Contacts of the helix formed by residues 141 - 154 (chain A) in PDB entry 1N54
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 ALA 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A VAL* 4.7 0.4 - - - -
140A ILE* 1.3 74.3 - - - +
142A ALA* 1.3 58.6 + - - +
143A PRO* 3.1 7.6 - - + -
144A SER* 2.7 41.3 + - - +
145A MET* 3.3 4.3 + - - +
265A GLN* 3.8 13.1 - - + +
266A HIS 2.7 20.4 + - - +
267A ASN* 4.3 14.1 - - - +
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Residues in contact with ALA 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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135A VAL* 3.7 23.3 - - + +
140A ILE 3.4 4.4 + - - -
141A ALA* 1.3 69.9 - - - +
143A PRO* 1.3 72.9 - - + +
145A MET* 3.7 6.4 + - - +
146A VAL* 3.7 3.2 - - - +
183A GLU* 5.0 13.0 - - - +
184A LEU* 3.3 26.1 - - + +
186A GLU* 5.1 7.4 - - - +
187A LYS* 5.1 11.9 - - + -
188A LYS* 5.9 0.2 - - - -
265A GLN* 5.6 0.6 - - - +
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Residues in contact with PRO 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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141A ALA* 3.4 10.3 - - + -
142A ALA* 1.3 92.5 - - + +
144A SER* 1.3 66.5 + - - +
145A MET 3.0 2.2 - - - -
146A VAL* 2.7 16.8 + - - +
147A ALA* 2.9 10.7 + - - +
187A LYS* 4.4 11.2 - - + -
188A LYS* 3.8 37.1 - - + +
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Residues in contact with SER 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ILE* 4.0 5.8 - - - -
141A ALA* 2.7 35.3 + - - +
143A PRO* 1.3 74.0 - - - +
145A MET* 1.3 55.2 + - - -
147A ALA* 3.2 23.9 - - - +
148A MET* 3.7 4.3 + - - +
267A ASN* 4.3 7.6 - - - +
268A LEU* 2.5 56.2 + - - +
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Residues in contact with MET 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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128A VAL* 4.9 7.6 - - + +
131A LEU* 4.3 29.6 - - + +
132A SER* 4.3 17.3 - - - +
135A VAL* 4.0 24.2 - - + -
140A ILE* 4.7 2.5 - - + -
141A ALA 3.3 2.0 + - - +
142A ALA 4.0 8.3 - - - +
143A PRO 2.8 4.9 + - - -
144A SER* 1.3 73.7 - - - +
146A VAL* 1.3 63.8 + - - +
147A ALA 3.0 2.0 + - - -
148A MET* 3.3 31.6 + - - +
149A PHE* 2.9 51.8 + - + +
180A VAL* 5.4 1.8 - - + -
184A LEU* 5.0 5.2 - - + -
268A LEU* 3.1 27.3 - - + +
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Residues in contact with VAL 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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142A ALA 3.7 14.8 - - - +
143A PRO 2.7 9.9 + - - +
145A MET* 1.3 74.0 - - - +
147A ALA* 1.3 64.6 + - - +
149A PHE* 3.8 8.7 - - + -
150A GLU* 2.8 50.1 + - + +
184A LEU* 3.7 24.2 - - + +
187A LYS 5.2 0.2 - - - +
188A LYS* 4.0 33.2 - - + -
191A GLU* 4.7 3.4 - - + -
192A MET* 4.0 23.6 - - + -
195A ILE* 5.0 1.8 - - + -
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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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143A PRO 2.9 10.3 + - - +
144A SER* 3.2 17.5 - - - +
145A MET 3.0 0.2 - - - -
146A VAL* 1.3 78.3 - - - +
148A MET* 1.3 61.7 + - - +
150A GLU* 3.4 22.4 + - - +
151A ASN* 3.1 17.6 + - - -
268A LEU 5.5 4.3 - - - +
270A PRO* 6.6 0.4 - - + -
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Residues in contact with MET 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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109A ILE* 4.2 25.8 - - + -
112A LEU* 5.3 7.0 - - + -
128A VAL* 5.7 0.4 - - - -
131A LEU* 5.1 1.8 - - + -
144A SER 3.7 6.1 + - - +
145A MET* 3.3 26.4 + - + +
146A VAL 3.3 0.2 - - - -
147A ALA* 1.3 75.6 - - - +
149A PHE* 1.3 56.0 + - - +
150A GLU 2.9 4.0 - - - -
151A ASN* 2.5 35.7 + - - +
152A PHE* 3.0 32.6 + - + -
268A LEU* 4.5 17.9 - - + -
269A PRO 5.3 2.5 - - - +
271A PHE* 3.3 55.0 - - + +
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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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128A VAL* 3.9 20.0 - - + -
132A SER* 3.4 26.5 - - - -
145A MET* 2.9 38.3 + - + +
146A VAL* 3.5 14.6 - - + +
148A MET* 1.3 74.8 - - + +
150A GLU* 1.3 61.1 + - - +
152A PHE* 3.4 19.8 + + - +
153A VAL* 3.2 28.4 + - - +
173A PHE* 3.4 45.9 - + + -
176A SER* 3.9 12.8 - - - -
177A LEU* 4.1 10.1 - - + -
180A VAL* 4.5 0.9 - - + -
184A LEU* 4.2 17.0 - - + -
192A MET* 5.2 0.7 - - - -
195A ILE* 4.9 2.5 - - + -
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Residues in contact with GLU 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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146A VAL* 2.8 39.3 + - + +
147A ALA* 3.4 15.3 - - - +
148A MET 2.8 0.2 + - - -
149A PHE* 1.3 76.2 - - - +
151A ASN* 1.3 53.6 + - - +
153A VAL* 3.2 3.8 + - - +
154A SER* 2.7 35.6 + - - -
188A LYS* 5.0 5.0 - - - +
191A GLU* 3.4 28.7 - - - +
194A ARG* 4.9 5.3 + - - -
195A ILE* 3.7 29.9 - - + +
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Residues in contact with ASN 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 ALA 3.1 22.6 + - - -
148A MET* 2.5 17.6 + - - +
150A GLU* 1.3 75.0 - - - +
152A PHE* 1.3 59.6 + - + +
154A SER* 3.4 15.2 + - - -
155A VAL* 3.2 21.3 + - - +
270A PRO* 5.9 0.6 - - - +
271A PHE 3.2 32.3 + - - +
272A THR* 4.9 7.3 - - - +
273A PRO* 3.9 14.3 - - + +
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Residues in contact with PHE 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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112A LEU* 5.3 4.0 - - + -
116A LEU* 6.2 0.9 - - + -
128A VAL* 3.8 26.5 - - + -
148A MET* 3.0 33.8 + - + -
149A PHE* 3.4 28.7 - + + +
150A GLU 3.2 0.2 - - - -
151A ASN* 1.3 76.4 - - - +
153A VAL* 1.3 65.4 + - + +
155A VAL* 3.7 7.7 + - - +
156A THR* 4.6 3.3 - - - +
168A TRP* 4.7 4.9 - + - -
169A TYR* 3.2 69.5 - + - +
172A ALA* 3.8 22.4 - - + -
173A PHE* 4.7 2.0 - - + -
271A PHE* 3.7 27.1 - + - -
273A PRO* 4.1 6.5 - - + -
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Residues in contact with VAL 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 PHE 3.2 8.3 + - - +
150A GLU 3.2 7.4 + - - +
152A PHE* 1.3 75.0 - - + +
154A SER* 1.3 57.2 + - - +
155A VAL 2.9 11.2 + - - -
156A THR* 2.9 35.8 + - + +
157A GLN* 3.4 1.1 - - - +
170A VAL* 5.4 7.6 - - + -
173A PHE* 4.6 16.6 - - + -
195A ILE* 3.2 34.1 - - + -
198A ASN* 4.0 23.8 - - + +
199A THR* 3.1 27.8 - - + +
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Residues in contact with SER 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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150A GLU 2.7 18.7 + - - -
151A ASN* 3.6 17.0 - - - -
152A PHE 3.3 0.6 - - - -
153A VAL* 1.3 74.3 - - - +
155A VAL* 1.3 59.7 + - - +
156A THR 3.2 0.4 - - - -
157A GLN* 3.3 29.6 + - - +
158A GLU* 4.1 2.1 + - - +
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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