Contacts of the helix formed by residues 144 - 152 (chain A) in PDB entry 4ZCU
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 TRP 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 GLU* 4.2 12.6 - - - -
91A MET* 4.0 2.0 - - + -
92A LYS* 3.6 61.4 - - + +
95A PHE* 3.5 36.1 - + + -
104A GLY 3.9 4.2 + - - +
143A ASP* 1.3 76.9 - - - +
145A ASN* 1.3 71.2 + - - +
147A TRP* 3.6 21.5 - + - -
148A ARG* 2.9 58.7 + - + +
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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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143A ASP* 3.1 15.7 + - - +
144A TRP* 1.3 89.8 - - - +
146A GLU* 1.3 57.6 + - + +
148A ARG* 3.9 10.6 + - - +
149A ASP* 2.9 42.7 + - - +
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Residues in contact with GLU 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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134A ILE* 4.4 7.5 - - - +
135A ASP* 2.7 34.1 - - - +
136A VAL* 2.8 20.4 + - + +
137A ASP* 3.6 20.1 + - - +
142A VAL* 3.7 31.4 - - + -
143A ASP* 3.1 17.5 + - - +
145A ASN* 1.3 75.1 - - + +
147A TRP* 1.3 59.9 + - - +
149A ASP* 3.8 5.0 - - - +
150A TYR* 2.9 33.0 + - - +
1004A CA 3.9 2.9 - - - -
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Residues in contact with TRP 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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91A MET* 3.0 26.8 + - + +
94A ALA* 4.0 11.7 - - + -
95A PHE* 3.5 19.9 - + + +
98A LEU* 3.4 31.9 - - + -
106A ILE* 3.8 15.0 - - + -
111A ILE* 6.0 0.9 - - + -
131A LEU* 6.1 1.3 - - + -
134A ILE* 4.2 11.4 - - + -
142A VAL* 3.7 9.8 - - + +
143A ASP 3.1 18.6 + - - +
144A TRP* 3.6 23.8 - + - +
146A GLU* 1.3 76.9 - - - +
148A ARG* 1.3 65.8 + - - +
150A TYR* 3.2 4.5 + - - +
151A PHE* 2.9 62.0 + + - +
159A ILE* 5.4 0.4 - - + -
162A ILE* 3.8 21.1 - - + -
166A TRP* 4.0 19.7 - + - -
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Residues in contact with ARG 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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23A ARG* 5.7 10.7 - - - +
24A TYR* 6.1 2.8 - - - -
88A GLU* 3.1 30.8 + - - +
91A MET* 5.6 2.0 - - - -
144A TRP* 2.9 48.9 + - + +
145A ASN* 3.9 10.3 + - - +
147A TRP* 1.3 81.4 - - - +
149A ASP* 1.3 79.7 + - - +
151A PHE* 3.7 1.9 - - - -
152A LEU* 2.9 52.4 + - + +
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Residues in contact with ASP 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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145A ASN* 2.9 27.9 + - - +
146A GLU* 3.9 5.7 - - - +
148A ARG* 1.3 106.8 + - - +
150A TYR* 1.3 63.1 + - - +
152A LEU* 3.5 19.2 + - - +
153A PHE* 4.9 2.6 + - - -
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Residues in contact with TYR 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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133A SER* 3.4 28.3 + - - -
134A ILE* 3.6 33.2 - - + +
146A GLU 2.9 19.6 + - - +
147A TRP 3.6 3.8 - - - +
149A ASP* 1.3 79.8 - - - +
151A PHE* 1.3 84.6 + + + +
152A LEU 3.7 0.3 + - - -
153A PHE 4.8 0.7 + - - -
154A ASN* 4.1 10.7 + - - +
165A PHE* 3.6 38.1 - + - -
166A TRP* 5.1 1.4 - - - -
169A SER* 4.2 9.2 + - - -
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Residues in contact with PHE 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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87A HIS* 2.7 33.3 + - - -
88A GLU* 5.0 0.2 - - - -
91A MET* 3.6 23.3 - - + -
134A ILE* 4.3 3.8 - - + -
147A TRP* 2.9 68.1 + + - +
148A ARG 3.7 1.6 - - - +
150A TYR* 1.3 98.8 - + + +
152A LEU* 1.3 54.3 + - - +
153A PHE 3.4 2.9 - - - -
154A ASN* 3.2 22.5 - - + +
156A VAL* 3.7 25.8 - - + -
162A ILE* 3.9 18.8 - - + -
165A PHE* 4.3 7.0 - + - -
166A TRP* 3.9 21.1 - - - -
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Residues in contact with LEU 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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24A TYR* 5.3 5.6 - - + -
27A LEU* 4.6 8.1 - - + -
83A TYR* 5.4 1.4 - - - -
84A LEU* 4.1 24.4 - - + +
87A HIS* 3.3 19.6 - - - -
88A GLU* 3.0 34.1 - - + +
148A ARG* 2.9 36.6 + - - +
149A ASP* 3.6 14.1 - - - +
150A TYR 3.4 2.2 - - - -
151A PHE* 1.3 76.8 - - - +
153A PHE* 1.3 89.9 + - + +
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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