Contacts of the helix formed by residues 129 - 144 (chain A) in PDB entry 1A7C
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 VAL 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A PHE* 3.4 19.1 - - - +
127A SER 3.2 3.7 + - - +
128A GLU* 1.3 72.9 - - - +
130A GLU* 1.3 70.3 + - + +
132A ALA* 3.2 5.0 + - - +
133A ARG* 2.9 29.9 + - + +
155A GLY 6.1 0.9 - - - +
157A VAL* 3.6 31.1 - - + +
158A ASP* 3.8 4.0 - - + -
159A GLN* 3.6 34.8 - - + +
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Residues in contact with GLU 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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128A GLU 3.5 0.8 - - - -
129A VAL* 1.3 86.9 - - + +
131A ARG* 1.3 57.4 + - - +
133A ARG* 2.9 38.9 + - - +
134A PHE* 3.1 29.5 + - - +
154A LYS* 3.3 35.8 + - - +
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Residues in contact with ARG 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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125A ASP 5.6 1.1 - - - +
128A GLU* 3.1 34.2 + - + +
130A GLU* 1.3 76.7 - - - +
132A ALA* 1.3 60.4 + - - +
134A PHE* 3.3 35.4 + - - +
135A ILE* 3.0 56.5 + - + +
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Residues in contact with ALA 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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124A VAL* 4.4 9.4 - - + -
125A ASP 3.7 22.2 - - - +
126A PHE* 3.8 31.0 - - + -
128A GLU 3.1 3.1 + - - +
129A VAL 3.7 6.7 - - - +
131A ARG* 1.3 80.5 - - - +
133A ARG* 1.3 62.7 + - - +
135A ILE* 3.3 11.7 + - - +
136A ILE* 3.2 30.1 + - - +
157A VAL* 5.7 0.2 - - + -
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Residues in contact with ARG 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 VAL* 2.9 17.9 + - - +
130A GLU* 2.9 40.3 + - - +
132A ALA* 1.3 77.2 - - - +
134A PHE* 1.3 58.3 + - - +
136A ILE* 3.5 5.8 + - - +
137A ASN* 2.9 43.4 + - - +
150A ASN* 3.8 11.9 + - - +
152A LEU* 2.7 41.1 + - + +
153A GLY* 3.5 26.6 - - - -
154A LYS* 3.7 25.6 - - - +
155A GLY 5.1 0.9 - - - +
157A VAL* 3.8 26.1 - - + +
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Residues in contact with PHE 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 GLU 3.1 19.2 + - - +
131A ARG* 3.6 31.9 - - - +
132A ALA 3.3 0.2 - - - -
133A ARG* 1.3 75.5 - - - +
135A ILE* 1.3 64.8 + - + +
137A ASN* 4.5 6.1 - - + +
138A ASP* 2.8 66.1 + - + +
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Residues in contact with ILE 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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98A PHE* 4.2 13.5 - - + -
124A VAL* 4.1 31.0 - - + -
131A ARG* 3.0 61.5 + - + +
132A ALA* 3.3 8.5 + - - +
134A PHE* 1.3 81.2 - - + +
136A ILE* 1.3 56.7 + - - +
138A ASP* 3.8 3.9 - - - +
139A TRP* 3.1 26.9 + - + +
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Residues in contact with ILE 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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98A PHE* 3.7 43.1 - - + -
124A VAL* 5.2 2.0 - - + -
126A PHE* 4.0 15.3 - - + -
132A ALA 3.2 17.7 + - - +
133A ARG* 3.9 3.6 - - - +
135A ILE* 1.3 75.3 - - + +
137A ASN* 1.3 64.6 + - - +
139A TRP* 3.1 3.8 + - - +
140A VAL* 3.0 31.3 + - + +
151A LEU* 5.1 0.7 - - + -
152A LEU* 3.8 26.0 - - + -
157A VAL* 5.3 0.7 - - + -
164A VAL* 3.9 37.7 - - + -
166A VAL* 4.6 5.2 - - + -
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Residues in contact with ASN 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 ARG* 2.9 34.4 + - - +
134A PHE* 3.9 6.4 - - + +
136A ILE* 1.3 78.0 - - - +
138A ASP* 1.3 57.6 + - - +
140A VAL* 3.5 6.6 + - - +
141A LYS* 3.0 28.1 + - - +
148A ILE 4.5 0.9 - - - +
149A SER 4.0 14.0 - - - +
150A ASN* 3.5 13.5 + - - -
151A LEU* 3.4 12.4 + - - +
152A LEU* 2.8 53.0 + - - +
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Residues in contact with ASP 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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134A PHE* 2.8 49.0 + - + +
135A ILE* 3.8 4.7 - - - +
137A ASN* 1.3 74.6 - - - +
139A TRP* 1.3 67.5 + - - +
141A LYS* 3.3 14.2 + - - +
142A THR* 3.0 35.3 + - - -
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Residues in contact with TRP 139 (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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94A THR* 3.5 46.9 - - + -
95A ASP 4.3 0.4 - - - -
96A ALA* 3.5 24.2 - - + -
98A PHE* 3.8 17.3 - + + -
119A SER* 5.2 0.4 - - - -
122A LYS* 3.6 25.0 - - + +
135A ILE 3.1 15.6 + - - +
136A ILE 3.5 7.6 - - - +
138A ASP* 1.3 78.7 + - - +
140A VAL* 1.3 69.8 + - + +
142A THR* 3.4 3.1 + - - -
143A HIS* 2.7 59.6 + + + -
166A VAL* 3.7 23.3 - - + -
168A ALA* 3.8 20.2 - - + -
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Residues in contact with VAL 140 (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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136A ILE* 3.0 21.8 + - + +
137A ASN 3.8 4.5 - - - +
139A TRP* 1.3 94.3 - - + +
141A LYS* 1.3 62.5 + - - +
143A HIS* 3.3 1.6 + - - -
144A THR* 2.8 36.8 + - + +
148A ILE* 3.8 31.2 - - + +
151A LEU* 3.7 33.7 - - + -
166A VAL* 4.6 6.3 - - + -
167A ASN 6.0 1.3 - - - +
168A ALA* 5.1 5.2 - - + -
905B SER 5.4 3.1 - - - +
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Residues in contact with LYS 141 (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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137A ASN 3.0 19.1 + - - +
138A ASP* 3.6 14.8 - - - +
139A TRP 3.3 0.2 - - - -
140A VAL* 1.3 76.6 - - - +
142A THR* 1.3 59.6 + - - +
144A THR* 3.4 0.7 + - - -
145A LYS 3.2 3.6 + - - -
146A GLY* 2.6 48.5 + - - -
148A ILE 3.2 12.7 + - - +
149A SER* 3.9 30.8 - - - +
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Residues in contact with THR 142 (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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138A ASP* 3.0 25.4 + - - -
139A TRP* 3.6 6.6 - - - -
141A LYS* 1.3 77.3 - - - +
143A HIS* 1.3 73.7 + - + +
145A LYS* 3.3 18.4 + - - +
146A GLY 4.9 0.4 - - - +
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Residues in contact with HIS 143 (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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92A SER* 4.7 9.8 + - - +
94A THR* 3.6 29.5 + - + +
139A TRP* 2.7 64.1 + + + +
140A VAL 3.3 1.3 + - - +
142A THR* 1.3 89.1 - - + +
144A THR* 1.3 61.2 + - - +
145A LYS* 3.4 3.7 - - - +
168A ALA* 3.7 27.4 - - + +
170A TYR* 4.1 12.0 - - - +
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Residues in contact with THR 144 (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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140A VAL* 2.8 24.9 + - + +
141A LYS 3.4 4.2 + - - -
142A THR 3.3 0.2 - - - -
143A HIS* 1.3 80.1 - - - +
145A LYS* 1.3 68.7 + - - +
147A MET* 2.9 17.2 + - - +
148A ILE* 3.1 34.4 + - + -
168A ALA* 4.2 9.4 - - + -
169A LEU 4.1 9.9 - - - +
170A TYR* 3.6 9.3 - - - -
904B SER* 3.6 17.5 + - - -
905B SER 3.7 23.6 - - - +
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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