Contacts of the helix formed by residues 153 - 160 (chain A) in PDB entry 1W57
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 THR 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A LEU* 4.5 5.1 - - + +
87A ILE* 3.8 25.6 - - + +
88A ASP* 5.4 0.7 - - - -
89A SER 2.7 25.2 + - - +
90A GLU* 2.9 16.9 + - - -
91A PHE 3.4 14.4 + - - -
92A VAL* 3.8 11.3 + - - +
151A SER 3.3 4.4 + - - -
152A LYS* 1.3 69.2 - - - +
154A LYS* 1.3 54.9 + - - +
156A LEU* 3.0 4.8 + - - +
157A LYS* 2.9 57.5 + - + +
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Residues in contact with LYS 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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90A GLU 4.4 0.8 + - - +
152A LYS* 3.1 4.4 + - + +
153A THR* 1.3 79.7 - - - +
155A LEU* 1.3 63.5 + - + +
157A LYS* 3.8 7.4 - - - +
158A LYS* 3.3 27.4 + - - +
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Residues in contact with LEU 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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118A ASP* 4.0 29.8 - - + +
152A LYS* 3.0 21.6 + - + +
154A LYS* 1.3 81.1 - - + +
156A LEU* 1.3 54.2 + - - +
158A LYS* 3.6 6.7 - - + +
159A ALA* 2.7 35.3 + - - +
173A ILE* 3.8 32.7 - - + +
176A MET* 5.3 11.3 - - + +
178A GLY* 4.5 10.8 - - - +
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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 LEU* 4.4 4.3 - - + -
84A LEU* 3.8 29.6 - - + -
92A VAL* 4.0 14.1 - - + -
94A VAL* 4.2 6.3 - - + -
151A SER* 4.1 7.4 - - - +
152A LYS 3.1 8.9 + - - +
153A THR* 3.0 8.5 + - - +
155A LEU* 1.3 75.6 - - - +
157A LYS* 1.3 64.0 + - - +
159A ALA* 3.2 1.7 + - + +
160A LEU* 3.2 37.4 + - + +
169A ASP* 3.6 45.8 - - + +
172A ALA* 4.6 9.6 - - + -
173A ILE* 3.6 23.5 - - + +
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Residues in contact with LYS 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 LYS* 5.1 6.0 + - - +
84A LEU* 3.8 41.5 + - + +
85A GLU* 3.7 33.5 + - - +
87A ILE 4.0 10.7 + - - -
153A THR* 2.9 35.5 + - + +
154A LYS* 3.8 8.3 - - - +
156A LEU* 1.3 75.5 - - - +
158A LYS* 1.3 62.8 + - - +
160A LEU* 3.4 12.7 + - - +
161A ASP* 3.4 11.6 + - - +
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Residues in contact with LYS 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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154A LYS* 3.3 19.4 + - - +
155A LEU* 3.7 7.0 - - + +
156A LEU 3.3 0.4 - - - -
157A LYS* 1.3 74.7 - - - +
159A ALA* 1.3 63.0 + - - +
160A LEU 3.0 4.7 - - - -
161A ASP* 3.0 29.2 + - - +
176A MET* 3.5 36.3 - - - +
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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 LEU* 2.7 23.2 + - + +
156A LEU* 3.2 11.8 + - - +
158A LYS* 1.3 72.6 - - - +
160A LEU* 1.3 57.3 + - + +
161A ASP 3.6 0.8 + - - -
162A GLN 5.3 0.2 + - - -
163A ASN* 4.3 2.8 + - - +
166A PHE* 3.6 22.3 - - - -
172A ALA* 3.7 32.9 - - + +
173A ILE* 4.2 7.6 - - + +
176A MET* 4.0 21.4 - - + +
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Residues in contact with LEU 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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77A ALA* 4.2 19.5 - - + +
80A LEU* 4.0 22.2 - - + -
81A LYS* 3.4 35.2 + - + +
84A LEU* 3.8 27.6 - - + -
156A LEU* 3.2 16.8 + - + +
157A LYS 3.4 6.5 + - - +
158A LYS 3.0 0.6 - - - -
159A ALA* 1.3 80.0 - - + +
161A ASP* 1.3 63.1 + - - +
162A GLN 3.4 1.8 - - - -
163A ASN 3.8 9.6 - - - +
164A LEU* 3.6 12.4 - - + +
166A PHE* 3.9 27.4 - - + -
172A ALA* 4.1 10.5 - - + -
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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