Contacts of the strand formed by residues 174 - 183 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B ILE* 4.7 0.7 - - - +
170B CYS* 2.9 19.6 + - - -
171B ASN* 3.0 9.5 + - - +
172B ILE 3.4 0.6 + - - -
173B PHE* 1.3 80.4 + - - +
175B THR* 1.3 62.2 + - - +
176B LYS* 3.7 17.6 - - - -
177B PHE* 4.4 2.9 - - - +
195B MET* 4.7 0.7 - - - -
196B ASP 4.1 0.2 + - - -
197B ASN* 3.0 22.5 + - - -
198B MET 4.5 0.3 + - - -
219B PHE* 3.5 26.7 - - - +
220B GLN 3.2 16.5 + - - -
221B PRO* 3.9 0.9 - - - +
222B ASP* 3.8 3.6 - - - +
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Residues in contact with THR 175 (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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114B ASN* 4.9 1.9 + - - -
174B SER* 1.3 73.5 - - - +
176B LYS* 1.3 61.6 + - - +
195B MET* 3.1 7.4 - - - +
196B ASP* 2.7 34.7 + - - +
197B ASN* 4.6 1.3 - - - +
220B GLN* 2.9 27.5 + - - +
221B PRO 4.6 1.8 + - - +
222B ASP* 4.0 30.7 - - + +
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Residues in contact with LYS 176 (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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174B SER* 3.7 3.2 - - - -
175B THR* 1.3 83.0 + - - +
177B PHE* 1.3 62.7 + - - +
178B THR* 3.6 20.1 + - - +
193B THR* 3.6 21.0 + - + +
194B TRP 3.3 4.7 - - - +
195B MET* 4.7 5.2 - - + -
218B THR* 5.0 8.1 - - + +
219B PHE* 3.1 5.4 - - - +
220B GLN* 2.8 67.5 + - + +
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Residues in contact with PHE 177 (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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88B ILE* 4.4 3.4 - - + -
142B PHE* 3.9 22.0 - + - -
167B ALA 3.9 12.6 - - - -
170B CYS* 3.8 21.3 - - + -
171B ASN* 3.2 53.6 - - + +
174B SER* 4.4 2.9 - - - +
176B LYS* 1.3 74.7 - - - +
178B THR* 1.3 61.7 + - - +
179B VAL* 3.4 26.0 - - + -
193B THR* 3.5 0.9 - - - -
194B TRP* 2.7 39.9 + + + -
217B ILE* 3.4 28.9 - - + -
218B THR 3.5 1.6 - - - -
219B PHE* 3.5 17.7 - - + -
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Residues in contact with THR 178 (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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176B LYS* 3.6 13.5 + - - +
177B PHE* 1.3 72.7 - - - +
179B VAL* 1.3 70.3 + - - +
180B GLU* 4.9 5.2 - - + +
191B LYS* 4.5 20.4 - - + -
192B GLN 3.5 7.4 - - - +
193B THR* 3.0 30.2 + - - +
216B CYS 4.1 0.5 - - - +
217B ILE* 3.3 8.7 - - - +
218B THR* 2.5 51.2 + - - +
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Residues in contact with VAL 179 (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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138B PRO* 4.5 4.5 - - + -
142B PHE* 3.4 49.4 - - + -
177B PHE* 3.4 33.4 + - + -
178B THR* 1.3 74.3 - - - +
180B GLU* 1.3 67.6 + - - +
181B THR* 4.9 2.7 - - + +
190B PHE* 3.6 17.1 - - + -
191B LYS* 3.3 4.5 - - - +
192B GLN 2.8 32.7 + - - -
194B TRP* 3.7 14.4 - - + -
215B THR* 6.0 0.9 - - + -
216B CYS 4.3 1.3 - - - -
217B ILE* 4.6 5.8 - - + +
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Residues in contact with GLU 180 (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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178B THR* 4.1 5.8 + - + +
179B VAL* 1.3 79.0 - - - +
181B THR* 1.3 61.4 + - - +
189B MET* 3.9 12.1 - - + +
190B PHE 3.4 14.8 - - - +
191B LYS* 3.3 35.3 + - + +
214B TYR* 3.2 29.6 + - + +
215B THR* 3.4 2.4 - - - +
216B CYS* 2.8 48.3 + - + +
217B ILE* 5.3 0.2 - - - +
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Residues in contact with THR 181 (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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124B GLY* 3.7 0.2 - - - -
125B ILE* 3.0 38.0 + - + +
127B VAL* 3.7 2.4 - - + +
138B PRO* 3.7 33.7 - - + -
179B VAL* 5.1 2.2 - - + -
180B GLU* 1.3 75.3 - - - +
182B ALA* 1.3 58.0 + - - +
189B MET* 3.6 2.9 - - - -
190B PHE* 2.8 42.9 + - + +
214B TYR* 3.3 5.6 + - - -
215B THR* 2.6 26.7 + - - -
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Residues in contact with ALA 182 (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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124B GLY* 3.6 7.4 - - - -
181B THR* 1.3 74.8 + - - +
183B SER* 1.3 55.0 + - - +
188B LYS 3.8 4.0 - - - -
189B MET* 4.1 7.2 - - + +
209B PHE* 3.6 28.7 - - + -
213B ASP* 2.5 27.4 - - - +
214B TYR* 2.8 44.3 + - + +
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Residues in contact with SER 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLY* 4.7 4.8 + - - -
125B ILE 3.5 23.9 + - - -
126B PRO* 4.4 1.4 - - - +
127B VAL* 4.2 9.2 - - - -
182B ALA* 1.3 75.6 - - - +
184B ARG* 1.3 64.5 + - - +
185B GLU* 3.8 6.6 + - - +
186B TYR* 3.5 25.2 + - - -
187B LYS 2.9 15.9 + - - -
188B LYS 2.9 21.3 + - - -
209B PHE* 4.0 3.3 - - - -
213B ASP* 3.6 5.9 + - - -
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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