Contacts of the helix formed by residues 137 - 156 (chain A) in PDB entry 4A9F
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 ALA 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A THR* 5.8 1.8 - - - -
79A LEU* 4.2 7.6 - - - -
135A TYR* 3.5 7.8 - - - +
136A TRP* 1.3 78.6 - - - +
138A ALA* 1.3 65.4 + - - +
139A SER* 3.9 16.8 - - - +
140A GLU* 3.2 29.1 + - + +
141A CYS 3.8 3.1 + - - -
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Residues in contact with ALA 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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76A THR* 5.2 1.4 + - - -
78A GLN* 3.1 49.8 + - + +
79A LEU* 4.0 13.8 - - - +
82A LEU* 3.7 10.9 - - + +
137A ALA* 1.3 69.7 - - - +
139A SER* 1.3 67.4 - - - +
141A CYS* 3.0 7.4 + - - +
142A MET* 3.0 26.8 + - - +
180A MET* 4.3 6.3 - - - -
178B ALA* 5.0 1.8 - - + -
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Residues in contact with SER 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ALA* 3.9 13.8 - - - +
138A ALA* 1.3 79.9 - - - +
140A GLU* 1.3 60.4 + - - +
142A MET* 3.3 13.9 + - - +
143A GLN* 2.8 39.0 + - - +
174B LEU 5.6 0.2 - - - -
175B GLN* 4.4 31.9 - - - +
178B ALA* 4.9 7.0 - - - +
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Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TYR* 4.9 0.9 - - - +
135A TYR* 3.6 15.8 - - + -
136A TRP* 2.7 45.8 + - - +
137A ALA* 3.2 24.9 + - + +
138A ALA 3.1 1.0 + - - -
139A SER* 1.3 79.2 + - - +
141A CYS* 1.3 61.4 + - - +
143A GLN* 3.5 9.3 + - - +
144A ASP* 3.2 24.9 + - - +
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Residues in contact with CYS 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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79A LEU* 4.3 4.0 - - + -
82A LEU* 3.8 22.0 - - + -
126A ILE* 4.0 4.7 - - - -
130A LEU* 3.9 13.2 - - - -
135A TYR* 3.6 41.3 - - + -
137A ALA 3.8 0.6 + - - -
138A ALA 3.0 8.8 + - - +
140A GLU* 1.3 76.0 - - - +
142A MET* 1.3 65.7 + - - +
144A ASP* 3.0 13.2 + - - +
145A PHE* 3.1 37.6 + - - -
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Residues in contact with MET 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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82A LEU* 4.1 15.9 - - + -
138A ALA 3.0 20.6 + - - +
139A SER* 3.5 9.6 - - - +
141A CYS* 1.3 76.7 - - - +
143A GLN* 1.3 55.7 + - - +
145A PHE* 3.3 4.0 + - - +
146A ASN* 2.9 27.9 + - - +
173A PHE* 3.9 23.2 - - + -
177A VAL* 3.6 27.6 - - + -
180A MET* 3.5 24.0 - - + +
174B LEU* 3.3 48.3 - - + +
177B VAL* 4.4 0.9 - - + -
178B ALA* 3.8 15.0 - - + +
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Residues in contact with GLN 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 SER* 2.8 32.2 + - - +
140A GLU* 3.7 8.3 - - - +
141A CYS 3.2 0.2 - - - -
142A MET* 1.3 73.1 - - - +
144A ASP* 1.3 59.2 + - - +
146A ASN* 3.5 6.7 + - - +
147A THR* 2.8 36.2 + - - +
171B LYS* 3.3 60.6 + - + +
174B LEU* 3.6 24.4 - - - +
175B GLN* 3.9 16.6 - - - +
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Residues in contact with ASP 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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121A MET* 3.2 30.8 - - + +
126A ILE* 3.7 13.7 - - + -
129A ARG* 2.9 25.8 + - - -
135A TYR* 2.7 32.4 + - - +
140A GLU 3.2 13.1 + - - +
141A CYS 3.0 9.4 + - - +
143A GLN* 1.3 75.7 - - - +
145A PHE* 1.3 65.6 + - - +
147A THR* 3.4 5.0 + - - -
148A MET* 3.0 19.2 + - - +
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Residues in contact with PHE 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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82A LEU* 5.0 5.8 - - + -
86A VAL* 4.2 12.3 - - + -
87A MET* 3.6 34.8 - - + -
90A LEU* 3.4 33.4 - - + -
123A MET* 4.4 7.6 - - + -
126A ILE* 3.6 18.8 - - + +
130A LEU* 5.1 0.4 - - + -
141A CYS* 3.1 44.0 + - - -
142A MET* 3.6 2.9 - - - +
144A ASP* 1.3 74.8 - - - +
146A ASN* 1.3 64.0 + - - +
148A MET* 3.2 15.9 + - + +
149A PHE* 3.1 32.7 + + + -
173A PHE* 3.5 36.1 - + + -
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Residues in contact with ASN 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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142A MET 2.9 17.0 + - - +
143A GLN* 3.5 13.9 + - - +
145A PHE* 1.3 78.4 - - - +
147A THR* 1.3 59.9 + - - +
149A PHE* 3.2 8.4 + - - +
150A THR* 2.8 43.8 + - - -
170A GLU* 4.4 7.0 - - - +
173A PHE* 5.0 3.7 - - + -
153B TYR* 5.1 1.6 + - - -
167B GLN* 5.5 4.0 + - - +
170B GLU* 3.0 37.3 + - - +
171B LYS* 4.7 13.9 - - - +
174B LEU* 3.5 21.6 - - + +
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Residues in contact with THR 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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119A GLN* 3.2 43.9 + - + +
121A MET* 4.0 10.1 - - + -
143A GLN* 2.8 25.1 + - - +
144A ASP* 3.7 8.5 + - - -
145A PHE 3.3 0.2 - - - -
146A ASN* 1.3 73.9 + - - +
148A MET* 1.3 58.6 + - - +
150A THR* 4.4 5.6 - - - -
151A ASN* 2.8 43.3 + - - +
171B LYS* 4.7 12.3 + - - -
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Residues in contact with MET 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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99A PHE* 4.0 27.6 - - + -
121A MET* 3.5 29.5 - - + +
122A ASP* 3.7 3.8 - - - -
123A MET* 3.5 49.4 - - + -
126A ILE* 4.7 1.8 - - - -
144A ASP 3.0 13.6 + - - +
145A PHE* 3.2 16.4 + - + +
147A THR* 1.3 77.5 - - - +
149A PHE* 1.3 103.0 + - + +
151A ASN* 3.5 4.8 + - - +
152A CYS* 3.3 18.4 + - - +
169A LEU* 5.6 0.2 - - + -
1183A MB3 5.9 0.7 - - - -
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Residues in contact with PHE 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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90A LEU* 4.5 8.7 - - + -
99A PHE* 5.0 2.5 - + - -
123A MET* 6.2 0.2 - - - -
145A PHE* 3.1 29.4 + + - -
146A ASN* 3.8 3.8 - - - +
148A MET* 1.3 101.8 - - + +
150A THR* 1.3 63.0 + - - +
152A CYS* 3.1 16.7 + - - +
153A TYR* 3.1 24.1 + - + +
166A ALA* 3.8 22.2 - - + -
169A LEU* 3.6 33.7 - - + -
170A GLU* 3.4 53.4 - - + +
173A PHE* 4.1 17.5 - + + -
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Residues in contact with THR 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 ASN* 2.8 39.9 + - - +
147A THR* 3.9 5.4 - - - -
149A PHE* 1.3 73.6 - - - +
151A ASN* 1.3 63.3 + - - +
153A TYR* 3.2 10.4 + - - +
154A ILE* 3.0 43.8 + - + +
170A GLU* 5.1 1.6 + - - -
153B TYR* 3.6 34.2 - - + -
167B GLN* 3.8 17.3 - - + +
170B GLU* 4.0 0.2 + - - -
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Residues in contact with ASN 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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113A TYR* 3.9 10.8 + - - +
117A ILE* 3.4 38.4 - - + +
118A LYS 5.6 0.2 + - - -
119A GLN* 2.8 29.5 + - - +
120A PRO* 3.6 0.6 - - - +
121A MET 3.6 17.4 + - - +
147A THR* 2.8 33.9 + - - +
148A MET* 3.7 5.9 - - - +
150A THR* 1.3 72.6 - - - +
152A CYS* 1.3 57.9 + - - +
154A ILE* 4.5 2.9 - - - +
155A TYR* 2.9 34.9 + - - +
167B GLN* 5.6 2.4 + - - -
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Residues in contact with CYS 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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99A PHE* 4.0 11.4 - - + -
113A TYR* 5.3 0.2 + - - -
148A MET 3.3 9.7 + - - +
149A PHE 3.1 10.6 + - - +
151A ASN* 1.3 80.1 - - - +
153A TYR* 1.3 62.8 + - - +
156A ASN* 2.9 48.0 + - - +
162A ILE* 3.6 40.2 - - - -
163A VAL* 4.3 4.5 - - - +
166A ALA* 3.8 13.9 - - + -
1183A MB3 4.0 10.1 - - - +
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Residues in contact with TYR 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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149A PHE* 3.1 21.6 + - + +
150A THR* 3.2 7.2 + - - +
152A CYS* 1.3 78.0 - - - +
154A ILE* 1.3 62.1 + - - +
156A ASN 3.7 11.8 - - - +
163A VAL* 3.8 22.9 - - + +
166A ALA* 3.5 23.6 - - + +
167A GLN* 3.3 37.6 + - + +
170A GLU* 2.6 40.4 + - - +
150B THR* 3.6 26.0 - - + -
153B TYR* 3.4 37.1 - + + +
154B ILE* 3.9 16.1 - - + +
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Residues in contact with ILE 154 (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 ILE* 4.1 3.8 - - + +
117A ILE* 4.0 16.4 - - + -
150A THR* 3.0 38.9 + - + +
151A ASN* 3.8 6.3 - - - +
153A TYR* 1.3 79.6 - - - +
155A TYR* 1.3 63.9 + - - +
156A ASN 4.2 2.1 - - - +
153B TYR* 3.9 22.9 - - + +
156B ASN 5.3 1.4 - - - +
158B PRO* 3.5 46.4 - - + +
163B VAL* 3.6 29.8 - - + -
167B GLN* 3.8 9.0 - - - +
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Residues in contact with TYR 155 (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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110A LEU* 3.5 35.0 - - + +
112A ASP* 2.7 39.9 + - - -
113A TYR* 3.6 41.1 - + + -
116A ILE* 3.8 27.7 - - + +
117A ILE* 3.9 12.1 - - + -
151A ASN 2.9 17.5 + - - +
154A ILE* 1.3 82.2 - - - +
156A ASN* 1.3 85.2 + - - +
1183A MB3 4.7 1.1 - + - -
158B PRO* 5.8 0.7 - - - +
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Residues in contact with ASN 156 (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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110A LEU* 5.9 0.2 - - - +
152A CYS* 2.9 28.7 + - - +
153A TYR 3.7 12.5 - - - +
154A ILE 4.2 1.7 - - - +
155A TYR* 1.3 99.6 - - - +
157A LYS* 1.3 65.5 + - - +
158A PRO* 3.7 4.2 - - - +
160A ASP* 3.5 11.8 - - - +
162A ILE* 3.4 29.0 - - + +
163A VAL* 3.9 8.4 - - + +
1183A MB3 2.9 34.5 + - - -
154B ILE* 5.4 1.0 - - - +
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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