Contacts of the strand formed by residues 146 - 152 (chain B) in PDB entry 1Z6Z
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 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B GLN 2.9 15.6 + - - +
91B ARG* 3.3 26.2 + - - +
92B LEU 2.9 26.3 + - - +
144B GLY 3.9 1.2 + - - -
145B LEU* 1.3 69.6 - - - +
147B ARG* 1.3 63.0 + - - +
148B THR* 2.7 25.9 + - - -
189B ARG* 4.1 8.6 - - - +
245B ASP* 3.1 31.7 + - - -
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Residues in contact with ARG 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A VAL* 6.0 0.6 - - - +
92B LEU* 3.6 20.9 - - + -
136B LEU* 3.3 33.8 + - + +
139B PHE 2.8 36.6 + - - -
140B PRO* 3.5 7.9 - - - +
141B ASP* 3.3 37.5 + - - +
145B LEU* 3.6 25.1 + - + +
146B ASN* 1.3 75.5 + - - +
148B THR* 1.3 61.5 + - - +
185B GLU* 3.9 14.3 + - - -
187B ASN* 4.3 14.6 + - - +
188B VAL* 3.5 32.2 - - + +
189B ARG* 2.9 25.5 + - - +
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Residues in contact with THR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ARG* 3.8 10.8 + - - -
92B LEU* 2.8 17.5 + - - +
93B LEU* 3.4 13.3 - - + +
94B LEU 3.1 23.7 + - - -
146B ASN* 2.7 25.6 + - - -
147B ARG* 1.3 71.4 + - - +
149B VAL* 1.3 70.1 + - - +
150B VAL* 4.2 7.0 - - + -
189B ARG* 3.2 22.8 - - + +
242B LEU* 3.8 28.5 - - + -
245B ASP* 4.8 1.7 + - - -
247B PHE* 4.6 7.2 - - + -
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Residues in contact with VAL 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU* 5.9 1.8 - - + -
94B LEU* 3.5 18.4 - - + +
132B THR* 4.0 13.7 - - + -
135B VAL* 5.7 1.1 - - + -
136B LEU* 4.0 26.7 - - + -
147B ARG 4.5 0.2 + - - -
148B THR* 1.3 79.6 - - - +
150B VAL* 1.3 64.4 + - - +
178B PHE* 3.6 24.5 - - + -
181B LEU* 3.7 22.9 - - + -
188B VAL* 4.1 4.9 - - + -
189B ARG 3.0 7.5 + - - +
190B VAL* 3.6 14.7 - - + -
191B LEU* 2.9 26.3 + - - +
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LEU* 4.3 8.1 - - + -
94B LEU 2.7 15.7 + - - +
95B ILE* 4.1 12.3 - - + -
96B ASN* 2.8 36.9 + - - -
148B THR* 4.2 6.3 - - + -
149B VAL* 1.3 78.7 - - - +
151B ASN* 1.3 61.3 + - - +
152B ILE* 3.9 26.0 - - + -
178B PHE* 3.7 3.1 - - - -
191B LEU* 3.3 16.2 - - + +
193B TYR* 4.5 4.7 - - + -
238B LEU* 4.2 15.9 - - + -
242B LEU* 4.0 27.4 - - + -
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Residues in contact with ASN 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ASN* 4.0 4.3 - - - -
128B MET* 3.5 13.1 - - + +
150B VAL* 1.3 73.7 - - - +
152B ILE* 1.3 64.2 + - - +
153B SER* 3.2 6.2 + - - +
174B ARG* 2.9 51.0 + - - +
175B ASP* 3.1 18.0 + - - -
178B PHE* 3.5 17.4 - - + -
191B LEU 2.9 6.5 + - - -
192B ASN* 2.8 27.6 + - - +
193B TYR* 2.9 26.2 + - - -
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Residues in contact with ILE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PHE* 3.9 21.3 - - + -
95B ILE* 4.0 9.0 - - + -
96B ASN 3.0 22.5 + - - +
97B ASN* 3.8 24.5 - - + +
150B VAL* 3.9 20.6 - - + -
151B ASN* 1.3 76.8 + - - +
153B SER* 1.3 60.8 + - - +
171B LYS* 3.0 23.4 + - - -
174B ARG* 3.4 1.9 + - - -
193B TYR* 3.4 9.6 - - + -
195B PRO* 3.8 20.0 - - + -
238B LEU* 4.2 7.4 - - + -
802B NAP 3.4 32.8 - - - +
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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