Contacts of the helix formed by residues 138 - 153 (chain A) in PDB entry 1R6W
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 GLU 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A TYR* 1.3 79.7 - - - +
139A ALA* 1.3 66.1 + - - +
140A VAL* 3.3 6.9 - - + +
141A ARG* 3.2 10.7 + - + +
142A ASP* 3.1 18.9 + - - -
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Residues in contact with ALA 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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137A TYR 3.9 0.2 + - - -
138A GLU* 1.3 73.9 - - - +
140A VAL* 1.3 57.1 + - - +
142A ASP* 3.2 10.2 + - - +
143A GLY 2.9 26.0 + - - -
166A TRP* 4.5 9.0 - - - +
170A LYS* 3.2 37.7 - - + +
173A GLN* 3.9 17.4 + - + +
174A PHE* 3.6 21.4 - - + +
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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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138A GLU* 3.3 5.9 - - + +
139A ALA* 1.3 75.4 - - - +
141A ARG* 1.3 58.3 + - - +
143A GLY* 3.8 0.7 - - - -
144A MET* 2.9 47.7 + - - +
173A GLN* 4.5 17.5 - - + +
177A TYR* 3.9 40.1 - - + +
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Residues in contact with ARG 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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112A GLY 4.9 7.1 + - - -
114A PRO* 4.4 18.2 - - - +
137A TYR* 3.8 60.0 + - + -
138A GLU* 3.2 14.5 + - + +
140A VAL* 1.3 79.9 - - - +
142A ASP* 1.3 67.3 + - - +
144A MET* 3.3 7.2 + - - +
145A VAL* 2.9 58.0 + - + +
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Residues in contact with ASP 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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133A ARG 4.8 1.6 - - - +
134A VAL* 3.3 22.9 - - + +
135A GLY* 2.8 29.3 + - - -
136A LEU 5.0 0.2 + - - -
137A TYR* 3.8 26.5 + - - +
138A GLU 3.1 14.7 + - - +
139A ALA* 3.2 7.7 + - - +
141A ARG* 1.3 80.5 + - - +
143A GLY* 1.3 57.6 + - - +
145A VAL* 3.9 4.0 - - - +
146A VAL* 2.9 34.5 + - - +
166A TRP* 3.9 5.7 - - - -
174A PHE* 3.7 17.5 - - + -
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Residues in contact with GLY 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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139A ALA 2.9 15.1 + - - -
140A VAL 3.8 2.2 - - - -
142A ASP* 1.3 69.7 - - - +
144A MET* 1.3 60.9 + - - +
146A VAL 3.5 0.2 + - - -
147A ASN* 2.9 30.5 + - - +
174A PHE* 3.4 35.3 - - - -
177A TYR* 3.6 10.5 - - - +
178A VAL* 3.8 5.9 - - - +
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Residues in contact with MET 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* 2.9 36.4 + - - +
141A ARG* 3.8 6.3 - - - +
143A GLY* 1.3 76.4 - - - +
145A VAL* 1.3 59.1 + - + +
147A ASN* 3.3 6.7 + - - +
148A LEU* 3.0 27.2 + - - +
177A TYR* 3.7 27.1 - - + +
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Residues in contact with VAL 145 (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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114A PRO* 3.8 33.9 - - + -
117A LEU* 6.4 0.2 - - + -
132A VAL* 6.1 4.3 - - + -
141A ARG* 2.9 50.3 + - + +
142A ASP* 3.9 4.3 - - - +
144A MET* 1.3 73.6 - - + +
146A VAL* 1.3 68.5 + - + +
148A LEU* 3.1 8.4 + - + +
149A LEU* 3.0 35.9 + - + +
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Residues in contact with VAL 146 (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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132A VAL* 5.5 3.6 - - + -
134A VAL* 4.5 5.8 - - + -
142A ASP 2.9 21.2 + - - +
143A GLY 3.9 3.4 - - - +
145A VAL* 1.3 76.0 - - + +
147A ASN* 1.3 64.7 + - - +
149A LEU* 3.2 11.2 + - + +
150A LEU* 3.0 44.7 + - + +
158A LEU* 4.1 10.3 - - + -
160A LEU* 4.0 24.0 - - + -
174A PHE* 3.9 16.4 - - + -
178A VAL* 4.1 13.7 - - + -
186A ILE* 4.3 12.6 - - + -
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Residues in contact with ASN 147 (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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143A GLY 2.9 10.7 + - - +
144A MET* 3.6 6.3 - - - +
146A VAL* 1.3 78.2 - - - +
148A LEU* 1.3 58.4 + - - +
150A LEU* 3.4 3.8 + - - +
151A GLU* 2.9 43.6 + - - +
177A TYR 3.3 24.9 + - - +
178A VAL* 3.6 5.1 - - - +
179A ASN* 2.8 36.3 + - - +
182A TYR* 3.4 15.4 - - - -
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Residues in contact with LEU 148 (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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114A PRO* 3.9 24.9 - - + -
115A ASP* 3.9 11.0 - - - +
118A ILE* 3.8 23.1 - - + -
144A MET 3.0 14.8 + - - +
145A VAL* 3.1 10.1 + - + +
147A ASN* 1.3 79.2 - - - +
149A LEU* 1.3 57.3 - - + +
151A GLU* 3.9 5.8 - - + +
152A ALA* 3.0 31.8 + - + +
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Residues in contact with LEU 149 (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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114A PRO* 4.0 15.9 - - + +
117A LEU* 4.0 31.4 - - + -
118A ILE* 3.6 28.0 - - + +
121A LEU* 4.7 4.5 - - + -
132A VAL* 4.6 13.2 - - + -
145A VAL* 3.0 32.7 + - + +
146A VAL* 3.6 7.0 - - + +
148A LEU* 1.3 76.9 - - + +
150A LEU* 1.3 63.3 + - - +
152A ALA* 3.3 3.3 + - - +
153A ILE* 3.2 20.0 + - + +
156A LEU* 3.8 21.7 - - + +
158A LEU* 4.0 20.6 - - + -
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Residues in contact with LEU 150 (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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146A VAL* 3.0 37.2 + - + +
147A ASN 4.0 2.5 - - - +
149A LEU* 1.3 76.1 - - - +
151A GLU* 1.3 61.9 + - - +
153A ILE 3.3 7.7 - - - +
154A PRO* 4.1 0.3 - - - +
156A LEU* 3.9 8.5 - - + +
158A LEU* 3.7 23.8 - - + -
178A VAL* 4.3 6.5 - - + -
182A TYR* 3.7 36.8 - - + +
185A ARG* 2.8 65.4 + - + +
186A ILE* 4.1 13.2 - - + +
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Residues in contact with GLU 151 (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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147A ASN* 2.9 28.2 + - - +
148A LEU* 4.0 6.1 - - + +
150A LEU* 1.3 77.4 - - - +
152A ALA* 1.3 62.7 + - - +
153A ILE 3.6 0.2 + - - -
154A PRO* 4.6 8.5 - - - +
179A ASN* 4.4 5.2 + - - -
182A TYR* 2.5 42.8 + - + +
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Residues in contact with ALA 152 (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 ILE* 3.7 36.1 - - + +
148A LEU 3.0 19.1 + - - +
149A LEU 3.7 4.9 - - - +
150A LEU 3.3 0.2 - - - -
151A GLU* 1.3 79.9 - - - +
153A ILE* 1.3 61.4 + - + +
154A PRO* 3.6 7.3 - - - +
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Residues in contact with ILE 153 (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 ILE* 3.7 25.6 - - + +
121A LEU* 3.4 39.0 - - + +
122A ALA* 3.9 12.1 - - + +
128A LYS* 3.6 21.3 - - + -
149A LEU 3.2 7.0 + - - +
150A LEU 3.3 2.6 - - - +
152A ALA* 1.3 86.7 - - + +
154A PRO* 1.3 63.7 - - + +
155A ASP* 3.5 20.2 - - - +
156A LEU* 3.0 24.0 + - + +
185A ARG* 3.0 19.6 + - - -
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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