Contacts of the helix formed by residues 146 - 159 (chain A) in PDB entry 4GUP
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 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A ALA 4.0 7.6 + - - +
143A TRP* 3.2 19.0 + - - +
144A GLU 4.1 0.9 - - - -
145A ALA* 1.4 73.5 - - - +
147A GLN* 1.3 63.1 + - - +
148A HIS 3.4 2.5 - - - +
149A GLU* 3.6 21.0 + - + +
150A LEU* 3.5 15.4 + - - +
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Residues in contact with GLN 147 (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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127A LEU* 5.2 8.3 - - + +
144A GLU 3.8 14.5 - - - +
145A ALA* 3.1 12.6 + - - +
146A ASN* 1.3 69.7 - - - +
148A HIS* 1.4 63.4 + - - +
150A LEU* 3.2 13.3 + - - +
151A LEU* 2.9 36.7 + - + +
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Residues in contact with HIS 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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146A ASN* 3.4 1.2 - - - +
147A GLN* 1.4 77.7 - - + +
149A GLU* 1.3 54.3 + - - +
151A LEU* 3.4 19.5 + - + +
152A TYR* 2.8 34.7 + - - +
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Residues in contact with GLU 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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143A TRP* 5.3 8.1 - - - +
146A ASN* 3.6 24.8 + - + +
148A HIS* 1.3 74.8 - - - +
150A LEU* 1.4 62.1 + - + +
152A TYR* 2.9 10.3 + - + +
153A GLN* 2.8 54.6 + - - +
302A CL 4.1 8.3 - - - +
303A PO4 2.9 45.1 + - - -
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Residues in contact with LEU 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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122A PHE* 3.9 9.5 - - + -
127A LEU* 3.4 54.4 - - + +
129A TRP* 3.5 30.1 - - + +
143A TRP* 3.7 15.5 - - + +
144A GLU* 3.9 29.4 - - + +
146A ASN 3.5 11.4 + - - +
147A GLN* 3.2 14.4 + - - +
149A GLU* 1.4 81.2 - - + +
151A LEU* 1.3 56.3 + - - +
153A GLN* 3.5 7.1 + - + +
154A LYS 2.9 23.6 + - - -
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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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127A LEU* 4.0 22.7 - - + -
147A GLN* 2.9 22.3 + - + +
148A HIS* 3.7 22.9 - - + +
149A GLU 3.2 0.2 - - - -
150A LEU* 1.3 73.5 - - - +
152A TYR* 1.4 56.3 + - - +
154A LYS* 3.6 15.9 - - + +
155A ASN* 2.8 38.3 + - - +
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Residues in contact with TYR 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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65A LEU* 5.2 8.7 - - - +
69A TRP* 5.0 13.3 - + - -
148A HIS 2.8 18.3 + - - +
149A GLU* 3.2 12.1 - - - +
151A LEU* 1.4 71.3 - - - +
153A GLN* 1.3 81.1 + - - +
155A ASN* 3.8 12.0 + - - +
156A TRP* 2.9 39.5 + + + +
160A GLU* 5.6 4.3 + - - -
301A 6FP 5.2 6.7 - - - -
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Residues in contact with GLN 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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94A ARG* 3.7 17.2 + - - +
96A ILE* 5.5 4.2 - - + +
110A LEU* 3.8 27.4 - - + -
122A PHE* 4.3 11.2 - - + -
129A TRP* 5.9 1.6 - - + -
149A GLU* 2.8 48.7 + - - +
150A LEU* 3.7 8.1 - - + +
152A TYR* 1.3 93.1 - - - +
154A LYS* 1.4 67.5 + - - +
156A TRP* 3.0 16.9 + - + +
157A LEU* 3.2 20.7 + - + +
301A 6FP 4.1 8.8 + - - -
302A CL 3.7 13.5 - - - +
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Residues in contact with LYS 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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122A PHE* 4.1 10.2 - - + -
124A LYS* 2.8 42.2 + - + +
125A ASP* 4.1 12.5 + - - +
127A LEU* 3.8 21.7 - - + +
150A LEU 2.9 21.8 + - - +
151A LEU* 3.3 17.9 + - + +
153A GLN* 1.4 73.2 - - - +
155A ASN* 1.4 56.5 + - - +
157A LEU* 3.3 6.4 + - - +
158A GLU* 2.9 37.2 + - + +
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Residues in contact with ASN 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 2.8 20.7 + - - +
152A TYR* 3.9 11.2 + - - +
154A LYS* 1.4 70.5 - - - +
156A TRP* 1.4 63.4 + - - +
158A GLU* 4.2 6.7 - - - -
159A GLU* 2.8 55.0 + - + +
160A GLU* 3.6 12.2 + - - +
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Residues in contact with TRP 156 (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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5A LEU* 4.9 3.1 - - + -
7A TYR* 4.1 24.5 - + - -
62A TYR* 5.0 0.6 + - - -
96A ILE* 3.6 34.1 - - + -
97A GLY* 3.9 13.9 - - - -
152A TYR* 2.9 35.9 + + + +
153A GLN* 3.0 8.2 + - - +
155A ASN* 1.4 76.1 - - - +
157A LEU* 1.3 70.1 + - + +
160A GLU* 3.4 47.5 + - + +
161A CYS* 2.6 73.5 + - + +
164A TRP* 4.6 6.6 - + - -
301A 6FP 4.1 29.5 + + - +
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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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96A ILE* 4.1 12.8 - - + -
97A GLY 3.7 15.9 - - - +
98A CYS* 4.6 6.9 - - - +
107A THR 4.9 4.5 - - - +
108A GLY* 4.0 5.8 - - - -
109A PHE* 3.2 34.8 - - - +
110A LEU* 4.8 3.8 - - + -
122A PHE* 4.0 29.2 - - + -
124A LYS* 4.3 21.3 - - + -
153A GLN* 3.2 19.8 + - + +
154A LYS 3.6 4.5 - - - +
156A TRP* 1.3 89.1 - - + +
158A GLU* 1.3 62.4 + - - +
159A GLU 3.3 2.8 + - - +
161A CYS* 3.7 14.0 - - - +
162A ILE* 4.3 6.4 + - - +
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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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106A THR* 5.4 4.5 + - - -
124A LYS* 4.6 16.1 - - - +
154A LYS* 2.9 30.1 + - + +
155A ASN* 4.0 5.4 - - - +
157A LEU* 1.3 72.1 - - - +
159A GLU* 1.4 75.0 + - + +
162A ILE* 5.4 6.0 - - - +
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Residues in contact with GLU 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 ASN* 2.8 37.3 + - - +
158A GLU* 1.4 98.0 - - + +
160A GLU* 1.4 67.5 + - - +
161A CYS 2.9 4.3 + - - -
162A ILE* 3.1 17.3 + - - +
163A ALA* 3.4 11.4 + - - +
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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