Contacts of the strand formed by residues 190 - 196 (chain A) in PDB entry 1ZA3
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 VAL 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A LYS 4.2 1.8 - - - +
149A VAL* 3.4 8.1 - - - +
150A ASP* 2.9 43.4 + - - +
151A ASN* 5.4 10.3 - - - +
189A LYS* 1.3 80.8 - - + +
191A TYR* 1.3 75.3 + - - +
192A ALA* 4.8 6.3 - - + +
207A SER* 4.7 9.0 - - - +
208A PHE 4.3 1.1 - - - +
209A ASN* 3.4 28.3 - - - +
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Residues in contact with TYR 191 (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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116A ILE* 3.6 6.3 - - - +
131A VAL* 4.4 9.2 - - + -
147A TRP* 5.0 1.3 - + + -
148A LYS 3.7 1.8 - - - -
149A VAL* 3.4 41.6 - - + +
178A LEU* 4.1 13.9 - - + -
180A LEU* 3.7 15.6 - - + +
184A ASP 4.0 0.3 + - - -
185A TYR* 3.0 50.9 + + - -
188A HIS* 3.6 15.4 - - - +
189A LYS 3.3 17.0 - - - -
190A VAL* 1.3 85.5 - - - +
192A ALA* 1.3 61.1 + - - +
207A SER* 2.9 24.4 - - - -
208A PHE* 3.0 49.0 + + + +
210A ARG* 4.5 1.3 - - + -
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Residues in contact with ALA 192 (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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116A ILE* 4.2 0.4 - - - -
146A GLN 4.0 0.2 - - - +
147A TRP* 3.5 9.5 - - - -
148A LYS* 2.9 50.4 + - + +
151A ASN* 5.9 1.8 - - - +
190A VAL* 4.9 6.1 - - + -
191A TYR* 1.3 75.2 - - - +
193A CYS* 1.3 58.5 + - - +
194A GLU* 6.2 0.2 - - + -
205A THR* 4.1 16.8 - - + +
206A LYS 3.3 6.5 - - - +
207A SER* 3.4 16.8 - - - -
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Residues in contact with CYS 193 (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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114A VAL* 4.1 13.2 - - - -
115A PHE 4.9 0.4 - - - -
116A ILE* 3.9 11.5 - - - +
133A CYS* 2.1 54.1 - - + -
145A VAL* 4.1 7.2 - - + -
146A GLN 3.3 10.3 - - - +
147A TRP* 4.1 11.0 - - + -
192A ALA* 1.3 74.3 - - - +
194A GLU* 1.3 59.9 + - - +
195A VAL* 4.1 2.2 - - - +
204A VAL 4.1 0.7 - - - +
205A THR* 3.4 4.6 + - - -
206A LYS 3.1 34.8 + - - +
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Residues in contact with GLU 194 (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 LYS 3.2 12.1 - - - +
145A VAL* 4.4 0.4 - - - -
146A GLN* 3.0 52.3 + - + +
148A LYS* 2.8 38.9 + - + +
192A ALA* 5.6 0.9 - - + +
193A CYS* 1.3 72.8 - - - +
195A VAL* 1.3 61.3 + - - +
196A THR* 4.1 7.8 + - - +
203A PRO* 4.3 22.7 - - + +
204A VAL 3.6 3.8 - - - +
205A THR* 3.4 18.1 + - - +
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Residues in contact with VAL 195 (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 PRO* 4.0 19.1 - - + -
114A VAL* 3.5 33.7 - - + -
133A CYS* 4.5 6.5 - - - -
135A LEU* 3.5 41.3 - - + -
143A ALA* 5.3 0.9 - - + -
144A LYS 3.4 5.2 - - - +
145A VAL* 4.6 4.3 - - + +
193A CYS* 4.6 1.3 - - - -
194A GLU* 1.3 75.3 - - - +
196A THR* 1.3 65.8 + - - +
197A HIS* 4.6 2.0 - - + -
200A LEU* 4.0 9.6 - - + +
203A PRO* 3.3 8.0 - - - +
204A VAL 2.8 33.6 + - - +
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Residues in contact with THR 196 (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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143A ALA* 3.8 4.5 - - - +
144A LYS* 2.8 48.1 + - + +
146A GLN* 5.8 0.5 + - - -
194A GLU* 4.1 11.1 + - - -
195A VAL* 1.3 78.2 + - - +
197A HIS* 1.3 64.1 + - - +
203A PRO* 4.0 26.9 - - + +
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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