Contacts of the strand formed by residues 174 - 183 (chain A) in PDB entry 1ZXN
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 SER 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A ILE* 4.8 0.3 - - - +
170A CYS* 2.7 21.6 + - - -
171A ASN 3.4 7.7 + - - +
173A PHE* 1.3 79.4 + - - +
175A THR* 1.3 61.6 + - - +
176A LYS 3.6 17.5 - - - -
177A PHE* 4.4 3.8 - - - -
195A MET 5.0 0.2 - - - -
197A ASN* 3.2 26.0 + - - -
198A MET 4.7 0.2 + - - -
219A PHE* 3.4 28.4 - - - +
220A GLN 3.1 13.6 - - - -
221A PRO* 4.1 0.2 - - - +
222A ASP* 3.5 5.6 - - - +
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Residues in contact with THR 175 (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 ASN* 5.2 0.9 + - - -
174A SER* 1.3 73.9 - - - +
176A LYS* 1.3 62.3 + - - +
195A MET* 3.1 9.2 - - - +
196A ASP* 2.9 31.5 + - - +
197A ASN* 4.7 1.1 - - - +
220A GLN* 2.6 31.0 + - - +
221A PRO 4.5 2.3 + - - +
222A ASP* 3.8 34.7 - - - +
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Residues in contact with LYS 176 (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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174A SER* 3.6 3.3 - - - -
175A THR* 1.3 83.6 + - - +
177A PHE* 1.3 62.1 + - - +
178A THR* 4.3 11.7 - - - +
193A THR* 3.8 26.7 - - + -
194A TRP 3.2 5.4 - - - +
195A MET* 4.7 5.4 - - + -
218A THR 4.6 0.4 - - - +
219A PHE* 3.3 4.7 - - - +
220A GLN* 2.9 61.4 + - + +
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Residues in contact with PHE 177 (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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88A ILE* 4.0 16.2 - - + -
142A PHE* 3.8 16.8 - + - -
167A ALA 3.6 13.9 - - - -
170A CYS* 3.6 24.2 - - - -
171A ASN* 3.3 55.0 - - + +
174A SER* 4.0 5.6 - - - -
176A LYS* 1.3 76.3 - - - +
178A THR* 1.3 64.3 + - - +
179A VAL* 3.8 26.0 - - + -
193A THR* 3.2 2.3 - - - -
194A TRP* 2.7 44.4 + + + -
217A ILE* 4.9 7.0 - - + -
218A THR 3.7 1.1 - - - -
219A PHE* 3.5 21.5 - + + -
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Residues in contact with THR 178 (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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176A LYS* 4.3 11.8 - - - +
177A PHE* 1.3 77.8 - - - +
179A VAL* 1.3 72.6 - - - +
180A GLU* 4.9 2.7 - - + +
191A LYS* 4.0 25.4 - - + -
192A GLN 3.3 7.4 - - - +
193A THR* 2.6 28.0 + - - +
216A CYS 3.6 1.6 - - - +
217A ILE* 3.4 6.8 - - - +
218A THR* 2.7 51.0 + - - +
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Residues in contact with VAL 179 (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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138A PRO* 5.0 3.6 - - + -
142A PHE* 3.7 42.0 - - + -
177A PHE* 3.8 21.3 - - + -
178A THR* 1.3 79.6 - - - +
180A GLU* 1.3 67.2 + - - +
181A THR* 4.2 5.4 - - + +
190A PHE* 3.7 16.4 - - + +
191A LYS* 3.1 5.2 - - - +
192A GLN 2.9 28.8 + - - -
194A TRP* 3.4 29.2 - - + -
215A THR* 5.3 4.7 - - + -
216A CYS 3.9 2.5 - - - +
217A ILE* 4.9 2.7 - - + +
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Residues in contact with GLU 180 (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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178A THR* 5.3 2.9 - - + +
179A VAL* 1.3 76.7 - - - +
181A THR* 1.3 61.0 + - - +
189A MET* 3.9 18.9 - - + +
190A PHE 3.2 9.6 - - - +
191A LYS* 3.5 28.7 + - + +
214A TYR* 2.7 35.1 + - + +
215A THR* 3.1 2.9 - - - +
216A CYS* 2.6 52.5 + - + +
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Residues in contact with THR 181 (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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125A ILE* 2.7 45.4 + - + +
127A VAL* 4.0 1.7 - - + +
138A PRO* 3.7 21.8 - - + -
179A VAL* 5.1 3.4 - - + -
180A GLU* 1.3 75.6 - - - +
182A ALA* 1.3 61.6 + - - +
189A MET* 3.7 2.6 - - - +
190A PHE* 2.8 52.4 + - + +
214A TYR* 3.3 6.0 + - - -
215A THR* 2.9 17.6 + - - -
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Residues in contact with ALA 182 (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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124A GLY* 3.4 7.5 - - - -
127A VAL* 5.0 0.2 - - - -
181A THR* 1.3 76.4 + - - +
183A SER* 1.3 60.3 + - - +
188A LYS 3.7 5.2 - - - +
189A MET* 4.5 5.4 - - + -
209A PHE* 3.6 33.0 - - + -
213A ASP* 3.1 25.1 - - - +
214A TYR* 2.8 36.4 + - + -
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Residues in contact with SER 183 (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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123A LYS* 6.1 0.2 - - - +
124A GLY 4.5 9.4 + - - -
125A ILE 3.9 22.4 - - - -
126A PRO* 4.6 3.0 - - - +
127A VAL* 4.4 10.4 - - - +
182A ALA* 1.3 73.0 - - - +
184A ARG* 1.3 67.2 + - - +
185A GLU* 3.6 19.6 + - - +
186A TYR* 4.0 9.0 + - - -
187A LYS 3.0 14.6 + - - -
188A LYS 3.3 16.8 + - - -
209A PHE* 3.9 4.0 - - - -
213A ASP* 4.5 3.6 - - - -
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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