Contacts of the helix formed by residues 140 - 157 (chain A) in PDB entry 4AUP
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 PHE 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A CYS* 3.9 10.5 - - - -
133A ASP 3.2 9.9 + - - +
135A PRO* 3.6 12.6 - - + -
138A PHE* 3.1 29.5 + - + -
139A ASN* 1.3 77.9 - - - +
141A LEU* 1.4 59.3 + - - +
142A ASP 3.4 2.7 - - - -
143A SER* 3.3 6.1 + - - -
144A CYS* 3.0 27.7 + - - -
176A LEU* 3.4 27.8 - - + -
179A GLU* 5.4 1.1 - - + -
180A CYS* 4.5 2.7 - - - -
194A CYS* 3.7 21.8 - - - -
197A ILE* 3.7 14.6 - - + -
198A ALA* 3.5 31.0 - - + -
201A TYR* 3.6 41.3 - + - -
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Residues in contact with LEU 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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125A ASP* 4.6 0.7 - - - +
127A GLY* 3.5 31.0 - - - -
128A CYS* 4.2 1.8 - - - -
133A ASP* 3.2 32.8 + - + +
134A ARG* 4.0 21.3 - - - +
139A ASN* 3.3 11.7 - - - +
140A PHE* 1.4 77.7 - - - +
142A ASP* 1.3 60.4 + - - +
144A CYS* 3.2 4.7 + - - -
145A LYS* 2.7 58.1 + - + +
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Residues in contact with ASP 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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106A MET* 3.6 35.4 - - + +
110A LEU* 3.5 29.1 - - + +
139A ASN* 2.8 30.8 + - - +
140A PHE 3.4 0.8 - - - -
141A LEU* 1.3 78.4 - - - +
143A SER* 1.3 60.8 + - - +
145A LYS* 3.2 18.2 + - - +
146A ARG 3.1 17.8 + - - -
179A GLU* 4.9 4.2 - - - +
182A LYS* 5.7 1.4 + - - -
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Residues in contact with SER 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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106A MET* 3.8 11.4 - - - +
139A ASN 5.1 1.1 + - - -
140A PHE* 3.3 4.6 + - - -
141A LEU 3.3 0.4 - - - -
142A ASP* 1.3 73.5 - - - +
144A CYS* 1.3 55.2 + - - +
146A ARG* 3.3 3.6 + - - +
147A HIS* 2.8 34.3 + - - +
172A PHE* 3.5 8.2 - - - +
175A ASP* 3.2 39.1 + - - +
176A LEU* 3.3 31.7 + - - +
179A GLU* 5.1 4.2 - - - +
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Residues in contact with CYS 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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127A GLY 3.6 2.9 - - - +
128A CYS* 2.1 64.8 - - - +
140A PHE* 3.0 12.8 + - - +
141A LEU 3.5 4.7 - - - +
143A SER* 1.3 75.3 - - - +
145A LYS* 1.3 55.2 + - - +
147A HIS* 3.1 3.0 + - - -
148A ASP* 2.7 43.5 + - - +
172A PHE* 3.7 25.1 - - - -
201A TYR* 4.8 2.5 - - - -
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Residues in contact with LYS 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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109A PHE* 4.1 6.0 - - + -
110A LEU* 4.2 16.9 - - + +
113A LYS* 3.7 36.3 + - + +
125A ASP* 3.7 24.8 - - - +
127A GLY* 4.9 0.4 - - - -
141A LEU* 2.7 50.8 + - + +
142A ASP* 3.4 16.3 + - - +
144A CYS* 1.3 72.9 - - - +
146A ARG* 1.3 56.8 + - - +
148A ASP* 3.4 8.8 + - - +
149A PHE* 2.9 27.2 + - - +
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Residues in contact with ARG 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 2.8 25.1 + - - -
101A LEU* 3.5 39.1 + - + +
104A THR 2.7 29.5 + - - -
105A ALA* 4.7 0.4 - - - +
106A MET* 3.7 20.8 - - + +
109A PHE* 3.6 41.0 - - + +
142A ASP 3.1 11.1 + - - +
143A SER 3.7 6.7 - - - +
145A LYS* 1.3 73.8 - - - +
147A HIS* 1.3 61.2 + - - +
149A PHE* 3.3 2.6 + - - +
150A GLY 3.0 23.0 + - - -
171A ASN* 4.0 3.7 - - - +
175A ASP* 2.8 43.3 + - - +
178A ASN* 5.6 1.0 - - - +
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Residues in contact with HIS 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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101A LEU* 5.5 0.4 - - - -
143A SER 2.8 20.5 + - - +
144A CYS* 3.6 5.3 - - - +
146A ARG* 1.3 74.5 - - - +
148A ASP* 1.3 60.9 + - - +
150A GLY* 3.3 1.9 + - - -
151A TYR* 3.0 60.4 + + - +
168A ILE* 3.5 24.7 - - + -
169A ASP* 2.6 25.5 + - - -
172A PHE* 3.5 40.1 - + + -
205A VAL* 3.7 25.8 - - + +
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Residues in contact with ASP 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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124A SER 4.5 1.1 - - - +
125A ASP* 3.2 30.1 - - + +
126A ASP* 3.4 15.0 - - - +
127A GLY* 2.6 28.4 + - - +
129A SER* 5.0 4.2 + - - -
144A CYS* 2.7 25.8 + - - +
145A LYS 3.6 4.7 - - - +
147A HIS* 1.3 74.0 + - - +
149A PHE* 1.4 58.3 + - - +
151A TYR* 3.4 5.8 + - - -
152A ARG* 2.8 53.3 + - - +
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Residues in contact with PHE 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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97A THR* 3.6 40.8 - - + -
100A LEU* 4.0 23.3 - - + -
101A LEU* 4.1 12.1 - - + -
109A PHE* 3.6 18.2 - + + -
113A LYS* 6.3 0.4 - - - +
121A LEU* 3.7 22.2 - - + -
122A ASP 3.7 6.1 - - - -
123A TRP* 3.4 39.9 - + + -
124A SER 5.2 2.2 + - - -
145A LYS 2.9 14.9 + - - +
146A ARG 3.3 8.3 - - - +
148A ASP* 1.4 73.7 - - - +
150A GLY* 1.3 63.8 + - - +
152A ARG* 5.0 0.7 - - - -
153A ASN* 2.9 54.1 + - - +
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Residues in contact with GLY 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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101A LEU* 3.8 31.6 - - - -
146A ARG 3.0 10.3 + - - -
147A HIS 3.7 2.9 - - - -
148A ASP 3.2 0.2 - - - -
149A PHE* 1.3 77.7 - - - +
151A TYR* 1.3 57.4 + - - +
153A ASN* 5.2 0.2 - - - -
154A TYR* 3.0 37.1 + - - +
168A ILE* 3.9 12.3 - - - -
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Residues in contact with TYR 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 HIS* 3.0 46.9 + + - +
148A ASP* 3.8 6.3 - - - +
150A GLY* 1.3 72.2 - - - +
152A ARG* 1.3 62.1 + - + +
154A TYR* 3.9 0.5 - - - -
155A LYS* 3.0 49.7 + - - +
160A PHE* 3.5 23.2 - + + -
165A ARG* 3.3 36.2 + - + -
168A ILE* 3.7 16.8 - - + -
169A ASP* 2.6 23.4 + - - -
205A VAL* 4.0 1.6 + - - +
209A GLY* 3.5 31.8 - - - -
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Residues in contact with ARG 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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122A ASP* 3.5 21.3 - - + +
124A SER* 3.2 50.9 + - - +
125A ASP* 3.8 4.8 - - - +
126A ASP* 3.2 45.5 + - - +
148A ASP* 2.8 29.3 + - - +
149A PHE* 4.6 1.6 - - - +
151A TYR* 1.3 75.0 - - + +
153A ASN* 1.3 56.3 + - - +
155A LYS* 3.7 7.7 + - + +
156A LYS* 3.1 36.9 + - + +
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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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97A THR* 4.1 12.3 - - + -
121A LEU* 3.0 16.9 - - - +
122A ASP* 2.7 51.9 + - - +
149A PHE* 2.9 45.4 + - - +
150A GLY 4.6 0.2 - - - +
152A ARG* 1.3 74.8 - - - +
154A TYR* 1.3 59.4 + - - +
156A LYS* 3.8 4.6 - - - +
157A GLN* 2.8 49.5 + - - +
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Residues in contact with TYR 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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97A THR* 3.8 7.4 - - + -
98A ASP* 2.7 19.4 + - - -
101A LEU* 3.5 21.1 - - + -
102A TYR* 3.1 23.7 + - - -
150A GLY 3.0 27.1 + - - +
153A ASN* 1.3 76.8 - - - +
155A LYS* 1.3 56.2 + - - +
157A GLN* 2.9 27.0 - - - +
159A ARG* 3.3 66.3 + - + -
160A PHE* 3.4 22.2 + - + -
164A ASN* 3.6 28.4 + - + -
167A ARG* 5.2 2.1 - - - -
168A ILE* 3.6 14.1 - - + -
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Residues in contact with LYS 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 TYR* 3.0 40.5 + - - +
152A ARG* 4.0 8.7 - - + +
154A TYR* 1.3 73.1 - - - +
156A LYS* 1.3 64.6 + - + +
157A GLN 2.8 13.5 - - - +
160A PHE* 3.5 45.6 - - + -
209A GLY 4.7 3.2 + - - -
210A TRP 6.0 1.3 - - - -
211A LEU* 4.3 17.5 + - - -
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Residues in contact with LYS 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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122A ASP* 2.8 30.9 + - + +
152A ARG* 3.1 29.6 + - - +
153A ASN* 4.2 8.1 - - - +
155A LYS* 1.3 79.9 - - + +
157A GLN* 1.3 60.7 + - + +
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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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93A PRO* 3.6 19.3 + - + +
94A VAL* 3.9 14.6 - - + -
97A THR* 2.9 25.8 + - - +
121A LEU* 4.6 3.2 - - - +
153A ASN* 2.8 37.3 + - - +
154A TYR* 2.9 14.6 - - - +
155A LYS 2.8 16.8 - - - +
156A LYS* 1.3 77.3 - - + +
158A HIS* 1.3 63.4 + - + +
159A ARG* 2.8 38.9 + - - +
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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