Contacts of the helix formed by residues 140 - 159 (chain A) in PDB entry 3ZDT
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 ASP 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LYS 4.1 1.0 - - - +
77A VAL* 3.9 4.2 - - - -
78A LYS* 3.0 40.0 + - + +
79A ASN* 2.7 41.0 + - - +
136A GLN 4.2 1.5 + - - +
137A PHE* 2.6 18.6 + - - +
138A THR 3.4 0.4 - - - -
139A GLU* 1.3 73.2 - - - +
141A LYS* 1.3 65.3 + - - +
142A PRO* 3.7 12.3 - - - +
143A THR* 3.0 22.0 + - - -
144A LEU 2.9 17.5 + - - -
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Residues in contact with LYS 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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137A PHE 4.6 0.4 - - - -
138A THR 4.9 10.5 - - - +
139A GLU 4.0 1.3 - - - -
140A ASP* 1.3 70.7 - - - +
142A PRO* 1.3 73.5 - - + +
144A LEU* 2.8 27.9 + - + +
145A ASN* 2.8 43.9 + - - +
236A ARG* 5.9 6.3 - - - +
237A GLU* 6.3 1.0 - - - +
240A ILE* 5.8 1.2 - - - +
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Residues in contact with PRO 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 4.2 15.8 - - + -
75A HIS* 3.2 28.7 - - + +
76A LYS* 4.2 8.3 - - + +
77A VAL* 4.1 12.3 - - + -
140A ASP* 3.7 9.9 - - - +
141A LYS* 1.3 93.3 - - + +
143A THR* 1.3 51.8 + - - +
145A ASN* 3.4 7.9 + - + +
146A PHE* 2.7 36.2 + - - +
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Residues in contact with THR 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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77A VAL* 3.2 15.1 - - - +
79A ASN* 4.6 2.7 - - + +
82A CYS* 5.4 0.4 - - + -
83A TYR* 2.7 30.8 + - + +
126A ILE* 3.5 10.5 - - + -
137A PHE* 3.3 33.6 - - + -
140A ASP* 3.0 28.5 + - - +
141A LYS 3.1 0.6 - - - -
142A PRO* 1.3 74.7 - - - +
144A LEU* 1.3 67.3 + - - +
146A PHE* 4.1 0.2 - - - -
147A PHE* 2.9 23.2 + - - +
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Residues in contact with LEU 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 LEU* 4.9 11.7 - - + +
137A PHE* 3.9 29.3 - - + +
138A THR* 4.6 16.2 - - - +
140A ASP 2.9 12.2 + - - +
141A LYS* 2.8 20.1 + - + +
143A THR* 1.3 77.6 - - - +
145A ASN* 1.3 53.9 - - - +
147A PHE* 3.2 5.7 + - + +
148A TYR* 2.8 31.1 + - - +
237A GLU* 4.6 20.0 - - + +
240A ILE* 4.1 35.7 - - + -
241A LEU* 5.1 8.1 - - + -
244A PHE* 4.6 8.7 - - + -
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Residues in contact with ASN 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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42A TYR 4.5 1.1 - - - +
43A PHE* 6.6 0.2 - - - -
44A GLU* 5.8 10.4 + - + +
141A LYS* 2.8 44.3 + - - +
142A PRO* 3.8 6.0 - - + +
144A LEU* 1.3 75.9 - - - +
146A PHE* 1.3 56.2 + - - +
148A TYR* 3.0 6.9 + - - +
149A GLN* 2.7 46.6 + - + +
178A ARG* 6.1 3.6 - - - -
240A ILE* 3.3 25.3 - - - +
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Residues in contact with PHE 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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41A HIS* 3.7 10.3 - - + -
42A TYR* 3.0 57.2 + + - +
43A PHE* 3.6 25.1 - + + +
83A TYR* 3.6 27.1 - + - +
124A LEU* 3.1 30.3 - - + -
125A ARG* 3.8 5.4 - - - -
126A ILE* 3.6 17.5 - - + -
142A PRO 2.7 22.3 + - - +
143A THR 3.8 1.3 - - - +
145A ASN* 1.3 73.5 - - - +
147A PHE* 1.3 58.3 + - - +
150A GLN* 2.9 44.7 + - - +
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Residues in contact with PHE 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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126A ILE* 3.8 31.9 - - + -
129A LEU* 3.6 27.6 - - + -
133A PHE* 4.2 14.1 - + - -
134A LEU* 4.3 5.2 - - + -
137A PHE* 5.0 12.1 - + + -
143A THR 2.9 19.1 + - - +
144A LEU* 3.5 5.8 - - + +
146A PHE* 1.3 75.2 - - - +
148A TYR* 1.3 67.2 + - - +
150A GLN* 3.2 9.3 + - - -
151A VAL* 2.8 45.6 + - + +
244A PHE* 3.4 41.7 - + - -
253A PHE* 3.7 26.9 - + - -
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Residues in contact with TYR 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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144A LEU 2.8 13.6 + - - +
145A ASN* 3.3 11.7 - - + +
147A PHE* 1.3 76.8 - - - +
149A GLN* 1.3 80.6 + - - +
151A VAL* 3.4 1.2 + - - +
152A LYS* 2.9 49.7 + - + +
174A LEU* 4.2 3.1 + - + -
175A GLU* 2.8 43.0 + - - +
178A ARG* 3.3 18.0 + - - -
240A ILE* 3.6 35.9 - - + -
243A PHE* 3.5 44.6 - + + -
244A PHE* 3.8 11.1 - + - -
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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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42A TYR* 3.8 29.0 - - + +
44A GLU* 3.8 19.5 + - + +
52A TRP* 3.9 28.8 - - + -
145A ASN* 2.7 26.1 + - + +
148A TYR* 1.3 88.3 - - - +
150A GLN* 1.3 62.6 + - - +
152A LYS* 3.4 25.2 + - - +
153A ASN* 3.0 26.0 + - - +
175A GLU* 4.9 0.5 - - - +
178A ARG* 3.3 30.4 + - - +
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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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42A TYR* 3.7 21.3 - - + -
125A ARG* 3.3 49.5 - - - +
126A ILE* 2.8 47.7 + - - +
146A PHE* 2.9 28.8 + - - +
147A PHE* 3.2 10.9 + - - +
149A GLN* 1.3 78.1 - - - +
151A VAL* 1.3 65.7 + - + +
153A ASN* 3.4 3.8 + - - +
154A ASP* 3.4 18.8 + - - +
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Residues in contact with VAL 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 PHE* 2.8 58.9 + - + +
148A TYR 4.0 1.8 - - - +
150A GLN* 1.3 71.2 - - + +
152A LYS* 1.3 68.2 + - - +
154A ASP* 2.9 20.3 + - - +
155A TYR* 2.9 9.5 + - - +
243A PHE* 4.9 1.6 - - + -
244A PHE* 3.8 13.7 - - + -
247A LEU* 3.9 27.8 - - + -
251A TYR* 4.5 5.2 - - + -
253A PHE* 4.1 25.1 - - + -
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Residues in contact with LYS 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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49A PRO* 5.9 5.9 - - - +
52A TRP* 6.0 0.4 - - - -
148A TYR* 2.9 46.3 + - + +
149A GLN* 3.5 27.4 + - - +
151A VAL* 1.3 75.7 - - - +
153A ASN* 1.3 63.5 + - - +
155A TYR* 3.1 12.6 - - + +
156A MET* 3.0 35.4 + - + +
175A GLU* 3.7 26.2 + - + +
205A ARG 5.7 2.6 + - - -
243A PHE* 4.0 26.6 - - + -
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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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42A TYR* 3.3 32.5 + - + -
149A GLN 3.0 18.0 + - - +
150A GLN 3.5 5.6 - - - +
151A VAL 2.9 1.0 + - - -
152A LYS* 1.3 75.7 - - - +
154A ASP* 1.3 64.3 + - - +
155A TYR 3.0 4.0 - - - -
156A MET* 3.0 17.3 + - - +
157A LEU* 3.0 38.8 + - - +
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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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42A TYR* 4.7 0.3 + - - -
86A ARG* 5.3 1.7 + - - -
125A ARG* 2.8 35.4 + - - -
150A GLN* 3.4 11.5 + - - +
151A VAL* 2.9 12.2 + - - +
153A ASN* 1.3 78.5 + - - +
155A TYR* 1.3 57.1 + - - +
157A LEU* 3.7 9.8 - - - +
158A GLU* 3.0 41.8 + - - +
251A TYR* 3.2 22.2 + - + +
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Residues in contact with TYR 155 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A VAL 2.9 11.6 + - - +
152A LYS* 3.1 15.5 - - + +
153A ASN 3.0 0.2 - - - -
154A ASP* 1.3 75.3 - - - +
156A MET* 1.3 85.3 + - - +
157A LEU 3.0 4.7 - - - -
159A ILE* 3.1 40.2 + - + -
160A ALA* 3.0 47.3 + - + -
163A VAL* 4.0 8.2 - - + +
167A ILE* 5.5 0.4 - - + -
168A ALA* 3.8 21.7 + - - +
171A LEU* 3.2 38.0 - - + +
206A PHE 5.8 1.1 - - - -
208A PRO* 5.7 1.9 - - + +
243A PHE* 5.0 7.0 - + - -
247A LEU* 3.5 28.0 - - + -
251A TYR* 4.4 4.4 + + + -
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Residues in contact with MET 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 LYS* 3.0 29.1 + - + +
153A ASN* 3.0 10.6 + - - +
155A TYR* 1.3 99.8 - - - +
157A LEU* 1.3 70.1 + - + +
158A GLU 3.5 0.4 + - - -
160A ALA* 3.9 14.6 - - + +
161A ASP* 6.2 0.2 - - - -
204A ARG* 4.2 17.3 + - - +
205A ARG 4.2 20.0 - - - +
206A PHE 4.2 10.5 - - - +
207A PHE 4.2 24.9 - - - -
208A PRO* 4.4 3.1 - - + -
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Residues in contact with LEU 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 ASN* 3.0 40.6 + - - +
154A ASP* 4.0 9.4 - - - +
155A TYR 3.0 1.2 - - - -
156A MET* 1.3 91.2 - - + +
158A GLU* 1.3 67.1 + - + +
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Residues in contact with GLU 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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154A ASP* 3.0 23.1 + - - +
155A TYR 3.2 0.6 + - - -
157A LEU* 1.3 89.6 - - + +
159A ILE* 1.3 64.5 + - + +
160A ALA 3.8 0.2 - - - -
161A ASP 5.3 0.8 + - - -
162A GLN* 3.5 18.4 + - - +
251A TYR* 3.0 31.8 + - + -
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Residues in contact with ILE 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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155A TYR* 3.1 30.8 + - + +
158A GLU* 1.3 81.9 - - + +
160A ALA* 1.3 69.7 + - - +
161A ASP 3.2 2.9 - - - -
162A GLN* 3.0 34.9 + - + +
163A VAL* 3.3 17.1 + - + +
247A LEU* 3.9 4.5 - - + -
250A VAL* 4.3 20.2 - - + +
251A TYR* 3.2 57.4 - - + -
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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