Contacts of the helix formed by residues 140 - 155 (chain A) in PDB entry 4B18
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 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A PRO* 4.7 18.0 + - - +
100A LEU* 5.6 5.2 - - - +
137A ARG* 2.7 25.9 + - + +
138A LYS 3.2 0.8 - - - -
139A GLU* 1.3 87.8 + - + +
141A CYS* 1.3 67.3 + - - +
142A THR* 3.5 15.6 + - - -
143A LEU* 3.5 30.3 + - + +
144A GLN* 3.2 26.5 + - - +
182A PHE* 4.7 0.4 - - - -
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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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139A GLU 4.1 2.0 + - - -
140A ASN* 1.3 69.8 + - - +
142A THR* 1.3 73.0 + - - +
144A GLN* 3.2 4.0 + - - +
145A PHE* 3.0 25.5 + - - +
182A PHE* 3.8 51.0 - - + -
184A ASP* 5.0 15.3 - - - -
185A VAL* 4.0 7.7 - - - +
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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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100A LEU* 4.0 29.2 - - + -
104A GLN* 4.6 4.3 - - - +
140A ASN* 3.5 7.8 + - - -
141A CYS* 1.3 79.9 - - - +
143A LEU* 1.3 58.7 + - - +
145A PHE* 2.9 12.0 + - + +
146A GLU* 2.9 43.5 + - + +
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Residues in contact with LEU 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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96A PRO 4.7 1.6 - - - +
99A GLN* 3.9 7.9 - - + +
100A LEU* 3.5 48.9 - - + +
103A THR* 4.0 4.7 - - - +
134A PHE* 3.7 37.2 - - + +
137A ARG* 3.7 44.2 - - + +
140A ASN* 3.5 23.0 + - + +
141A CYS 3.4 0.2 - - - -
142A THR* 1.3 77.9 - - - +
144A GLN* 1.3 63.7 + - - +
146A GLU* 4.2 1.0 - - - +
147A SER* 2.9 29.8 + - - -
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Residues in contact with GLN 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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134A PHE 3.7 14.1 + - - +
135A LEU* 2.6 36.5 + - - +
136A LYS* 4.1 1.2 - - - +
137A ARG 3.7 13.6 - - - +
138A LYS* 3.8 23.9 - - - +
140A ASN 3.2 21.3 + - - +
141A CYS 3.2 3.6 + - - +
143A LEU* 1.3 75.8 - - - +
145A PHE* 1.3 57.4 + - - +
147A SER* 3.6 3.3 - - - -
148A ALA* 2.9 29.7 + - - +
177A LEU* 3.4 23.7 - - + +
180A SER* 4.8 1.8 + - - -
182A PHE* 4.0 20.3 - - - -
185A VAL* 4.0 16.6 - - + +
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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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107A ARG* 5.6 0.2 - - - -
141A CYS* 3.0 13.8 + - - +
142A THR* 2.9 13.6 + - + +
144A GLN* 1.3 73.7 - - - +
146A GLU* 1.3 79.2 + - + +
147A SER 3.1 1.1 - - - -
148A ALA* 3.1 6.9 + - - +
149A TRP* 2.8 60.2 + + - +
184A ASP* 3.7 43.5 - - + -
185A VAL* 4.2 11.2 - - + +
188A GLN* 4.0 12.6 - - + -
239B ARG* 3.8 27.4 - - - -
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Residues in contact with GLU 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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100A LEU* 4.0 16.6 - - + -
103A THR* 3.6 22.0 - - + +
104A GLN* 3.7 17.5 - - + +
107A ARG* 2.5 54.0 + - - +
142A THR* 2.9 29.7 + - + +
143A LEU 4.2 1.3 - - - +
145A PHE* 1.3 86.5 - - + +
147A SER* 1.3 57.8 + - - +
149A TRP* 3.1 7.6 + - - +
150A VAL* 2.9 31.0 + - - +
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Residues in contact with SER 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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103A THR* 4.0 10.4 - - - +
131A PHE* 4.1 17.4 + - - -
134A PHE* 3.3 29.1 - - - +
135A LEU* 4.0 13.0 - - - -
143A LEU 2.9 21.8 + - - -
144A GLN* 3.6 4.0 - - - -
146A GLU* 1.3 76.0 - - - +
148A ALA* 1.3 65.1 + - - +
150A VAL* 3.3 6.0 + - - +
151A LEU* 3.0 28.6 + - - +
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Residues in contact with ALA 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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135A LEU* 3.8 8.9 - - + +
144A GLN 2.9 17.4 + - - +
145A PHE* 3.1 6.5 + - - +
147A SER* 1.3 75.6 - - - +
149A TRP* 1.3 57.3 + - - +
151A LEU* 3.3 1.6 + - - +
152A THR* 2.8 32.9 + - - -
174A PHE* 3.7 24.2 - - + -
177A LEU* 5.5 2.5 - - + -
185A VAL* 5.3 3.8 - - + +
188A GLN* 3.7 25.1 - - + -
189A ALA* 4.7 1.3 - - + +
192A ALA* 4.5 0.7 - - - +
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Residues in contact with TRP 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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107A ARG* 3.5 49.6 - - + +
111A SER* 4.0 10.1 + - - -
145A PHE* 2.8 40.6 + + - +
146A GLU* 3.2 11.2 - - - +
148A ALA* 1.3 76.8 - - - +
150A VAL* 1.3 62.6 + - - +
152A THR* 3.0 10.6 + - - -
153A ASN* 3.0 22.7 + - - +
188A GLN* 3.6 16.3 - - + +
239B ARG* 3.2 72.4 + - + +
241B ALA 4.0 25.1 - - - -
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Residues in contact with VAL 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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103A THR* 4.0 13.5 - - + +
106A PHE* 4.0 7.4 - - + -
107A ARG* 3.6 34.3 - - + +
110A LEU* 3.8 18.1 - - + +
131A PHE* 3.7 36.8 - - + -
146A GLU 2.9 15.4 + - - +
147A SER* 3.3 8.9 + - - +
149A TRP* 1.3 75.0 - - - +
151A LEU* 1.3 65.0 + - - +
153A ASN* 3.1 13.1 + - - +
154A ILE* 3.1 23.0 + - + +
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Residues in contact with LEU 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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128A VAL* 4.1 26.2 - - + -
131A PHE* 4.1 23.3 - - + -
132A VAL* 4.1 14.8 - - + +
135A LEU* 3.9 19.3 - - + -
147A SER 3.0 21.0 + - - +
148A ALA 3.9 0.2 - - - +
150A VAL* 1.3 74.3 - - + +
152A THR* 1.3 61.1 + - - +
154A ILE* 4.1 11.7 - - + +
155A ALA* 2.9 32.3 + - - +
165A VAL* 4.2 20.0 - - + +
170A ALA* 4.8 0.2 - - + -
174A PHE* 3.8 33.0 - - + -
192A ALA* 4.8 2.1 - - - +
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Residues in contact with THR 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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148A ALA 2.8 20.3 + - - -
149A TRP 3.0 6.3 + - - -
151A LEU* 1.3 80.3 - - - +
153A ASN* 1.3 66.7 + - - +
155A ALA* 3.2 4.2 + - - -
156A SER 3.0 20.6 + - - -
188A GLN* 3.0 27.4 + - - +
191A TRP* 3.7 20.2 - - + +
192A ALA* 3.1 27.0 + - - +
195A ASN* 3.1 28.0 + - - +
239B ARG* 4.5 3.1 - - + +
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Residues in contact with ASN 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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107A ARG 4.9 0.4 + - - -
110A LEU* 3.1 41.5 + - + +
116A PRO* 6.1 1.6 - - + -
118A ILE* 4.0 7.6 - - + +
149A TRP* 3.0 25.6 + - - +
150A VAL* 3.1 6.2 + - - +
152A THR* 1.3 76.7 - - - +
154A ILE* 1.3 57.9 + - - +
155A ALA 3.1 0.9 - - - -
156A SER* 2.2 39.9 + - - +
238B PRO* 3.4 12.3 - - - +
239B ARG* 2.9 45.0 + - - -
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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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110A LEU* 4.3 16.5 - - + +
118A ILE* 4.1 17.2 - - + +
121A VAL* 4.1 22.7 - - + -
122A ILE* 4.0 18.4 - - + -
128A VAL* 4.2 11.9 - - + -
131A PHE* 5.0 1.3 - - + -
150A VAL* 3.1 31.3 + - + +
151A LEU* 4.1 14.8 - - + +
153A ASN* 1.3 72.4 - - - +
155A ALA* 1.3 63.5 + - - +
156A SER 3.0 11.4 + - - +
161A GLN* 3.6 28.7 - - - +
162A THR* 4.1 4.2 + - - -
164A ILE* 5.6 0.4 - - + -
165A VAL* 3.7 13.2 - - + -
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Residues in contact with ALA 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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151A LEU 2.9 21.9 + - - +
152A THR* 3.4 7.4 - - - +
153A ASN 3.1 0.4 - - - -
154A ILE* 1.3 77.0 - - - +
156A SER* 1.3 55.6 + - - +
162A THR* 3.7 12.6 - - + +
165A VAL* 4.4 9.8 - - + +
192A ALA* 4.6 2.0 - - - +
195A ASN* 3.5 14.4 - - + +
196A ILE* 4.0 27.1 - - + -
236B LYS* 3.0 27.5 + - - +
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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