Contacts of the strand formed by residues 153 - 158 (chain A) in PDB entry 4Z1H
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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146A GLN* 5.1 2.3 + - - -
147A THR* 3.7 1.7 - - - -
148A ASN* 2.9 51.7 + - - +
151A LYS* 3.3 20.3 - - + +
152A GLY* 1.3 73.2 - - - +
154A ILE* 1.3 63.4 + - - +
155A THR* 4.4 5.7 + - - -
254A ILE* 4.3 12.0 - - + +
255A ILE 3.1 9.6 - - - +
256A HIS* 3.2 37.9 - - + +
257A LEU* 4.5 4.5 - - - -
265A SER* 3.9 5.9 - - - -
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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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112A PHE* 4.0 16.2 - - + -
113A ILE* 4.1 24.2 - - + -
145A LEU* 4.7 8.7 - - + -
146A GLN 3.4 13.7 - - - +
147A THR* 4.6 2.5 - - + -
153A THR* 1.3 72.4 - - - +
155A THR* 1.3 69.4 + - - +
156A ILE* 6.1 1.3 - - + -
253A ILE 3.8 1.2 - - - +
255A ILE* 2.9 55.5 + - + +
257A LEU* 4.2 7.4 - - + -
264A PHE 3.5 25.1 - - - +
270A VAL* 4.0 21.8 - - + -
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Residues in contact with THR 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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75A ILE* 4.2 15.4 - - + +
144A HIS 3.8 0.3 - - - +
145A LEU* 3.3 7.1 - - - +
146A GLN* 2.9 52.8 + - - +
153A THR* 4.4 5.2 + - - -
154A ILE* 1.3 77.9 - - - +
156A ILE* 1.3 65.0 + - - +
252A LYS* 3.9 25.3 - - + -
253A ILE 3.2 10.1 - - - +
254A ILE* 3.7 32.8 - - + +
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Residues in contact with ILE 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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113A ILE* 4.9 0.7 - - - +
116A LEU* 3.7 37.7 - - + +
117A ILE* 3.6 36.3 - - + +
120A ALA* 4.5 4.5 - - + -
143A ILE* 4.1 10.3 - - + -
144A HIS 3.3 3.6 - - - +
145A LEU* 3.7 29.4 - - + -
154A ILE* 6.1 1.6 - - + -
155A THR* 1.3 75.7 - - - +
157A GLN* 1.3 63.6 + - - +
158A ASP* 5.0 2.4 - - - +
251A THR 3.8 1.9 - - - +
252A LYS* 3.7 0.9 - - - -
253A ILE* 2.9 50.1 + - + +
255A ILE* 5.1 2.2 - - + -
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Residues in contact with GLN 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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74A ILE* 3.5 29.4 + - + +
75A ILE* 3.4 35.3 - - + +
76A SER 4.9 0.3 + - - -
79A GLU* 5.8 0.8 + - - -
142A GLU 4.0 0.3 - - - +
143A ILE* 3.6 3.5 - - - +
144A HIS* 2.9 34.1 + - + +
155A THR 4.2 0.4 - - - -
156A ILE* 1.3 75.4 - - - +
158A ASP* 1.3 71.8 + - - +
159A THR* 5.4 2.0 - - + +
248A ARG* 4.0 28.3 + - - +
249A THR 5.6 1.2 + - - -
251A THR 3.2 11.0 - - - +
252A LYS* 3.8 30.8 + - + +
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Residues in contact with ASP 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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120A ALA* 3.6 35.4 - - + +
123A ALA* 3.9 8.7 - - - +
124A LEU* 4.5 2.9 - - + -
142A GLU 3.6 10.1 - - - +
143A ILE* 4.6 0.9 - - + -
156A ILE* 5.0 2.6 - - - +
157A GLN* 1.3 81.4 - - - +
159A THR* 1.3 60.9 + - - +
160A GLY* 3.3 16.1 + - - +
161A ILE 4.2 0.7 - - - +
249A THR 3.9 0.9 - - - +
250A GLY* 3.1 4.3 - - - -
251A THR* 2.9 43.1 + - - +
253A ILE* 6.0 0.7 - - - +
601A 4KP 3.2 22.6 + - - -
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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