Contacts of the strand formed by residues 168 - 173 (chain A) in PDB entry 1ZSV
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 LYS 168 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLY 5.0 2.1 + - - +
143A GLU 3.0 6.5 + - - +
144A THR* 3.4 26.4 - - + +
145A VAL 2.9 26.2 + - - -
163A LYS* 4.4 0.4 - - - +
167A CYS* 1.3 73.5 - - - +
169A VAL* 1.3 63.2 + - - +
170A VAL* 4.1 13.0 - - + -
188A ASP* 3.4 24.2 - - + +
189A VAL* 4.3 10.9 - - - +
206A ALA 2.6 31.3 + - - -
207A SER* 4.0 9.1 + - - +
208A PRO* 5.0 4.0 - - - +
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Residues in contact with VAL 169 (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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145A VAL* 3.5 9.2 - - + +
147A VAL* 3.9 14.8 - - + -
159A GLY* 3.7 23.3 - - - +
162A ALA* 3.5 32.1 - - + -
163A LYS* 3.8 17.5 - - + -
167A CYS 4.0 1.3 - - - +
168A LYS* 1.3 76.3 - - - +
170A VAL* 1.3 66.0 + - - +
187A PHE* 3.7 29.4 - - + +
188A ASP* 3.1 13.4 + - - +
189A VAL 3.3 23.0 + - - +
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Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A THR* 4.3 5.8 - - + -
145A VAL 2.9 8.4 + - - +
146A MET* 3.4 14.7 - - - +
147A VAL* 2.8 33.1 + - - +
168A LYS* 4.1 24.0 - - - -
169A VAL* 1.3 79.7 - - - +
171A GLY* 1.3 54.9 + - - +
189A VAL* 3.3 15.5 - - + +
191A PHE* 4.2 13.9 - - + -
206A ALA* 3.9 25.6 - - + +
211A TYR* 3.7 31.2 - - + +
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Residues in contact with GLY 171 (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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146A MET* 4.7 0.2 - - - -
147A VAL* 3.2 7.4 - - - -
150A ALA* 3.9 12.3 - - - -
169A VAL 4.1 0.6 - - - -
170A VAL* 1.3 75.3 - - - +
172A ALA* 1.3 60.8 + - - +
187A PHE* 4.2 12.3 - - - -
189A VAL 2.8 10.8 + - - +
190A VAL* 3.3 9.3 - - - -
191A PHE* 3.1 30.0 + - - -
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A MET* 3.7 10.5 - - + -
147A VAL 3.2 7.0 + - - +
148A ASN* 4.4 1.8 - - - -
149A ALA 3.3 9.4 + - - -
150A ALA* 3.1 24.2 + - - +
171A GLY* 1.3 74.3 - - - +
173A VAL* 1.3 62.4 + - - +
191A PHE* 3.4 22.4 - - + -
193A TYR* 4.8 0.9 - - + -
222A PHE* 3.6 33.4 - - + -
407A CL 3.9 4.4 - - + +
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Residues in contact with VAL 173 (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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151A ALA* 3.8 22.0 - - + +
172A ALA* 1.3 77.9 - - - +
174A GLY* 1.3 59.2 + - - +
175A SER 2.8 28.9 - - - +
178A LYS* 3.4 13.2 - - + +
179A VAL* 3.6 14.6 - - + +
182A LEU* 3.6 33.0 - - + -
190A VAL* 4.2 4.5 - - + -
191A PHE 3.1 9.3 + - - +
192A ASN* 3.2 3.7 - - - +
193A TYR* 2.8 33.1 + - - -
407A CL 4.6 0.2 - - - -
422A CL 4.0 5.4 - - + -
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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