Contacts of the strand formed by residues 179 - 192 (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 ARG 179 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C VAL* 5.0 1.0 - - - +
91C ASP* 3.2 19.9 + - - -
93C SER* 3.3 25.5 + - - -
133D ARG* 3.6 28.5 + - - +
134D SER* 3.8 19.4 + - - +
135D VAL* 3.5 9.6 - - - +
136D ASP* 3.0 47.3 + - - +
175D ALA* 3.4 4.6 - - - -
176D LEU 2.9 28.6 + - - +
177D GLU 2.9 9.6 + - - +
178D ASP* 1.3 80.0 - - + +
180D LEU* 1.3 63.4 + - - +
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Residues in contact with LEU 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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133D ARG* 4.0 4.0 - - - +
134D SER* 3.0 44.9 + - - +
139D ASN* 3.1 39.3 - - - +
140D ILE 3.6 9.4 - - - +
141D VAL* 5.0 1.1 - - + -
173D ASN* 4.2 20.9 - - + +
174D PHE* 3.4 16.4 - - - +
175D ALA* 4.4 0.9 - - - +
179D ARG* 1.3 77.7 - - - +
181D GLU* 1.3 76.9 + - - +
182D SER* 4.1 1.1 - - - +
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Residues in contact with GLU 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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42C PHE* 3.6 11.0 - - - -
77D ARG* 3.6 18.4 + - - -
131D ILE* 3.5 31.5 - - + +
132D VAL 3.5 19.1 - - - +
133D ARG* 2.8 42.8 + - - +
173D ASN* 3.4 2.9 - - - +
174D PHE* 2.8 50.8 + - + +
176D LEU* 3.6 19.4 - - + +
180D LEU* 1.3 76.9 - - - +
182D SER* 1.3 59.3 + - - +
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Residues in contact with SER 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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131D ILE* 4.2 1.6 - - - -
132D VAL* 3.1 33.9 + - - -
140D ILE 3.6 21.3 - - - -
141D VAL* 3.8 6.0 - - - -
142D LEU* 3.1 30.5 + - - +
171D PRO* 3.7 6.6 - - - +
173D ASN* 2.9 26.7 + - - -
180D LEU* 4.1 1.2 - - - +
181D GLU* 1.3 72.6 - - - +
183D LYS* 1.3 58.1 + - - +
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Residues in contact with LYS 183 (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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152C ASN* 4.7 5.6 - - - +
154C ASP* 3.3 28.8 + - - -
79D VAL* 4.5 10.3 - - + -
129D TYR* 3.5 33.5 - - + -
130D LEU 3.2 8.1 - - - +
131D ILE* 3.8 17.0 - - + -
171D PRO* 3.4 21.3 - - - +
172D ALA* 3.4 20.6 + - + +
173D ASN* 3.6 0.4 + - - -
174D PHE* 4.0 22.4 - - + -
181D GLU 4.2 0.2 + - - -
182D SER* 1.3 73.7 + - - +
184D LEU* 1.3 70.5 + - - +
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Residues in contact with LEU 184 (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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20D THR* 3.0 31.2 - - + +
129D TYR* 3.6 6.8 - - - +
130D LEU* 2.7 37.0 + - + +
142D LEU* 3.7 27.6 - - + +
143D ALA 4.0 9.6 - - - +
144D VAL* 3.7 17.5 - - + -
168D VAL 3.2 26.9 - - - +
169D VAL 3.9 8.5 - - - +
171D PRO* 4.1 13.2 - - + -
183D LYS* 1.3 83.5 - - - +
185D ASP* 1.3 61.6 + - - +
186D TYR* 4.1 11.4 - - + -
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Residues in contact with ASP 185 (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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127D HIS* 3.2 14.0 + - - -
128D ILE 4.3 0.2 - - - -
129D TYR* 3.4 27.5 + - + -
167D ALA* 3.5 1.5 - - - +
168D VAL* 3.0 40.3 + - + +
184D LEU* 1.3 81.4 - - - +
186D TYR* 1.3 66.8 + - - +
187D GLN* 3.1 36.5 + - - +
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Residues in contact with TYR 186 (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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20D THR* 2.8 40.4 + - - -
22D ILE* 3.7 35.9 - - + -
127D HIS* 3.4 3.3 - - - -
128D ILE* 2.9 46.8 + - + +
130D LEU* 3.6 19.7 - - + -
144D VAL* 4.5 3.0 - - + +
149D VAL* 3.9 13.3 - - + +
165D PHE* 3.8 33.8 - + + -
166D THR 3.7 3.8 - - - -
167D ALA* 3.8 24.0 - - + -
184D LEU* 4.1 18.3 - - + +
185D ASP* 1.3 83.7 - - - +
187D GLN* 1.3 59.0 + - - +
188D LEU 4.2 0.5 + - - -
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Residues in contact with GLN 187 (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 THR* 4.3 3.5 - - + +
126D LEU 3.5 4.9 - - - +
127D HIS* 3.7 18.5 - - + +
164D SER 3.5 2.6 - - - +
165D PHE* 3.5 6.8 - - - -
166D THR* 2.9 38.4 + - - +
167D ALA* 5.5 0.4 - - - -
168D VAL* 3.3 24.4 - - + +
185D ASP* 3.1 38.5 + - - +
186D TYR* 1.3 71.3 - - - +
188D LEU* 1.3 60.0 + - - +
189D ARG* 3.1 39.5 + - - +
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Residues in contact with LEU 188 (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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24D LEU* 4.2 19.5 - - + -
27D CYS* 3.8 27.8 - - + -
37D PHE* 4.4 12.1 - - + -
125D THR* 4.5 0.4 - - - -
126D LEU* 2.6 70.1 + - + +
128D ILE* 5.8 3.6 - - + -
151D LYS* 5.1 0.2 - - + -
157D LEU* 5.6 1.6 - - + -
162D ILE* 3.4 32.1 - - + -
164D SER 3.5 9.9 - - - +
165D PHE* 3.8 16.2 - - + -
186D TYR 4.2 0.4 + - - -
187D GLN* 1.3 70.5 - - - +
189D ARG* 1.3 57.8 + - - +
190D ILE* 4.5 7.4 - - + -
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Residues in contact with ARG 189 (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* 6.5 0.2 - - - -
124D GLN 3.2 7.2 - - - +
125D THR* 3.4 33.5 + - - +
162D ILE* 3.8 2.1 - - - +
163D GLU* 2.9 37.0 + - + +
164D SER* 3.1 28.8 + - - +
166D THR* 3.0 27.3 + - - -
187D GLN* 3.1 38.1 + - - +
188D LEU* 1.3 73.0 - - - +
190D ILE* 1.3 64.0 + - - +
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Residues in contact with ILE 190 (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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30D LEU* 3.3 33.4 - - + -
123D SER* 3.2 5.2 - - - -
124D GLN* 2.6 55.7 + - + +
126D LEU* 3.8 17.9 - - + -
157D LEU* 3.9 12.3 - - + -
160D TRP* 3.6 21.3 - - + -
161D ASP 3.2 14.1 - - - +
162D ILE* 3.9 20.4 - - + -
163D GLU* 3.8 4.5 - - - -
188D LEU* 4.5 10.3 - - + -
189D ARG* 1.3 82.9 - - - +
191D SER* 1.3 60.1 + - - +
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Residues in contact with SER 191 (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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122D ASP 3.8 0.7 - - - -
123D SER* 3.0 21.1 - - - +
160D TRP* 3.4 4.5 - - - -
161D ASP* 2.8 51.0 + - - +
163D GLU* 3.4 16.1 + - - -
190D ILE* 1.3 72.9 - - - +
192D ARG* 1.3 65.4 + - - +
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Residues in contact with ARG 192 (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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32D ASP* 2.5 45.3 + - - -
116D PHE* 4.1 2.8 - - - -
119D TYR* 3.2 23.9 - - - -
120D PRO* 3.7 20.5 - - - +
121D PHE* 5.5 1.2 - - - -
122D ASP* 2.4 72.7 + - - +
159D GLY 3.6 9.6 + - - +
160D TRP* 3.1 34.6 - - + +
161D ASP* 4.8 1.5 - - - +
191D SER* 1.3 74.3 - - - +
193D GLN* 1.3 67.3 - - - +
194D TYR* 3.1 19.4 + - - +
197D TYR* 3.9 23.6 + - + -
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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