Contacts of the strand formed by residues 174 - 183 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84D ILE* 5.0 0.7 - - - +
170D CYS* 2.6 23.3 + - - -
171D ASN* 3.0 10.7 + - - +
172D ILE 3.3 1.0 + - - -
173D PHE* 1.3 78.9 + - - +
175D THR* 1.3 64.5 + - - +
176D LYS* 3.2 20.6 + - - -
177D PHE* 4.4 2.2 - - - -
194D TRP 5.4 0.2 - - - +
195D MET* 4.6 0.5 - - - -
196D ASP 3.9 0.9 + - - -
197D ASN 3.2 19.5 + - - -
198D MET 4.4 0.9 + - - -
219D PHE* 3.6 26.6 - - - +
220D GLN 3.5 8.5 - - - -
221D PRO* 4.0 2.6 - - - +
222D ASP* 3.8 3.1 - - - +
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Residues in contact with THR 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D ASN* 5.2 0.9 + - - -
174D SER* 1.3 72.8 - - - +
176D LYS* 1.3 60.6 + - - +
195D MET* 3.0 7.4 - - - +
196D ASP* 2.4 43.8 + - - +
197D ASN 4.5 0.2 - - - +
220D GLN* 3.0 26.1 + - - +
221D PRO 4.4 2.2 + - - +
222D ASP* 3.8 31.6 - - + +
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Residues in contact with LYS 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D SER* 3.6 4.3 - - - -
175D THR* 1.3 84.3 + - - +
177D PHE* 1.3 61.4 + - - +
178D THR* 4.3 2.2 - - - +
193D THR* 4.9 6.7 - - + -
194D TRP 3.2 7.4 - - - +
195D MET* 4.1 7.2 - - + +
218D THR 4.8 0.4 - - - -
219D PHE* 3.4 4.0 - - - +
220D GLN* 2.9 51.2 + - + +
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Residues in contact with PHE 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D ILE* 4.2 6.3 - - + -
142D PHE* 3.7 17.3 - + + -
167D ALA 3.8 12.6 - - - -
170D CYS* 3.5 26.2 - - + -
171D ASN* 3.4 57.2 - - + +
174D SER* 4.4 3.1 - - - +
176D LYS* 1.3 75.1 - - - +
178D THR* 1.3 61.4 + - - +
179D VAL* 3.6 26.7 - - + -
193D THR* 3.4 0.7 - - - +
194D TRP* 2.6 41.7 + + - +
217D ILE* 3.8 24.5 - - + -
218D THR 3.9 2.0 - - - -
219D PHE* 3.5 16.4 - - + -
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Residues in contact with THR 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D LYS* 5.2 1.7 - - - +
177D PHE* 1.3 74.9 + - - +
179D VAL* 1.3 70.2 + - - +
180D GLU* 5.1 3.8 - - + +
191D LYS* 4.0 23.3 - - - -
192D GLN 3.3 8.3 - - - +
193D THR* 2.7 33.3 + - - +
216D CYS 3.9 0.7 - - - +
217D ILE* 3.4 9.5 - - - +
218D THR* 2.8 45.8 + - - +
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Residues in contact with VAL 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D ILE* 5.1 0.4 - - + -
138D PRO* 4.7 4.9 - - + +
142D PHE* 3.4 59.7 - - + -
177D PHE* 3.6 18.6 - - + -
178D THR* 1.3 73.5 - - - +
180D GLU* 1.3 68.1 + - - +
181D THR* 4.7 5.2 - - + -
190D PHE* 4.0 16.6 - - + -
191D LYS* 3.2 4.2 - - - +
192D GLN 2.8 33.4 + - - +
194D TRP* 3.8 15.3 - - + -
216D CYS 4.1 1.3 - - - -
217D ILE* 4.3 8.1 - - + -
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Residues in contact with GLU 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D THR* 5.1 4.0 - - + +
179D VAL* 1.3 77.1 - - - +
181D THR* 1.3 58.8 + - - +
189D MET* 2.9 24.2 - - + +
190D PHE 3.5 5.4 - - - +
191D LYS* 3.5 32.4 + - + +
214D TYR* 2.8 35.5 + - + +
215D THR* 3.4 1.8 - - - +
216D CYS* 2.6 54.1 + - + +
218D THR* 5.8 0.2 + - - -
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Residues in contact with THR 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D GLY 3.7 0.2 - - - -
125D ILE* 2.8 46.1 + - + +
127D VAL* 4.1 0.8 - - + +
138D PRO* 3.8 20.9 - - + -
179D VAL* 4.7 3.4 - - + -
180D GLU* 1.3 74.6 - - - +
182D ALA* 1.3 62.0 + - - +
189D MET* 3.5 4.0 - - - +
190D PHE* 2.8 54.3 + - + +
214D TYR* 3.3 7.2 - - - -
215D THR* 3.2 15.4 + - - -
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Residues in contact with ALA 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D GLY* 3.3 16.1 - - - -
127D VAL* 4.8 0.7 - - - -
181D THR* 1.3 76.0 + - - +
183D SER* 1.3 54.6 + - - +
188D LYS 3.8 4.5 - - - -
189D MET* 4.2 3.4 - - + -
209D PHE* 3.7 27.4 - - + -
213D ASP* 2.7 23.1 - - - +
214D TYR* 2.8 43.7 + - + +
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Residues in contact with SER 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D GLY* 4.7 6.0 + - - -
125D ILE 3.8 19.5 - - - -
126D PRO* 4.6 1.7 - - - +
127D VAL* 4.2 4.0 - - - -
182D ALA* 1.3 74.9 - - - +
184D ARG* 1.3 58.7 + - - +
185D GLU* 3.6 7.1 + - - +
186D TYR* 3.1 33.7 + - - -
187D LYS* 2.8 24.6 + - - -
188D LYS 3.0 20.6 + - - -
209D PHE* 4.3 4.0 - - - -
213D ASP* 3.0 4.0 + - - -
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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