Contacts of the strand formed by residues 160 - 176 (chain D) in PDB entry 5J0Z
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 TRP 160 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D LEU* 3.7 36.4 + - + +
32D ASP* 3.9 2.3 + - - -
114D LEU* 5.4 0.7 - - + -
116D PHE* 5.9 0.2 - + - -
122D ASP* 3.7 9.4 - - - -
124D GLN* 3.8 26.7 - - + -
157D LEU* 2.8 48.0 + - + +
158D THR 3.6 12.9 + - - -
159D GLY* 1.3 85.6 + - - +
161D ASP* 1.3 65.4 + - - +
162D ILE* 4.2 3.3 + - - +
190D ILE* 3.6 18.2 - - + -
191D SER 3.4 9.6 - - - +
192D ARG* 3.1 74.1 - - + +
193D GLN* 3.4 15.1 + - - -
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Residues in contact with ASP 161 (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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160D TRP* 1.3 73.5 - - - +
162D ILE* 1.3 61.3 + - - +
163D GLU* 3.8 6.7 - - - +
190D ILE* 3.2 7.8 - - - +
191D SER* 2.8 50.7 + - - +
192D ARG 4.8 1.0 - - - +
193D GLN* 3.5 30.2 + - - +
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Residues in contact with ILE 162 (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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27D CYS* 5.2 2.5 - - - -
151D LYS* 4.5 20.2 + - + +
155D VAL* 3.5 43.3 - - + +
156D PHE* 4.3 0.2 - - - -
157D LEU* 3.9 25.8 - - + +
160D TRP 4.5 1.6 - - - +
161D ASP* 1.3 79.4 - - - +
163D GLU* 1.3 70.0 + - - +
188D LEU* 3.4 32.5 - - + -
189D ARG 3.8 3.6 - - - +
190D ILE* 3.9 10.8 - - + -
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Residues in contact with GLU 163 (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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123D SER* 5.8 0.2 - - - -
151D LYS* 3.4 13.9 + - - -
161D ASP* 3.8 5.4 - - - +
162D ILE* 1.3 77.4 - - - +
164D SER* 1.3 63.4 + - - +
189D ARG* 2.9 26.7 + - + +
190D ILE 3.8 3.5 + - - -
191D SER* 3.4 37.9 + - - -
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Residues in contact with SER 164 (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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151D LYS* 4.0 6.5 - - - +
163D GLU* 1.3 82.1 - - - +
165D PHE* 1.3 60.1 + - - +
166D THR* 4.3 14.8 - - - -
188D LEU* 3.5 8.9 - - - +
189D ARG* 3.1 57.6 + - - +
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Residues in contact with PHE 165 (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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22D ILE* 3.3 31.2 - - + -
24D LEU* 3.6 33.0 - - + -
128D ILE* 4.3 11.0 - - + -
149D VAL* 4.2 13.1 - - + +
150D GLY* 3.3 24.2 - - - +
151D LYS* 3.5 26.7 - - + +
164D SER* 1.3 73.6 - - - +
166D THR* 1.3 64.8 + - - +
186D TYR* 3.8 39.9 - + + -
187D GLN 3.5 20.4 - - - -
188D LEU* 3.8 15.9 - - + -
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Residues in contact with THR 166 (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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149D VAL* 4.8 6.3 - - - -
164D SER* 4.1 14.3 + - - -
165D PHE* 1.3 81.0 - - - +
167D ALA* 1.3 65.0 + - - +
186D TYR* 3.7 4.9 - - - +
187D GLN* 2.9 27.4 + - - +
189D ARG* 3.0 28.4 + - - -
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Residues in contact with ALA 167 (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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144D VAL* 4.0 24.7 - - + -
146D LEU* 5.1 5.9 - - + +
149D VAL* 4.9 3.8 - - + +
166D THR* 1.3 81.4 - - - +
168D VAL* 1.3 61.1 + - - +
169D VAL* 2.9 19.2 + - - +
184D LEU* 5.6 0.2 - - + -
185D ASP 3.5 8.1 - - - +
186D TYR* 3.8 29.8 - - + -
187D GLN* 4.6 1.3 - - - +
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Residues in contact with VAL 168 (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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167D ALA* 1.3 66.5 - - - +
169D VAL* 1.3 67.1 + - + +
170D LYS* 3.2 23.0 + - + +
184D LEU* 3.2 20.5 - - - +
185D ASP* 3.0 27.1 + - + +
187D GLN* 3.3 33.3 - - - +
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Residues in contact with VAL 169 (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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143D ALA* 4.7 3.6 - - - +
144D VAL* 3.8 22.5 + - + +
146D LEU* 4.0 32.8 - - + -
167D ALA 2.9 15.6 + - - +
168D VAL* 1.3 72.5 - - + +
170D LYS* 1.3 73.4 + - + +
171D PRO* 3.3 12.3 - - - +
184D LEU* 3.9 6.4 - - - +
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Residues in contact with LYS 170 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168D VAL* 3.2 21.8 - - + +
169D VAL* 1.3 91.3 - - + +
171D PRO* 1.3 67.2 - - + +
172D ALA* 3.3 3.8 + - - +
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Residues in contact with PRO 171 (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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141D VAL* 4.3 7.6 - - + -
142D LEU 3.1 27.6 - - - +
143D ALA* 5.2 1.6 - - + -
169D VAL 3.3 10.5 - - - +
170D LYS* 1.3 82.7 - - + +
172D ALA* 1.3 60.7 + - - +
173D ASN* 3.0 26.5 + - - +
182D SER* 3.7 9.2 - - - +
183D LYS 3.4 21.1 - - - +
184D LEU* 4.1 13.5 - - + -
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Residues in contact with ALA 172 (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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170D LYS 3.3 6.6 + - - +
171D PRO* 1.3 69.8 - - - +
173D ASN* 1.3 64.2 + - - +
174D PHE* 3.9 7.2 - - + -
183D LYS* 3.4 27.5 + - - +
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Residues in contact with ASN 173 (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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141D VAL* 3.3 30.7 - - - +
171D PRO* 3.0 19.5 + - - +
172D ALA* 1.3 77.0 - - - +
174D PHE* 1.3 66.8 + - - +
180D LEU* 4.2 16.2 - - + +
181D GLU 3.4 11.7 - - - +
182D SER* 2.9 29.9 + - - -
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Residues in contact with PHE 174 (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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23C TYR* 6.0 1.1 - - - -
152C ASN* 6.1 4.5 - - - -
131D ILE* 4.4 13.2 - - + -
172D ALA* 3.9 9.2 - - + -
173D ASN* 1.3 82.0 - - - +
175D ALA* 1.3 70.6 + - - +
176D LEU* 3.9 27.8 - - + -
180D LEU* 3.4 11.4 - - - +
181D GLU* 2.8 45.1 + - + +
183D LYS* 4.0 33.4 - - + -
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Residues in contact with ALA 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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174D PHE* 1.3 80.7 - - - +
176D LEU* 1.3 60.4 + - - +
177D GLU 4.3 0.4 + - - -
178D ASP* 5.3 7.6 - - - +
179D ARG 3.4 11.7 - - - +
180D LEU* 4.4 1.3 - - - +
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Residues in contact with LEU 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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23C TYR* 3.4 50.0 - - + +
25C ILE* 5.9 1.1 - - + -
42C PHE* 3.6 22.0 - - + -
152C ASN* 5.1 2.2 - - - +
131D ILE* 5.5 2.0 - - + -
133D ARG* 3.1 12.8 + - - +
174D PHE* 3.8 22.8 + - + -
175D ALA* 1.3 75.1 - - - +
177D GLU* 1.3 80.9 + - + +
178D ASP 3.4 0.4 - - - -
179D ARG 2.9 16.5 + - - +
181D GLU* 3.6 32.5 - - + +
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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