Contacts of the helix formed by residues 144 - 155 (chain A) in PDB entry 3LEZ
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 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A LYS* 3.8 6.1 - - - -
118A TYR 3.8 4.5 - - - -
119A SER* 3.2 9.3 - - - -
120A PRO* 4.4 6.7 - - + -
121A ILE* 2.8 34.1 + - + -
122A THR* 2.8 36.4 + - - -
138A ALA* 3.2 20.7 + - + +
139A ALA* 3.9 2.0 + - - -
142A TYR 3.2 2.5 - - - -
143A SER* 1.3 76.3 - - - +
145A ASN* 1.3 59.6 + - - +
146A THR 3.2 2.3 + - - -
147A ALA* 2.9 28.0 + - + +
148A GLY 3.1 20.1 + - - -
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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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85A SER* 4.1 2.8 + - - -
88A LYS* 2.8 23.5 + - - +
116A VAL* 3.6 12.6 - - + -
117A THR* 2.9 29.7 + - - +
118A TYR* 3.0 23.6 + - - +
143A SER 3.7 4.0 + - - +
144A ASP* 1.3 70.3 + - - +
146A THR* 1.3 65.5 + - - +
148A GLY* 3.1 3.6 + - - -
149A ASN* 3.1 17.7 + - - -
179A GLU* 3.2 33.1 + - + +
180A THR* 3.8 11.1 - - - +
183A ASN* 5.0 1.9 + - - +
305A EPE 5.7 3.2 - - - -
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Residues in contact with THR 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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110A TYR* 4.9 5.8 - - + -
114A ASP* 4.0 18.2 - - + +
115A LEU* 3.3 13.3 - - + -
116A VAL* 2.9 24.9 + - - +
119A SER* 2.7 19.5 + - - -
122A THR* 3.3 20.2 - - - +
144A ASP* 3.2 0.2 + - - -
145A ASN* 1.3 74.5 - - - +
147A ALA* 1.3 60.8 + - - +
149A ASN* 3.0 8.6 + - + +
150A LEU* 2.8 46.0 + - + +
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Residues in contact with ALA 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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122A THR* 3.7 12.4 - - + +
135A ILE* 3.4 35.5 - - + +
138A ALA* 4.1 2.2 - - + -
139A ALA* 3.7 13.5 - - + +
144A ASP* 2.9 27.9 + - + +
146A THR* 1.3 75.6 - - - +
148A GLY* 1.3 63.4 + - - +
150A LEU* 3.2 2.2 + - - -
151A LEU* 3.0 26.3 + - - +
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Residues in contact with GLY 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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87A PHE* 4.1 13.7 - - - -
88A LYS* 4.1 21.1 - - - -
139A ALA* 4.2 0.8 - - - +
144A ASP 3.1 10.6 + - - -
145A ASN 3.1 8.6 + - - -
147A ALA* 1.3 76.6 - - - +
149A ASN* 1.3 57.3 + - - +
151A LEU* 3.3 9.9 + - - +
152A LEU* 3.0 30.7 + - - +
179A GLU* 4.9 0.7 - - - -
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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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114A ASP 5.2 2.4 + - - +
116A VAL* 3.8 19.6 - - - +
145A ASN 3.1 9.1 + - - +
146A THR* 3.0 14.2 + - + +
148A GLY* 1.3 73.9 - - - +
150A LEU* 1.3 59.8 + - + +
152A LEU* 3.3 4.4 + - - +
153A GLU* 2.9 46.0 + - - +
178A TYR* 3.4 20.8 - - + +
179A GLU* 2.8 51.7 + - - +
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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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108A ILE* 4.3 16.7 - - + +
109A THR 5.2 0.9 - - - +
110A TYR* 3.8 43.7 - - + -
114A ASP* 6.1 1.6 - - + -
122A THR* 4.3 7.6 - - + -
132A LEU* 4.7 3.0 - - + +
135A ILE* 3.8 34.5 - - + -
146A THR* 2.8 30.8 + - + +
147A ALA* 3.2 6.0 + - - +
149A ASN* 1.3 76.1 - - + +
151A LEU* 1.3 57.8 + - - +
153A GLU* 3.5 17.8 + - + +
154A ALA* 2.9 29.5 + - - +
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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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88A LYS* 4.2 9.4 - - + +
91A ALA* 4.0 16.2 - - + -
92A VAL* 3.7 22.9 - - + -
95A VAL* 4.1 21.5 - - + -
132A LEU* 4.2 11.7 - - + +
135A ILE* 3.9 14.8 - - + -
136A ALA* 4.3 14.1 - - + +
139A ALA* 3.6 30.1 - - + -
147A ALA 3.0 13.6 + - - +
148A GLY* 3.5 9.4 - - - +
150A LEU* 1.3 75.0 - - - +
152A LEU* 1.3 66.3 + - - +
154A ALA* 3.2 5.1 + - - +
155A MET* 3.1 28.7 + - - +
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Residues in contact with LEU 152 (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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87A PHE* 3.8 28.7 - - + -
91A ALA* 5.0 0.2 - - + -
148A GLY 3.0 17.8 + - - +
149A ASN* 3.6 13.7 - - - +
151A LEU* 1.3 74.5 - - - +
153A GLU* 1.3 61.5 + - - +
155A MET* 3.1 13.0 + - - +
156A GLY 3.3 0.3 + - - -
157A GLY* 2.8 24.2 + - - -
158A PRO* 4.3 17.7 - - + -
161A LEU* 3.7 28.3 - - + -
175A MET* 4.3 8.7 - - + -
177A ARG 4.0 16.4 - - - +
178A TYR* 3.7 30.1 - - + -
182A LEU* 4.4 2.5 - - + -
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Residues in contact with GLU 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 ASN* 2.9 34.3 + - - +
150A LEU* 3.9 17.9 + - + +
152A LEU* 1.3 76.8 - - - +
154A ALA* 1.3 62.1 + - - +
156A GLY* 2.9 15.0 + - - -
157A GLY 4.3 4.0 - - - +
178A TYR* 3.6 23.5 - - + +
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Residues in contact with ALA 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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95A VAL* 4.8 4.3 - - + -
99A LYS* 2.8 32.3 + - - +
108A ILE* 6.1 2.5 - - + -
132A LEU* 3.8 32.1 - - + -
150A LEU 2.9 18.8 + - - +
151A LEU* 3.2 6.0 + - - +
153A GLU* 1.3 76.2 - - - +
155A MET* 1.3 59.4 + - - +
156A GLY 3.6 0.5 + - - -
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Residues in contact with MET 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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91A ALA 4.5 4.3 - - - +
94A ALA* 3.7 15.7 - - + +
95A VAL* 3.7 32.3 - - + -
98A THR* 3.5 26.2 - - + +
99A LYS* 4.4 4.0 - - - -
151A LEU 3.1 13.7 + - - +
152A LEU* 3.7 7.4 - - - +
153A GLU 3.1 1.0 - - - -
154A ALA* 1.3 80.0 - - - +
156A GLY* 1.3 56.5 + - - +
157A GLY 3.5 0.7 - - - -
160A GLU* 3.4 18.4 - - - +
161A LEU* 4.1 29.4 + - + -
164A ILE* 3.1 37.4 - - + +
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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