Contacts of the strand formed by residues 157 - 163 (chain A) in PDB entry 1JZ3
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 ARG 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A TRP* 3.2 3.0 - - - -
154A CYS 2.8 37.2 + - - +
155A ASN* 3.2 7.8 - - + +
156A GLY* 1.3 83.7 - - - +
158A TRP* 1.3 64.0 + - - +
159A VAL* 3.5 2.4 + - - +
175A ALA* 3.3 29.7 + - - +
176A PHE* 3.8 42.9 + - + +
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Residues in contact with TRP 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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24A LEU* 3.8 32.5 - - + -
25A ASN* 3.5 26.9 - - - -
151A HIS* 3.0 29.1 + + - -
152A LEU 3.6 12.6 - - - -
153A TRP* 3.4 36.1 - + + +
156A GLY 4.1 0.2 + - - -
157A ARG* 1.3 70.5 - - - +
159A VAL* 1.3 59.8 - - - +
160A GLY* 3.4 25.8 + - - -
176A PHE* 3.4 13.9 - - - -
13D ARG* 5.1 12.8 - - - -
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Residues in contact with VAL 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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25A ASN* 2.9 28.8 + - + +
152A LEU* 2.8 25.6 + - + +
153A TRP 4.1 0.7 - - - -
154A CYS* 3.7 31.6 - - + +
157A ARG 3.7 0.2 - - - +
158A TRP* 1.3 77.1 - - - +
160A GLY* 1.4 59.2 - - - +
171A PHE* 3.8 30.5 - - + -
172A ASP 4.6 2.7 - - - +
173A LEU* 3.9 12.1 - - + -
176A PHE* 3.5 37.4 - - + -
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Residues in contact with GLY 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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24A LEU 3.4 11.7 - - - -
151A HIS* 3.4 1.4 - - - -
152A LEU* 2.8 29.7 + - - +
158A TRP* 3.4 23.0 + - - -
159A VAL* 1.4 83.6 - - - +
161A TYR* 1.4 60.2 - - - -
171A PHE* 4.0 12.1 - - - -
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Residues in contact with TYR 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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15A ASP* 3.9 21.1 - - + -
16A TRP* 3.1 23.4 - + - +
21A VAL* 4.0 11.2 - - + -
22A THR 4.4 0.2 - - - -
23A GLN* 3.1 20.0 - - - +
24A LEU* 2.8 43.8 + - + +
149A ALA* 3.5 6.7 - - + +
150A PHE* 3.0 34.5 - - - -
151A HIS* 3.3 40.2 - + + -
160A GLY* 1.4 74.1 - - - +
162A GLY* 1.3 58.5 + - - +
163A GLN* 2.7 42.7 + - + -
171A PHE* 3.7 12.3 - - - -
189A LEU* 4.6 6.3 - - + -
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Residues in contact with GLY 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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22A THR 3.9 3.4 - - - -
26A ARG* 3.8 14.4 - - - -
149A ALA* 3.1 5.9 - - - +
150A PHE* 2.9 57.1 + - - -
161A TYR* 1.3 77.6 - - - +
163A GLN* 1.3 64.1 + - - +
169A SER* 4.3 1.6 - - - -
171A PHE* 4.7 0.7 - - - -
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Residues in contact with GLN 163 (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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16A TRP* 3.9 0.9 - - - -
21A VAL 3.8 7.1 + - - -
22A THR* 2.9 31.4 + - + +
26A ARG* 2.9 21.2 + - - -
146A VAL 5.6 0.4 - - - -
148A SER 3.8 8.3 - - - +
149A ALA* 3.8 7.9 - - + -
161A TYR* 2.7 26.5 + - + +
162A GLY* 1.3 76.4 - - - +
164A ASP* 1.3 74.5 + - - +
169A SER* 4.5 0.7 + - - -
192A SER* 4.4 3.6 - - - +
193A ASP* 2.8 27.3 + - - +
194A GLY* 3.6 17.0 - - - +
435A ALA* 6.1 0.2 - - - +
439A ARG* 4.6 4.8 - - - +
3002A MG 2.2 25.5 - - - -
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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