Contacts of the helix formed by residues 121 - 137 (chain A) in PDB entry 1SNG
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 ASN 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A ASP* 3.3 8.3 + - + +
120A THR* 1.3 86.3 + - - +
122A PRO* 1.3 62.8 - - - +
123A GLU* 3.7 8.3 - - - +
124A GLY* 3.3 26.4 - - - +
125A VAL* 3.0 30.0 + - + +
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Residues in contact with PRO 122 (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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118A PHE 3.5 17.7 - - - +
119A ARG 4.6 2.2 - - - +
120A THR 3.9 4.0 - - - +
121A ASN* 1.3 89.2 - - - +
123A GLU* 1.3 61.1 + - + +
125A VAL* 3.3 2.9 + - + -
126A ARG* 2.9 23.0 + - - +
150A VAL* 3.4 46.0 - - + +
151A THR* 4.3 0.4 - - - -
152A PRO* 3.9 24.7 - - + -
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Residues in contact with GLU 123 (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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121A ASN* 3.4 6.8 - - - +
122A PRO* 1.3 80.8 - - + +
124A GLY* 1.3 61.1 + - - +
126A ARG* 3.2 45.4 + - - +
127A ALA* 3.0 27.4 + - - +
147A GLN* 3.9 23.0 + - - +
148A GLY* 4.0 7.8 + - - -
150A VAL 4.9 5.5 - - - +
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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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121A ASN* 3.3 27.1 + - - +
123A GLU* 1.3 76.3 - - - +
125A VAL* 1.3 62.9 + - - +
127A ALA* 3.3 7.4 + - - +
128A THR* 3.0 26.4 + - - -
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Residues in contact with VAL 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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116A ALA* 3.8 13.5 - - + -
117A ASP* 3.4 35.9 - - + +
118A PHE* 3.7 31.0 - - + +
121A ASN* 3.0 20.9 + - + +
122A PRO 3.3 7.8 + - - +
124A GLY* 1.3 73.3 - - - +
126A ARG* 1.3 61.2 + - - +
128A THR* 3.1 7.1 + - - -
129A VAL* 2.8 46.3 + - + +
150A VAL* 4.2 6.5 - - + -
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Residues in contact with ARG 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 PRO 2.9 15.2 + - - +
123A GLU* 3.2 39.5 + - - +
124A GLY 3.3 0.2 - - - -
125A VAL* 1.3 76.3 - - - +
127A ALA* 1.3 58.4 + - - +
129A VAL* 3.4 4.2 + - - +
130A ASN* 2.9 51.8 + - - +
143A GLU* 3.0 23.6 + - - +
145A LEU* 3.0 30.7 + - + +
146A PRO 3.3 20.6 - - - -
147A GLN* 3.6 28.9 - - - +
148A GLY 4.6 1.3 - - - +
150A VAL* 3.9 18.6 - - + +
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Residues in contact with ALA 127 (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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123A GLU 3.0 14.2 + - - +
124A GLY* 3.6 11.0 - - - +
126A ARG* 1.3 76.5 - - - +
128A THR* 1.3 57.2 + - - +
130A ASN* 3.9 5.0 - - - +
131A ALA* 2.9 32.4 + - - +
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Residues in contact with THR 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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90A TRP* 3.9 24.0 - - + -
114A ARG* 4.2 15.3 - - - +
124A GLY 3.0 14.3 + - - -
125A VAL* 3.6 10.5 - - - -
127A ALA* 1.3 76.0 - - - +
129A VAL* 1.3 64.4 + - - +
131A ALA* 3.4 4.7 + - - +
132A ASP* 3.0 23.2 + - - +
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Residues in contact with VAL 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 TRP* 3.5 50.3 - - + +
125A VAL* 2.8 38.2 + - + +
126A ARG 3.7 3.4 - - - +
128A THR* 1.3 72.4 - - - +
130A ASN* 1.3 64.9 + - - +
132A ASP* 3.2 5.0 + - - +
133A ILE* 3.1 25.0 + - + +
144A LEU* 5.1 0.9 - - + -
145A LEU* 3.6 30.3 - - + -
157A ILE* 4.8 3.1 - - + -
159A THR* 3.8 16.2 - - + +
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Residues in contact with ASN 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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126A ARG* 2.9 37.0 + - - +
127A ALA* 4.0 4.7 - - - +
129A VAL* 1.3 77.0 - - - +
131A ALA* 1.3 57.3 + - - +
133A ILE* 3.5 5.7 + - - +
134A ALA* 2.9 30.1 + - - +
142A ARG 3.8 16.7 - - - +
143A GLU* 3.4 10.7 - - - +
144A LEU* 3.3 12.3 + - - +
145A LEU* 2.9 54.3 + - - +
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Residues in contact with ALA 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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127A ALA 2.9 19.1 + - - +
128A THR* 3.8 5.2 - - - +
130A ASN* 1.3 73.5 - - - +
132A ASP* 1.3 64.0 + - - +
134A ALA* 3.7 7.0 - - - +
135A ASP* 3.0 27.0 + - - +
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Residues in contact with ASP 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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86A ARG* 3.0 42.5 + - - +
88A VAL* 3.2 13.5 - - - +
90A TRP* 3.9 17.9 - - + -
114A ARG* 3.4 15.1 + - - +
128A THR 3.0 14.5 + - - +
129A VAL 3.2 10.1 + - - +
131A ALA* 1.3 77.3 - - - +
133A ILE* 1.3 64.8 + - - +
135A ASP* 4.2 2.5 - - - +
136A ALA* 3.2 25.5 + - - +
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Residues in contact with ILE 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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86A ARG* 3.7 37.2 - - + +
88A VAL* 5.4 0.7 - - + -
90A TRP* 5.9 0.2 - - - +
129A VAL* 3.1 17.1 + - + +
130A ASN 3.9 3.8 - - - +
132A ASP* 1.3 78.3 - - - +
134A ALA* 1.3 59.3 + - - +
136A ALA 3.8 0.2 - - - -
137A THR* 2.7 36.9 + - + +
141A ILE* 3.7 21.3 - - + +
144A LEU* 4.0 26.0 - - + -
159A THR* 4.1 22.0 - - - +
161A ALA* 3.6 27.8 - - + +
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Residues in contact with ALA 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 ASN 2.9 19.1 + - - +
131A ALA* 3.7 9.0 - - - +
132A ASP 3.3 0.2 - - - -
133A ILE* 1.3 75.9 - - - +
135A ASP* 1.3 57.6 - - - +
137A THR* 3.2 7.0 + - - -
139A GLY* 2.7 33.1 + - - +
141A ILE 3.2 17.8 + - - +
142A ARG* 3.9 20.9 - - + +
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Residues in contact with ASP 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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131A ALA 3.0 14.9 + - - +
132A ASP* 4.2 2.5 - - - +
134A ALA* 1.3 78.8 - - - +
136A ALA* 1.3 59.7 + - - +
138A ARG* 3.0 20.3 + - - +
139A GLY* 4.7 1.8 - - - +
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Residues in contact with ALA 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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84A ALA* 3.5 17.5 - - - +
85A SER 4.5 4.7 - - - +
86A ARG* 3.6 38.1 - - + +
132A ASP 3.2 17.3 + - - +
133A ILE 4.0 1.3 - - - +
135A ASP* 1.3 79.3 - - - +
137A THR* 1.3 58.6 + - - +
138A ARG* 3.3 4.3 + - - +
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Residues in contact with THR 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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84A ALA* 3.8 20.6 - - - +
86A ARG* 4.9 6.1 - - + -
133A ILE* 2.7 24.6 + - + +
134A ALA 3.2 4.7 + - - -
135A ASP 3.2 0.2 - - - -
136A ALA* 1.3 77.1 - - - +
138A ARG* 1.3 70.7 + - - +
140A MET* 3.1 18.0 + - - +
141A ILE* 3.1 32.8 + - + -
161A ALA* 3.8 29.4 - - + +
163A TRP* 4.0 12.0 - - + -
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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