Contacts of the strand formed by residues 160 - 171 (chain B) in PDB entry 1RX0
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 HIS 160 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156B LYS* 3.6 2.8 - - - +
157B GLN* 2.8 38.4 + - - +
158B GLY 3.4 0.2 - - - -
159B ASP* 1.3 95.1 + - + +
161B TYR* 1.3 61.9 + - - +
162B ILE* 4.8 4.3 - - + -
230B ALA* 4.3 17.0 - - + -
231B VAL 3.2 14.1 - - - +
232B PRO* 3.7 32.3 - - + +
233B VAL* 3.6 9.1 - - - +
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Residues in contact with TYR 161 (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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154B ALA* 3.7 22.2 - - + -
155B LYS 3.4 1.8 - - - -
156B LYS* 3.9 23.7 - - + -
160B HIS* 1.3 73.7 - - - +
162B ILE* 1.3 60.5 + - - +
163B LEU* 3.7 17.6 + - + +
185B THR* 3.8 15.3 - - + -
196B ILE* 3.7 21.3 - - + -
229B CYS 3.3 2.6 - - - +
230B ALA* 3.4 1.4 - - - -
231B VAL* 2.7 35.5 + - + +
232B PRO 4.5 2.2 - - - -
233B VAL* 3.7 36.3 - - + +
236B ARG* 2.8 33.9 + - + -
240B GLU* 2.5 32.5 + - - +
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Residues in contact with ILE 162 (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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153B SER* 3.4 4.3 + - - +
155B LYS* 2.8 51.3 + - - +
157B GLN* 3.5 39.3 - - + +
160B HIS* 4.8 5.2 - - + -
161B TYR* 1.3 74.8 - - - +
163B LEU* 1.3 62.8 + - - +
164B ASN* 4.0 8.8 + - - +
228B ASP* 3.8 38.1 - - + +
229B CYS 3.6 1.1 - - - -
230B ALA* 3.7 28.7 - - + +
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Residues in contact with LEU 163 (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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152B THR* 4.9 3.1 - - + -
153B SER 3.1 10.1 - - - +
154B ALA* 3.9 12.1 - - + -
161B TYR* 3.7 29.2 - - + +
162B ILE* 1.3 75.9 - - - +
164B ASN* 1.3 62.3 + - - +
181B VAL* 4.6 10.8 - - + -
183B CYS* 4.8 9.0 - - + -
196B ILE* 4.6 5.8 - - + -
198B VAL* 3.9 27.4 - - + -
226B PHE* 3.6 37.0 - - + +
228B ASP 3.3 7.4 + - - -
229B CYS 2.8 38.6 + - - +
231B VAL* 4.0 9.4 - - + -
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Residues in contact with ASN 164 (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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151B LEU 4.4 0.9 - - - +
152B THR* 3.3 5.6 - - - -
153B SER* 2.9 42.9 + - - +
155B LYS* 6.3 0.2 - - - +
162B ILE* 4.0 12.7 + - - +
163B LEU* 1.3 80.9 + - - +
165B GLY* 1.3 58.8 + - - +
226B PHE* 3.4 4.3 - - - +
227B GLU* 3.6 6.2 - - - -
228B ASP* 2.9 42.2 + - - +
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Residues in contact with GLY 165 (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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151B LEU 5.6 0.2 - - - -
152B THR* 3.8 12.8 - - - -
164B ASN* 1.3 76.1 - - - +
166B SER* 1.3 62.7 + - - -
225B ILE* 3.8 3.3 - - - +
226B PHE* 2.9 35.8 + - - +
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Residues in contact with SER 166 (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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140B GLU* 3.3 29.2 + - - +
141B PRO* 3.8 19.9 - - - +
152B THR* 3.5 3.2 + - - -
165B GLY* 1.3 76.1 - - - -
167B LYS* 1.3 67.3 + - - +
223B ALA* 5.7 2.0 - - - -
224B VAL 3.3 9.6 - - - -
225B ILE* 4.3 16.6 - - - -
226B PHE* 4.9 0.4 - - - -
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Residues in contact with LYS 167 (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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137B CYS* 3.7 24.9 + - + +
138B LEU* 2.9 23.5 + - - +
139B THR 3.2 13.2 - - - +
140B GLU* 2.8 29.1 + - + +
141B PRO* 4.8 1.1 - - - -
150B LEU* 4.1 5.9 - - - +
152B THR* 3.6 7.6 - - - -
166B SER* 1.3 76.9 - - - +
168B ALA* 1.3 60.2 + - - +
170B ILE* 3.8 20.0 - - + -
181B VAL* 4.0 8.3 - - - -
182B MET 2.8 28.4 + - - -
223B ALA* 3.2 10.0 - - - +
224B VAL* 2.7 33.8 + - + +
226B PHE* 4.1 14.6 - - + -
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Residues in contact with ALA 168 (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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139B THR* 2.8 20.4 + - - +
140B GLU* 4.0 3.8 - - - +
141B PRO* 4.1 28.0 - - + -
167B LYS* 1.3 73.9 - - - +
169B PHE* 1.3 91.9 + - + +
170B ILE* 3.2 14.1 + - - +
223B ALA* 4.5 7.0 - - + +
399B FAD 4.0 0.7 + - - -
2003B EDO 4.2 11.7 - - - +
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Residues in contact with PHE 169 (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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139B THR* 4.0 7.6 - - + -
168B ALA* 1.3 82.9 - - + +
170B ILE* 1.3 60.4 + - - +
171B SER 3.1 0.2 + - - -
211B GLU* 5.4 2.0 + - - -
221B THR* 3.6 20.3 - - + +
222B ARG 4.3 5.5 + - - -
223B ALA* 4.8 0.2 - - - +
399B FAD 2.8 77.0 + + + +
2003B EDO 3.4 24.7 + - - -
353D GLY* 3.5 24.5 - - - -
354D TYR* 3.6 52.3 - + - -
357D LEU* 3.6 18.8 - - + -
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Residues in contact with ILE 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B SER* 3.7 27.4 - - - -
136B TYR 3.5 20.6 - - - +
137B CYS* 3.7 24.5 - - - -
138B LEU 4.3 0.4 - - - +
139B THR 4.5 0.4 - - - +
167B LYS* 3.8 17.9 - - + -
168B ALA 3.3 16.4 - - - +
169B PHE* 1.3 75.0 - - - +
171B SER* 1.3 64.1 + - - +
173B ALA* 3.2 22.8 + - + +
220B PRO 3.4 1.9 - - - +
221B THR* 4.4 1.1 - - - -
222B ARG 3.2 26.0 + - - +
224B VAL* 3.6 21.1 - - + -
399B FAD 3.6 11.9 - - + +
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Residues in contact with SER 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B TYR* 4.0 9.8 - - - -
103B ILE* 3.8 16.7 - - - +
135B SER* 2.7 31.4 + - - -
136B TYR 4.9 0.2 + - - -
169B PHE 3.1 1.6 + - - -
170B ILE* 1.3 70.5 - - - +
172B GLY* 1.3 53.3 + - - +
173B ALA 3.2 0.2 - - - -
216B TRP* 3.9 0.2 - - - -
219B GLN* 2.9 28.5 + - - -
220B PRO 3.5 6.1 - - - -
221B THR* 4.8 2.8 + - - +
399B FAD 3.0 43.0 + - - +
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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