Contacts of the helix formed by residues 144 - 165 (chain A) in PDB entry 4QNW
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 THR 144 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ARG* 4.7 4.5 - - - +
142A ALA 4.7 3.6 - - - +
143A LEU* 1.3 76.7 - - - +
145A GLU* 1.3 67.0 + - - +
146A ASP* 3.5 8.4 + - - +
147A GLU* 3.0 38.2 + - - +
148A ILE* 2.9 23.9 + - - +
191A ARG* 4.6 0.4 - - - +
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Residues in contact with GLU 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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143A LEU 4.2 0.2 + - - -
144A THR* 1.3 73.5 - - - +
146A ASP* 1.3 73.5 + - - +
148A ILE* 3.2 9.6 + - - +
149A GLN* 2.9 44.0 + - + +
191A ARG* 4.4 5.0 - - - +
193A ASP* 4.9 4.4 + - - +
194A ARG* 2.8 32.2 + - - +
195A TRP* 2.8 29.1 + - - -
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Residues in contact with ASP 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A THR* 3.3 7.5 + - - +
145A GLU* 1.3 85.9 - - - +
147A GLU* 1.3 59.2 + - + +
149A GLN* 3.3 10.9 + - - +
150A GLN* 2.9 27.4 + - - +
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Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LYS* 4.5 10.6 + - - -
141A ARG* 2.9 45.8 + - - -
143A LEU* 3.6 22.5 - - + +
144A THR* 3.0 34.3 + - - +
146A ASP* 1.3 75.7 - - + +
148A ILE* 1.3 58.9 + - - +
150A GLN* 3.4 7.1 + - - +
151A CYS* 2.9 28.8 + - - +
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Residues in contact with ILE 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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143A LEU* 3.9 15.0 - - + -
144A THR 2.9 16.0 + - - +
145A GLU* 3.2 6.9 + - - +
147A GLU* 1.3 74.3 - - - +
149A GLN* 1.3 65.8 + - - +
151A CYS* 3.1 7.2 + - - +
152A ILE* 3.0 30.7 + - + +
183A PHE* 3.8 16.6 - - + -
191A ARG* 3.5 34.5 - - - +
195A TRP* 3.6 54.3 - - + +
205A PHE* 3.8 13.0 - - + -
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Residues in contact with GLN 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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145A GLU* 2.9 40.2 + - + +
146A ASP* 3.6 11.9 - - - +
148A ILE* 1.3 77.0 - - - +
150A GLN* 1.3 59.5 + - - +
152A ILE* 3.4 8.4 + - - +
153A ALA* 3.0 27.4 + - - +
194A ARG* 3.4 3.2 - - - +
195A TRP* 3.9 8.7 - - - -
406A GOL 2.6 48.9 + - - -
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Residues in contact with GLN 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 ASP 2.9 16.1 + - - +
147A GLU* 3.7 8.3 - - - +
149A GLN* 1.3 79.0 - - - +
151A CYS* 1.3 50.5 + - - +
153A ALA* 3.3 12.1 + - - +
154A ASP* 2.7 70.9 + - - +
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Residues in contact with CYS 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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67A ILE* 4.2 8.3 - - - -
71A ALA* 6.2 1.6 - - - -
109A ALA* 5.1 2.0 - - - -
143A LEU* 5.2 5.8 - - + -
147A GLU 2.9 17.9 + - - +
148A ILE* 3.1 7.1 + - - +
150A GLN* 1.3 74.6 - - - +
152A ILE* 1.3 63.2 + - - +
154A ASP* 3.1 10.8 + - - +
155A PHE* 3.0 40.5 + - - -
179A LEU* 4.0 15.0 - - - -
205A PHE* 3.8 25.8 - - + -
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Residues in contact with ILE 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 ILE* 3.0 24.5 + - + +
149A GLN* 3.5 11.2 - - - +
151A CYS* 1.3 75.9 - - - +
153A ALA* 1.3 65.1 + - - +
155A PHE* 3.3 4.9 + - - +
156A ALA* 3.2 19.9 + - - +
195A TRP* 3.8 22.0 - - + -
205A PHE* 4.3 5.4 - - + -
208A GLU* 3.6 30.7 - - + +
209A VAL* 4.1 26.2 - - + +
212A ALA* 3.4 27.3 - - + +
406A GOL 4.3 16.2 - - - +
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Residues in contact with ALA 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 GLN 3.0 14.9 + - - +
150A GLN* 3.6 18.6 - - - +
152A ILE* 1.3 79.6 - - - +
154A ASP* 1.3 57.0 + - - +
156A ALA* 3.3 9.2 + - - +
157A GLN* 3.0 28.8 + - - +
212A ALA* 5.4 0.2 - - - -
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Residues in contact with ASP 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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67A ILE* 3.9 13.8 - - + +
68A THR* 3.2 34.9 + - + +
150A GLN* 2.7 57.5 + - - +
151A CYS* 3.1 9.7 + - - +
153A ALA* 1.3 72.4 - - - +
155A PHE* 1.3 57.5 + - - +
157A GLN* 3.3 6.4 + - - +
158A ALA* 2.9 29.8 + - - +
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Residues in contact with PHE 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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67A ILE* 3.5 19.7 - - + +
107A LEU* 3.6 46.1 - - + +
108A TRP* 4.0 20.6 - - - -
109A ALA* 4.0 6.7 - - + -
151A CYS* 3.0 38.3 + - - -
152A ILE 3.3 7.2 + - - +
154A ASP* 1.3 76.3 - - - +
156A ALA* 1.3 63.9 + - - +
158A ALA* 3.2 5.2 + - - +
159A ALA* 3.0 23.0 + - - +
172A ILE* 4.7 4.9 - - + -
173A HIS 5.5 0.2 - - - -
179A LEU* 5.3 1.1 - - + -
180A ILE* 3.9 25.8 - - + -
205A PHE* 4.8 1.8 - + - -
209A VAL* 3.6 31.4 - - + -
213A VAL* 3.8 17.1 - - + +
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Residues in contact with ALA 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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152A ILE 3.2 9.8 + - - +
153A ALA* 3.6 11.0 - - - +
155A PHE* 1.3 79.0 - - - +
157A GLN* 1.3 57.5 + - - +
159A ALA* 3.2 4.6 + - - +
160A ARG* 2.9 25.5 + - - +
212A ALA* 3.5 30.7 - - + +
213A VAL* 4.0 8.6 - - - +
216A ALA* 3.6 15.3 - - + +
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Residues in contact with GLN 157 (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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153A ALA 3.0 16.3 + - - +
154A ASP* 3.9 7.0 - - - +
155A PHE 3.2 0.2 - - - -
156A ALA* 1.3 72.9 - - - +
158A ALA* 1.3 67.1 + - - +
160A ARG* 3.3 16.9 + - - +
161A ASN* 2.9 59.9 + - - +
164A ASN* 5.9 0.6 - - - +
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Residues in contact with ALA 158 (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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67A ILE* 3.6 33.9 - - + +
80A ILE* 4.0 14.5 - - + +
81A TRP* 6.2 0.2 - - - +
107A LEU* 3.9 13.4 - - + +
154A ASP 2.9 18.2 + - - +
155A PHE 3.2 3.3 + - - +
157A GLN* 1.3 77.9 - - - +
159A ALA* 1.3 55.7 + - - +
161A ASN* 3.2 11.7 + - - +
162A ALA* 2.9 28.9 + - - +
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Residues in contact with ALA 159 (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 LEU* 3.8 12.1 - - + +
155A PHE 3.0 13.0 + - - +
156A ALA* 3.2 9.8 + - - +
158A ALA* 1.3 74.5 - - - +
160A ARG* 1.3 67.5 + - - +
162A ALA* 3.3 2.6 + - - +
163A ILE* 3.0 19.9 + - - +
170A VAL* 4.0 8.7 - - + -
213A VAL* 3.8 27.4 - - + -
216A ALA* 4.4 1.8 - - + -
217A VAL* 3.6 20.8 - - + +
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Residues in contact with ARG 160 (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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156A ALA 2.9 18.1 + - - +
157A GLN* 3.3 23.8 + - - +
159A ALA* 1.3 77.7 - - - +
161A ASN* 1.3 56.5 + - - +
163A ILE* 3.4 15.8 + - - +
164A ASN* 2.8 60.3 + - - +
216A ALA* 2.8 40.3 + - + +
217A VAL* 4.1 4.3 - - - +
221A ARG* 4.1 0.8 - - - +
405A SO4 2.8 43.8 + - - -
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Residues in contact with ASN 161 (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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80A ILE* 2.8 33.8 + - + +
81A TRP* 3.8 15.2 + - - +
86A ARG* 3.8 38.2 + - - +
157A GLN* 2.9 46.8 + - - +
158A ALA* 3.2 9.3 + - - +
160A ARG* 1.3 75.0 - - - +
162A ALA* 1.3 63.8 + - - +
164A ASN* 3.4 7.5 + - - +
165A ALA* 2.9 23.6 + - - +
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Residues in contact with ALA 162 (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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80A ILE* 3.7 12.0 - - + +
105A CYS* 4.2 6.3 - - + -
107A LEU* 5.2 0.4 - - + -
158A ALA 2.9 13.3 + - - +
159A ALA 3.5 8.3 - - - +
161A ASN* 1.3 76.7 - - - +
163A ILE* 1.3 61.8 + - - +
165A ALA 3.1 10.9 + - - -
167A PHE* 3.1 44.2 + - + -
170A VAL* 3.5 25.4 - - + -
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Residues in contact with ILE 163 (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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159A ALA 3.0 20.0 + - - +
160A ARG* 3.9 13.9 - - - +
162A ALA* 1.3 75.4 - - + +
164A ASN* 1.3 59.9 + - - +
166A GLY* 2.9 21.3 + - - -
167A PHE 3.9 17.2 - - - +
169A GLY* 4.2 14.8 - - - -
170A VAL* 4.0 18.8 - - + -
217A VAL* 3.6 24.0 - - + -
221A ARG* 3.5 40.2 - - + +
405A SO4 3.8 20.6 - - - +
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Residues in contact with ASN 164 (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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86A ARG* 4.4 19.8 - - - +
90A ARG* 5.3 3.8 - - - +
157A GLN* 5.9 0.6 - - - +
160A ARG* 2.8 53.4 + - - +
161A ASN* 3.7 7.7 + - - +
163A ILE* 1.3 77.5 - - - +
165A ALA* 1.3 57.8 + - - +
166A GLY 3.3 0.9 + - - -
405A SO4 4.1 4.9 + - - -
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Residues in contact with ALA 165 (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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80A ILE* 4.8 2.5 - - + -
86A ARG* 3.8 25.1 - - + +
89A TRP* 4.4 5.2 - - + -
90A ARG* 3.5 39.3 - - - +
93A VAL* 3.8 8.7 - - - +
161A ASN 2.9 13.6 + - - +
162A ALA* 3.1 10.2 + - - +
164A ASN* 1.3 74.3 - - - +
166A GLY* 1.3 58.0 + - - +
167A PHE* 3.6 11.7 - - + -
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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
------------------------------------------------------------
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