Contacts of the helix formed by residues 154 - 163 (chain A) in PDB entry 4NTX
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 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A PHE* 1.3 83.6 - - - +
155A MET* 1.3 59.7 + - - +
156A LEU* 2.8 13.3 + - - +
157A GLU* 2.6 46.0 + - + +
158A PHE* 2.9 28.2 + - - +
335A TYR* 3.6 30.5 - - - +
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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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99A PHE* 4.1 13.5 - - + -
112A ALA* 4.6 1.8 - - - -
115A LEU* 3.9 25.8 - - + -
153A PHE* 3.7 26.4 - - + -
154A ASN* 1.3 70.8 + - - +
156A LEU* 1.3 60.3 + - - +
158A PHE* 3.6 8.3 - - + +
159A TYR* 2.8 65.5 + - + +
239A GLU* 5.6 0.4 - - + -
327A VAL* 3.7 20.1 - - + +
335A TYR* 5.7 1.2 - - - +
336A CYS 4.0 12.3 + - - +
338A PRO* 4.0 15.7 - - + +
341A TYR* 3.9 24.5 - - + -
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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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154A ASN* 2.8 13.2 + - - +
155A MET* 1.3 70.8 - - - +
157A GLU* 1.3 62.1 + - - +
159A TYR* 3.4 1.3 + - - +
160A ASP* 2.9 29.6 + - + +
189A PHE* 3.8 40.4 - - + -
327A VAL* 3.4 35.2 - - + +
335A TYR* 3.5 32.5 - - + +
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Residues in contact with GLU 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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153A PHE* 5.6 1.4 - - - -
154A ASN* 2.6 33.4 + - + +
156A LEU* 1.3 73.9 - - - +
158A PHE* 1.3 57.8 + - - +
160A ASP* 3.4 8.4 + - + +
161A ARG* 2.8 73.9 + - - +
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Residues in contact with PHE 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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99A PHE* 3.3 45.1 - + - -
104A VAL* 4.3 14.4 - - + -
108A ASP* 3.4 42.8 - - + -
112A ALA* 4.2 17.5 - - + -
116A LEU* 4.3 9.2 - - + -
153A PHE* 3.5 24.0 - + + -
154A ASN 2.9 19.0 + - - +
155A MET* 3.6 11.2 - - - +
157A GLU* 1.3 79.3 - - - +
159A TYR* 1.3 58.4 + - - +
161A ARG* 3.8 6.3 - - - +
162A ALA* 2.8 52.5 + - + +
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Residues in contact with TYR 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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98A GLU* 2.9 32.9 + - + -
99A PHE* 3.3 34.9 - + - -
155A MET* 2.8 43.4 + - + +
156A LEU 3.8 3.8 - - - +
158A PHE* 1.3 72.4 - - - +
160A ASP* 1.3 59.3 + - - +
163A GLY* 2.8 30.9 + - - +
189A PHE* 4.0 17.0 - + + -
190A THR 5.5 1.8 - - - -
191A ARG 4.2 6.7 + - - -
193A GLY* 3.5 31.0 - - - -
194A LYS* 3.8 7.7 - - - +
239A GLU* 3.9 11.6 + - - +
327A VAL* 3.5 24.9 - - + -
341A TYR* 4.4 11.2 - + - -
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Residues in contact with ASP 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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100A ARG* 5.4 0.7 + - - -
156A LEU* 2.9 19.5 + - + +
157A GLU* 3.7 10.1 - - + +
159A TYR* 1.3 77.2 - - - +
161A ARG* 1.3 60.5 + - - +
163A GLY 4.9 0.5 - - - +
187A VAL* 5.3 0.9 - - - +
189A PHE* 3.9 20.9 - - + -
194A LYS* 2.8 45.3 + - - +
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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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100A ARG* 3.1 23.1 + - - -
103A ARG* 3.4 26.8 + - + +
105A THR* 4.0 10.8 + - - +
108A ASP* 2.7 44.2 + - - -
153A PHE* 4.9 1.8 - - - -
157A GLU* 2.8 54.0 + - - +
158A PHE* 3.8 15.1 - - - +
160A ASP* 1.3 80.1 - - - +
162A ALA* 1.3 58.5 + - - +
163A GLY 3.5 0.2 - - - -
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Residues in contact with ALA 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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99A PHE* 4.1 14.8 - - + -
100A ARG* 2.8 35.7 + - - +
103A ARG* 3.8 22.0 - - + +
104A VAL 5.1 0.2 - - - +
158A PHE* 2.8 47.5 + - + +
161A ARG* 1.3 73.6 - - - +
163A GLY* 1.3 61.3 + - - +
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Residues in contact with GLY 163 (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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98A GLU 3.4 19.6 + - - -
100A ARG* 3.0 19.6 + - - -
159A TYR* 2.8 20.6 + - - +
160A ASP 4.9 0.5 - - - +
161A ARG 4.1 0.7 - - - +
162A ALA* 1.3 78.8 - - - +
164A HIS* 1.3 70.1 + - - +
165A ASP* 4.3 0.3 - - - -
194A LYS* 4.4 16.8 + - - +
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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