Contacts of the strand formed by residues 153 - 162 (chain A) in PDB entry 1Z59
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 PRO 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A PRO* 3.3 45.8 - - + +
88A ASN* 3.4 16.6 - - - +
91A GLY* 3.6 11.4 - - - +
92A ARG* 3.7 15.7 - - - +
144A LEU* 5.1 1.8 - - + -
145A LYS 3.7 6.1 - - - +
152A GLU* 1.3 99.4 - - + +
154A ILE* 1.3 62.3 + - - +
155A ILE* 4.1 8.9 + - + +
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Residues in contact with ILE 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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144A LEU* 3.4 6.2 - - - +
145A LYS* 2.7 52.1 + - + +
146A ILE 4.4 3.8 - - - +
147A ASP* 3.8 43.3 - - + +
152A GLU* 5.8 0.7 - - + -
153A PRO* 1.3 77.4 - - - +
155A ILE* 1.3 68.1 - - - +
156A VAL* 3.5 16.3 + - + +
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Residues in contact with ILE 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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87A PRO* 3.9 31.2 - - + -
142A PHE* 4.7 8.1 - - + -
143A LYS 4.0 1.6 - - - +
144A LEU* 4.2 18.8 - - + -
153A PRO* 4.1 6.0 + - + +
154A ILE* 1.3 80.9 - - - +
156A VAL* 1.3 63.6 + - - +
157A GLU 3.8 19.7 - - - +
158A ARG* 3.9 40.4 - - + +
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Residues in contact with VAL 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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126A PRO* 4.5 13.2 - - + -
143A LYS* 2.9 24.6 + - + +
145A LYS* 4.3 26.7 - - + -
154A ILE* 4.2 17.9 - - + +
155A ILE* 1.3 76.1 - - - +
157A GLU* 1.3 71.9 + - + +
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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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142A PHE* 3.4 5.1 - - - +
143A LYS* 3.0 68.6 + - + +
155A ILE* 3.8 5.9 - - - +
156A VAL* 1.3 85.8 - - - +
158A ARG* 1.3 63.9 + - - +
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Residues in contact with ARG 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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83A PRO 5.8 0.6 + - - -
87A PRO* 4.2 22.0 - - - +
141A THR* 3.5 7.0 - - - +
142A PHE* 4.0 21.9 - - + -
155A ILE* 3.9 30.2 - - + +
157A GLU* 1.3 79.7 - - - +
159A GLY* 1.3 63.3 + - - +
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Residues in contact with GLY 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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140A TYR* 3.7 5.7 - - - +
141A THR* 2.9 39.7 + - - +
142A PHE* 5.6 0.5 - - - -
158A ARG* 1.3 79.6 - - - +
160A SER* 1.3 65.0 + - - -
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Residues in contact with SER 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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138A ARG* 2.8 35.0 + - - -
139A ILE 3.2 13.7 - - - -
140A TYR* 3.9 19.3 - - - -
141A THR* 3.9 3.2 + - - +
159A GLY* 1.3 76.0 - - - -
161A VAL* 1.3 71.0 + - - +
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Residues in contact with VAL 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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138A ARG* 3.2 11.7 - - - +
139A ILE* 2.8 45.0 + - + +
141A THR* 5.3 9.9 - - + -
160A SER* 1.3 79.7 - - - +
162A GLU* 1.3 75.5 + - + +
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Residues in contact with GLU 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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137A LYS 3.8 8.3 - - - +
138A ARG* 3.6 22.4 + - - +
139A ILE* 4.8 4.0 - - - +
161A VAL* 1.3 87.7 - - + +
163A ASN* 1.3 72.2 + - - +
164A THR* 5.1 2.4 - - - +
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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