - +
127A ASN* 3.0 28.0 + - + +
111B LEU* 3.9 23.4 - - + +
114B PHE* 4.2 22.2 - - + -
115B GLN* 4.4 30.5 - - + +
118B ILE* 4.4 14.6 - - + -
119B ASN* 5.3 4.5 - - - +
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Residues in contact with GLY 124 (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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65A VAL* 3.5 31.8 - - - +
66A THR* 4.6 1.8 - - - -
119A ASN 3.0 13.1 + - - -
120A VAL 3.6 13.3 + - - -
122A LEU 3.4 0.6 - - - -
123A ILE* 1.3 73.7 - - - +
125A THR* 1.3 60.2 + - - +
127A ASN* 3.4 2.7 + - - +
128A VAL* 3.1 28.6 + - - +
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Residues in contact with THR 125 (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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90A ASN* 3.8 27.4 - - + +
92A ALA 4.8 7.6 + - - -
120A VAL 4.1 1.5 + - - -
121A ASN 3.2 23.4 + - - -
122A LEU 3.4 3.9 + - - -
123A ILE 3.4 0.6 - - - -
124A GLY* 1.3 73.7 - - - +
126A PHE* 1.4 62.1 + - - +
128A VAL* 3.4 4.0 + - - +
129A ILE* 3.1 30.4 + - + +
152A ASN* 3.9 25.8 - - + +
153A THR 5.7 0.9 + - - +
175A ILE* 4.5 14.3 - - + +
178A MET* 4.1 10.1 - - + -
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Residues in contact with PHE 126 (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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122A LEU 3.1 8.9 + - - +
123A ILE 3.8 4.0 - - - +
125A THR* 1.4 76.5 - - - +
127A ASN* 1.3 57.7 + - - +
129A ILE* 3.3 4.7 + - + +
130A ARG* 2.9 52.3 + - + +
178A MET* 4.1 7.4 - - + +
182A ILE* 4.0 23.3 - - + -
100B THR* 4.0 28.0 - - + -
109B HIS* 3.8 36.6 - + + -
110B THR 4.8 0.2 - - - -
111B LEU* 5.0 3.1 - - + -
114B PHE* 3.4 66.0 - + + -
166B ALA* 4.3 5.2 - - + -
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Residues in contact with ASN 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL 3.3 19.9 + - - +
66A THR* 4.3 2.9 - - - -
67A SER 3.6 26.1 + - - -
68A GLU* 3.8 3.8 - - - +
71A VAL* 3.9 9.5 - - - +
123A ILE* 3.0 17.5 + - + +
124A GLY* 3.6 5.6 - - - +
125A THR 3.3 0.2 - - - -
126A PHE* 1.3 73.2 - - - +
128A VAL* 1.3 64.0 + - - +
130A ARG* 2.8 45.4 + - - +
131A LEU* 3.4 32.7 + - - +
111B LEU* 3.7 17.3 - - + +
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Residues in contact with VAL 128 (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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14A VAL* 5.8 4.3 - - + -
16A THR* 3.9 26.5 - - + -
40A LEU* 5.3 2.9 - - + -
65A VAL* 4.0 15.9 - - + -
71A VAL* 4.4 24.9 - - + -
75A LEU* 4.9 6.6 - - + +
88A ALA* 5.1 8.3 - - + -
89A VAL 6.3 0.4 - - - -
90A ASN* 3.4 25.6 - - - +
124A GLY 3.1 15.2 + - - +
125A THR 3.9 1.8 - - - +
126A PHE 3.4 0.2 - - - -
127A ASN* 1.3 76.4 - - - +
129A ILE* 1.3 62.1 + - - +
131A LEU* 4.0 0.5 - - - +
132A VAL* 3.0 33.7 + - + +
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Residues in contact with ILE 129 (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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90A ASN* 3.9 13.0 - - - +
125A THR* 3.1 23.5 + - + +
126A PHE* 3.3 8.7 + - + +
128A VAL* 1.3 75.1 - - - +
130A ARG* 1.3 63.8 + - - +
132A VAL* 3.8 8.9 - - - +
133A ALA* 3.1 24.6 + - - +
150A ILE* 4.0 21.5 - - + -
152A ASN* 3.5 26.2 - - - +
178A MET* 4.2 14.8 - - + -
182A ILE* 4.0 35.0 - - + -
186A LEU* 5.0 1.3 - - + -
193A VAL* 5.4 1.3 - - + -
100B THR* 4.2 10.1 - - + -
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Residues in contact with ARG 130 (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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68A GLU* 3.0 39.6 + - - +
126A PHE* 2.9 45.7 + - + +
127A ASN* 2.8 34.6 + - - +
129A ILE* 1.3 74.7 - - - +
131A LEU* 1.3 75.8 + - - +
133A ALA* 3.7 11.0 + - - +
134A GLY* 4.0 3.8 + - - -
100B THR* 4.2 15.5 - - - +
101B TYR* 5.2 1.2 - - - +
108B VAL* 3.3 42.8 - - + +
109B HIS 3.1 25.3 + - - +
110B THR* 4.1 2.2 - - - +
111B LEU* 3.8 26.9 - - - +
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Residues in contact with LEU 131 (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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68A GLU* 4.1 19.5 - - + +
71A VAL* 3.7 22.0 - - + -
72A GLN* 3.8 29.3 - - - +
75A LEU* 3.8 16.3 - - + +
127A ASN* 3.4 31.2 + - - +
128A VAL 4.2 0.7 - - - +
129A ILE 3.3 0.8 - - - -
130A ARG* 1.3 101.5 - - + +
132A VAL* 1.3 64.1 + - - +
133A ALA 3.4 0.5 + - - -
134A GLY* 3.5 9.5 + - - -
135A VAL* 3.8 14.2 + - - +
108B VAL* 4.8 10.1 - - + -
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Residues in contact with VAL 132 (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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14A VAL* 5.6 1.3 - - + -
75A LEU* 3.8 17.7 - - + +
85A ILE* 4.0 37.9 - - + -
88A ALA* 3.9 20.9 - - + -
128A VAL* 3.0 24.1 + - + +
129A ILE* 3.8 7.4 - - - +
131A LEU* 1.3 73.2 - - - +
133A ALA* 1.3 67.5 + - - +
135A VAL* 3.2 3.9 + - + +
136A MET* 3.0 31.8 + - + +
150A ILE* 3.9 21.1 - - + -
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Residues in contact with ALA 133 (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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129A ILE 3.1 18.4 + - - +
130A ARG* 3.9 7.2 - - - +
131A LEU 3.3 0.4 - - - -
132A VAL* 1.3 80.3 - - - +
134A GLY* 1.3 58.7 + - - +
136A MET* 3.5 2.1 + - - -
137A GLY* 3.0 24.1 + - - -
150A ILE* 4.9 1.3 - - + -
186A LEU* 4.2 34.3 - - + -
189A ILE* 4.3 4.0 - - + +
191A ILE* 3.7 16.1 - - + +
100B THR* 5.1 1.6 - - + -
101B TYR* 4.5 10.3 - - + -
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Residues in contact with GLY 134 (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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130A ARG 4.0 4.6 + - - -
131A LEU 3.5 6.7 + - - -
132A VAL 3.3 0.6 - - - -
133A ALA* 1.3 78.8 - - - +
135A VAL* 1.3 61.0 + - - +
137A GLY* 3.4 9.0 + - - -
138A GLN* 3.6 17.9 + - - +
101B TYR* 4.2 31.4 + - - -
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Residues in contact with VAL 135 (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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72A GLN* 5.3 5.6 - - - +
75A LEU* 4.7 16.8 - - + +
79A LYS* 4.8 14.4 - - + -
84A ARG* 5.4 0.9 - - - -
85A ILE* 3.8 39.6 + - + +
131A LEU 3.8 13.0 - - - +
132A VAL* 3.2 11.1 + - + +
134A GLY* 1.3 72.1 - - - +
136A MET* 1.3 66.4 + - - +
138A GLN* 3.1 37.9 + - - +
139A ASN* 4.0 5.5 + - - +
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Residues in contact with MET 136 (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 ILE* 3.7 15.7 - - + +
86A ASP 3.9 12.3 - - - +
87A VAL 3.9 3.6 - - - +
88A ALA* 3.7 33.4 - - + +
132A VAL* 3.0 30.1 + - + +
135A VAL* 1.3 74.7 - - - +
137A GLY* 1.3 56.6 + - - +
139A ASN* 2.9 36.1 + - - +
147A ARG* 3.8 18.8 - - - +
148A GLY* 4.1 13.2 - - - -
149A VAL 3.8 10.8 - - - +
150A ILE* 3.9 24.5 - - + -
191A ILE* 3.7 23.3 - - + -
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Residues in contact with GLY 137 (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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133A ALA 3.0 15.5 + - - -
134A GLY* 3.4 8.0 + - - -
135A VAL 3.2 0.8 - - - -
136A MET* 1.3 75.9 - - - +
138A GLN* 1.3 59.3 + - - +
139A ASN 3.5 0.5 + - - +
147A ARG* 3.6 23.9 + - - -
189A ILE* 4.3 16.7 - - - +
191A ILE* 4.5 0.6 - - - +
101B TYR* 5.6 4.3 - - - -
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Residues in contact with GLN 138 (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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79A LYS* 4.3 21.0 + - - +
134A GLY 3.6 15.9 + - - +
135A VAL* 3.3 28.6 - - - +
136A MET 3.0 0.8 + - - -
137A GLY* 1.3 75.5 - - - +
139A ASN* 1.3 63.8 + - - +
140A GLU 3.8 1.2 + - - -
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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