Contacts of the helix formed by residues 137 - 156 (chain B) in PDB entry 4A9J
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ARG* 4.6 4.7 - - - +
76B THR* 5.5 2.0 - - - -
79B LEU* 3.9 12.9 - - - +
135B TYR* 3.5 1.4 - - - +
136B TRP* 1.3 93.7 - - + +
138B ALA* 1.3 65.9 + - - +
139B SER* 3.2 15.3 - - - +
140B GLU* 3.1 27.5 + - + +
141B CYS 3.7 2.8 + - - -
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ALA* 5.0 1.6 - - + -
76B THR* 4.9 1.4 + - - -
78B GLN* 3.4 45.5 + - + +
79B LEU* 3.8 15.7 - - - +
82B LEU* 3.6 13.1 - - + +
137B ALA* 1.3 72.5 - - - +
139B SER* 1.3 63.4 + - - +
141B CYS* 3.1 6.8 + - - +
142B MET* 3.0 25.7 + - - +
180B MET* 4.2 10.1 - - + -
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Residues in contact with SER 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU 5.1 0.7 - - - -
175A GLN* 4.3 28.7 - - - +
178A ALA* 4.3 15.4 - - - +
137B ALA* 4.0 13.2 - - - +
138B ALA* 1.3 77.8 - - - +
140B GLU* 1.3 61.8 + - - +
142B MET* 3.3 13.5 + - - +
143B GLN* 2.9 36.8 + - - +
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B TYR* 4.6 2.6 - - + +
135B TYR* 3.6 22.4 - - + -
136B TRP* 2.9 38.1 + - - +
137B ALA* 3.1 20.0 + - + +
139B SER* 1.3 82.3 + - - +
141B CYS* 1.3 62.5 + - - +
143B GLN* 3.4 11.0 + - - +
144B ASP* 3.2 20.3 + - - +
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Residues in contact with CYS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU* 4.0 5.2 - - + -
82B LEU* 3.7 22.7 - - + -
126B ILE* 3.9 11.7 - - - -
130B LEU* 3.9 21.5 - - - -
135B TYR* 3.5 26.0 - - + -
137B ALA 3.7 0.8 + - - -
138B ALA 3.1 9.0 + - - +
140B GLU* 1.3 77.5 - - - +
142B MET* 1.3 63.7 + - - +
144B ASP* 3.0 14.0 + - - +
145B PHE* 3.1 34.2 + - - -
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Residues in contact with MET 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 3.2 50.0 - - + +
177A VAL* 4.3 1.8 - - + -
178A ALA* 3.8 25.4 - - - +
82B LEU* 4.2 15.0 - - + -
138B ALA 3.0 18.0 + - - +
139B SER* 3.6 6.7 - - - +
141B CYS* 1.3 75.1 - - - +
143B GLN* 1.3 56.5 + - - +
145B PHE* 3.3 5.8 + - - +
146B ASN* 3.0 27.7 + - - +
173B PHE* 4.0 23.2 - - + -
177B VAL* 3.9 24.9 - - + -
180B MET* 3.9 17.9 - - - +
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Residues in contact with GLN 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LYS* 3.1 53.8 + - + +
174A LEU* 3.5 22.1 - - - +
175A GLN* 3.6 20.8 + - - +
139B SER 2.9 27.8 + - - +
140B GLU* 3.5 11.9 - - - +
141B CYS 3.2 0.2 - - - -
142B MET* 1.3 76.2 - - - +
144B ASP* 1.3 58.4 + - - +
146B ASN* 3.2 7.1 + - - +
147B THR* 2.9 32.9 + - - +
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Residues in contact with ASP 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLN* 4.1 14.4 - - - +
121B MET* 3.2 21.1 - - + +
126B ILE* 3.7 13.5 - - + -
129B ARG* 2.7 29.1 + - - -
135B TYR* 2.6 32.8 + - - +
140B GLU 3.2 8.2 + - - +
141B CYS 3.0 10.1 + - - +
143B GLN* 1.3 78.4 - - - +
145B PHE* 1.3 65.0 + - - +
147B THR* 3.3 3.9 + - - -
148B MET* 3.1 18.7 + - - +
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Residues in contact with PHE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 4.9 6.1 - - + -
86B VAL* 4.6 6.3 - - + -
87B MET* 3.3 44.9 - - + -
90B LEU* 3.4 28.9 - - + -
123B MET* 4.1 6.7 - - + -
126B ILE* 3.6 12.7 - - + +
130B LEU* 5.3 0.2 - - + -
141B CYS* 3.1 44.2 + - - -
142B MET* 3.3 7.4 + - - +
144B ASP* 1.3 74.5 - - - +
146B ASN* 1.3 64.1 + - - +
148B MET* 3.2 20.1 + - + +
149B PHE* 3.1 32.4 + + + -
173B PHE* 3.5 35.7 - + + -
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Residues in contact with ASN 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A TYR* 5.1 1.4 + - - -
167A GLN* 5.5 4.4 + - - +
170A GLU* 3.0 38.1 + - - +
171A LYS* 4.9 12.3 - - - +
174A LEU* 3.4 31.8 - - + +
142B MET 3.0 6.6 + - - +
143B GLN* 3.2 13.0 + - - +
145B PHE* 1.3 76.8 - - - +
147B THR* 1.3 60.0 + - - +
149B PHE* 3.3 7.8 + - - +
150B THR* 2.8 45.1 + - - +
170B GLU* 4.6 6.2 - - - +
173B PHE* 5.2 2.9 - - + -
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Residues in contact with THR 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LYS* 5.7 5.4 - - - -
119B GLN* 3.3 54.2 + - + +
121B MET* 3.9 8.5 - - + -
143B GLN* 2.9 18.1 + - - +
144B ASP* 3.3 10.8 + - - -
146B ASN* 1.3 79.5 + - - +
148B MET* 1.3 57.0 + - - +
150B THR* 3.9 4.2 - - - -
151B ASN* 2.9 43.6 + - - +
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Residues in contact with MET 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B PHE* 4.0 28.1 - - + -
121B MET* 3.5 28.4 - - + +
122B ASP* 3.7 3.8 - - - -
123B MET* 3.5 49.8 - - + -
126B ILE* 4.9 1.1 - - + -
144B ASP 3.1 12.1 + - - +
145B PHE* 3.4 16.2 - - + +
147B THR* 1.3 79.7 - - - +
149B PHE* 1.3 102.1 + - + +
151B ASN* 3.6 4.5 - - - +
152B CYS* 3.3 17.3 + - - +
1187B TYL 5.9 1.9 - - + +
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Residues in contact with PHE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LEU* 4.7 4.0 - - + -
99B PHE* 5.2 3.6 - + - -
123B MET* 5.8 0.7 - - - -
145B PHE* 3.1 34.7 + + - -
146B ASN* 3.9 5.4 - - - +
148B MET* 1.3 100.2 - - + +
150B THR* 1.3 64.3 + - - +
152B CYS* 3.0 18.4 + - - +
153B TYR* 3.2 21.6 + - + -
166B ALA* 3.7 34.3 - - + -
169B LEU* 3.8 22.0 - - + -
170B GLU* 3.3 52.9 - - + +
173B PHE* 4.2 17.5 - + + -
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Residues in contact with THR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A TYR* 3.6 33.3 - - + -
167A GLN* 3.9 16.4 - - + +
146B ASN* 2.8 45.7 + - - +
147B THR* 3.9 4.7 - - - -
149B PHE* 1.3 73.4 - - - +
151B ASN* 1.3 63.0 + - - +
153B TYR* 3.0 11.9 + - - +
154B ILE* 2.9 44.7 + - + +
170B GLU* 5.3 0.9 + - - -
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Residues in contact with ASN 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLN* 5.9 0.5 + - - -
113B TYR* 4.1 11.5 + - - +
117B ILE* 3.4 39.4 - - + +
119B GLN* 2.8 29.4 + - - +
120B PRO* 3.7 0.4 - - - +
121B MET 3.6 16.3 + - - +
147B THR* 2.9 29.8 + - - +
148B MET* 3.6 5.5 - - - +
150B THR* 1.3 76.9 - - - +
152B CYS* 1.3 63.6 + - - +
154B ILE* 4.6 4.5 - - - +
155B TYR* 3.0 29.3 + - - +
1187B TYL 5.6 0.2 - - - -
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Residues in contact with CYS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B PHE* 4.0 11.2 - - + -
148B MET 3.3 8.5 + - - +
149B PHE 3.0 11.5 + - - +
151B ASN* 1.3 79.8 - - - +
153B TYR* 1.3 63.5 + - - +
156B ASN* 2.9 48.4 + - - +
162B ILE* 3.7 43.7 - - - -
163B VAL* 4.3 4.6 - - - +
166B ALA* 3.9 13.7 - - + -
1187B TYL 4.3 7.4 - - + +
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Residues in contact with TYR 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A THR* 3.6 20.0 - - + -
153A TYR* 3.5 38.1 - + + +
154A ILE* 3.9 28.6 - - + +
149B PHE* 3.3 22.1 - - + +
150B THR* 3.0 8.8 + - - +
152B CYS* 1.3 78.2 - - - +
154B ILE* 1.3 62.3 + - - +
156B ASN 3.6 13.7 - - - +
163B VAL* 3.8 23.2 - - + +
166B ALA* 3.5 13.2 - - + -
167B GLN* 3.3 36.6 + - + +
170B GLU* 2.6 41.4 + - - +
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Residues in contact with ILE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A TYR* 4.1 18.3 - - + +
156A ASN 5.4 2.1 - - - +
158A PRO* 3.5 49.1 - - + +
163A VAL* 3.9 24.0 - - + -
167A GLN* 4.0 9.2 - - - +
116B ILE* 4.2 11.0 - - + +
117B ILE* 4.2 9.0 - - + -
150B THR* 2.9 41.5 + - + +
151B ASN* 3.9 7.2 - - - +
153B TYR* 1.3 79.3 - - - +
155B TYR* 1.3 60.7 + - - +
156B ASN 4.4 1.6 - - - +
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Residues in contact with TYR 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 3.4 36.8 - - + +
112B ASP* 2.9 29.6 + - - -
113B TYR* 3.7 42.4 - + + -
116B ILE* 3.8 33.2 - - + +
117B ILE* 4.0 12.6 - - + -
151B ASN 3.0 16.6 + - - +
154B ILE* 1.3 79.3 - - - +
156B ASN* 1.3 83.0 - - - +
157B LYS* 4.2 0.5 + - - +
1187B TYL 4.5 1.8 - + - -
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Residues in contact with ASN 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE 5.4 0.9 - - - +
152B CYS* 2.9 30.1 + - - +
153B TYR 3.6 13.6 - - - +
154B ILE 4.4 1.6 - - - +
155B TYR* 1.3 91.5 - - - +
157B LYS* 1.3 65.6 + - - +
158B PRO* 3.8 2.9 - - - +
160B ASP* 3.5 12.4 - - - +
162B ILE* 3.4 26.3 - - + +
163B VAL* 4.0 8.8 - - + +
1187B TYL 3.1 51.1 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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