Contacts of the helix formed by residues 148 - 162 (chain A) in PDB entry 4L28
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 GLY 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A THR* 2.8 13.6 + - - -
147A SER* 1.3 80.8 - - - +
149A ASN* 1.3 54.3 + - - +
150A THR 3.3 1.8 - - - -
151A GLY* 2.9 4.3 + - - -
152A ILE* 2.6 42.3 + - - +
169A MET* 3.5 17.9 - - - -
177A LYS* 4.1 7.0 - - - -
181A LEU* 4.8 1.9 - - - +
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Residues in contact with ASN 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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117A SER* 3.3 29.5 + - - +
119A LYS* 3.3 22.7 - - + +
120A ASP* 4.3 0.2 - - - +
147A SER* 3.8 3.0 + - - -
148A GLY* 1.3 76.1 - - - +
150A THR* 1.3 62.6 + - - +
152A ILE* 3.3 9.3 + - - +
153A GLY* 3.0 18.4 + - - -
177A LYS* 4.6 5.8 - - - +
376A ASP* 3.3 15.6 + - - +
379A ARG* 5.4 0.9 + - - -
380A ASN* 2.9 25.3 + - - +
381A TYR* 4.6 0.6 + - - -
601A PLP 2.8 41.4 + - - +
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Residues in contact with THR 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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119A LYS* 2.9 27.4 - - - +
122A ILE* 4.0 12.3 - - + -
123A SER* 3.1 13.3 + - - +
126A MET* 5.0 3.4 - - + -
144A GLU* 4.4 5.6 - - + +
146A THR* 3.4 13.1 + - - -
148A GLY 3.3 0.2 - - - -
149A ASN* 1.3 77.5 - - - +
151A GLY* 1.3 57.4 + - - +
154A LEU* 2.9 42.6 + - + +
222A GLN* 2.7 37.4 + - + +
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Residues in contact with GLY 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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144A GLU* 5.6 0.4 - - - -
146A THR* 3.5 15.5 + - - -
148A GLY 2.9 7.6 + - - -
150A THR* 1.3 78.8 - - - +
152A ILE* 1.3 59.1 - - - +
154A LEU* 4.5 2.9 - - - -
155A ALA* 2.9 30.5 + - - +
167A ILE* 3.6 25.5 - - - +
181A LEU* 3.3 8.6 - - - +
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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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115A GLY* 4.0 24.2 - - - +
117A SER* 5.7 1.1 - - - +
120A ASP* 5.1 0.7 - - - +
148A GLY 2.6 21.1 + - - +
149A ASN* 3.7 16.6 - - - +
150A THR 3.3 0.2 - - - -
151A GLY* 1.3 74.2 - - - +
153A GLY* 1.3 59.1 + - - +
155A ALA* 3.4 1.6 + - - +
156A LEU* 2.9 28.6 + - + +
177A LYS* 4.3 18.4 - - + -
180A VAL* 4.2 26.9 - - + -
181A LEU* 3.7 23.6 - - + -
184A LEU* 3.9 4.9 - - + +
379A ARG* 4.3 8.1 - - - +
380A ASN* 4.1 19.1 - - - +
345C LEU* 5.6 2.0 - - + -
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Residues in contact with GLY 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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81A LEU* 5.4 0.5 - - - +
120A ASP* 3.6 21.5 + - - -
123A SER* 3.4 21.1 - - - -
149A ASN 3.0 12.4 + - - -
152A ILE* 1.3 76.0 - - - +
154A LEU* 1.3 57.0 + - - +
156A LEU* 3.4 7.9 + - - +
157A ALA* 3.0 29.3 + - - +
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Residues in contact with LEU 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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123A SER* 3.3 33.8 + - - +
126A MET* 4.9 3.6 - - + -
127A ILE* 3.7 20.9 - - + +
142A ILE* 4.6 13.0 - - + +
144A GLU* 3.6 42.8 - - + +
150A THR* 2.9 27.0 + - + +
151A GLY* 3.9 4.3 - - - +
153A GLY* 1.3 76.3 - - - +
155A ALA* 1.3 60.1 + - - +
157A ALA* 3.8 3.0 - - - +
158A ALA* 2.8 30.9 + - - +
165A CYS* 4.2 10.3 - - - -
167A ILE* 5.1 0.2 - - + -
220A LEU* 4.0 11.7 - - + -
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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 GLY 2.9 19.3 + - - +
152A ILE 3.8 2.5 - - - +
154A LEU* 1.3 73.8 - - - +
156A LEU* 1.3 60.9 + - - +
158A ALA* 3.7 2.6 - - - +
159A ALA* 2.9 28.4 + - - +
165A CYS* 3.7 11.1 - - - -
181A LEU* 3.7 17.9 - - + -
184A LEU* 4.0 17.6 - - + +
186A ALA* 3.8 20.2 - - + +
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Residues in contact with LEU 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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80A ILE* 4.3 6.3 - - + -
81A LEU* 4.2 16.2 - - + -
84A ILE* 5.6 2.7 - - + -
114A ALA* 4.3 13.7 - - + +
115A GLY* 4.0 31.2 - - - +
120A ASP* 5.3 2.0 - - - -
152A ILE* 2.9 17.6 + - + +
153A GLY* 3.5 7.4 - - - +
155A ALA* 1.3 74.7 - - - +
157A ALA* 1.3 65.5 + - - +
159A ALA* 3.1 4.7 + - + +
160A VAL* 3.0 26.5 + - + +
184A LEU* 4.1 19.0 - - + +
343C GLY* 3.3 41.7 - - - +
345C LEU* 5.7 3.1 - - + -
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Residues in contact with ALA 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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81A LEU* 3.7 28.9 - - + -
123A SER 5.3 2.7 - - - +
124A LEU* 5.3 8.5 - - + -
127A ILE* 3.8 26.0 - - + -
153A GLY 3.0 17.6 + - - +
154A LEU* 3.9 0.4 - - - +
156A LEU* 1.3 77.7 - - - +
158A ALA* 1.3 58.5 + - - +
160A VAL* 3.3 0.5 + - - +
161A ARG* 2.8 35.8 + - + +
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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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127A ILE* 4.9 0.6 - - - +
142A ILE* 5.0 4.5 - - + -
154A LEU 2.8 19.1 + - - +
155A ALA 3.7 4.5 - - - +
157A ALA* 1.3 74.0 - - - +
159A ALA* 1.3 62.1 + - - +
162A GLY* 2.8 27.5 + - - -
163A TYR* 3.1 45.4 + - + +
165A CYS* 3.9 18.2 - - + -
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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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155A ALA 2.9 19.2 + - - +
156A LEU* 3.4 7.0 - - - +
158A ALA* 1.3 78.2 - - - +
160A VAL* 1.3 61.7 + - + +
162A GLY* 4.0 2.6 + - - -
163A TYR 5.4 0.2 - - - -
184A LEU* 3.6 18.8 - - + +
94C LYS* 2.7 23.0 + - - -
339C ILE 4.8 4.7 - - - +
340C ALA 3.6 23.3 - - - +
341C GLN 4.0 3.0 - - - +
343C GLY* 5.5 1.6 - - - -
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Residues in contact with VAL 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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79A ASP* 4.1 29.4 - - + +
80A ILE* 4.4 15.3 - - + -
81A LEU* 4.1 17.7 - - + -
156A LEU 3.0 17.0 + - - +
157A ALA 3.7 6.5 - - - +
158A ALA 3.1 0.2 - - - -
159A ALA* 1.3 79.4 - - - +
161A ARG* 1.3 64.0 + - + +
162A GLY 3.5 0.2 + - - -
93C ASN* 5.7 1.8 - - - +
94C LYS* 3.3 22.9 + - - +
341C GLN 4.5 2.5 - - - +
342C GLU* 3.9 27.4 - - - +
343C GLY* 4.6 2.0 - - - -
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Residues in contact with ARG 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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79A ASP* 5.5 2.6 + - - -
81A LEU* 3.9 19.2 - - + +
82A LYS* 3.7 20.6 - - - +
124A LEU* 4.3 6.9 - - - +
127A ILE* 4.9 5.8 - - - +
128A GLU* 3.2 34.8 + - - +
131A GLU* 2.6 41.8 + - - -
138A PRO* 6.1 0.5 - - - +
157A ALA* 2.8 20.6 + - + +
160A VAL* 1.3 80.8 - - + +
162A GLY* 1.3 60.7 + - - +
163A TYR* 3.7 22.3 - - + -
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Residues in contact with GLY 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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139A GLY* 3.8 21.0 + - - -
158A ALA 2.8 11.5 + - - -
159A ALA* 4.0 4.0 + - - -
160A VAL 3.3 3.6 + - - -
161A ARG* 1.3 79.2 - - - +
163A TYR* 1.3 59.9 + - - -
94C LYS* 5.5 2.5 - - - -
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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