Contacts of the strand formed by residues 164 - 175 (chain B) in PDB entry 1XHU
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 PHE 164 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B THR* 4.0 11.9 - - + -
85B LEU* 4.6 7.4 - - + -
88B LEU* 3.4 26.2 - - + -
122B PHE* 3.6 7.6 - - - -
123B TYR* 2.7 20.6 - - + +
125B LEU* 3.9 13.0 - - + -
151B THR* 3.6 22.0 - - + -
155B MET* 3.7 33.0 - - + -
160B GLU* 4.6 5.2 - - + -
162B ASP* 5.0 1.6 - - - -
163B LEU* 1.3 87.4 + - + +
165B ASP* 1.3 71.7 + - - +
166B ILE* 3.5 31.4 - - + -
191B PHE* 4.0 9.8 - + - -
223B ARG* 3.8 10.8 + - - -
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Residues in contact with ASP 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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2B SER 4.6 9.7 + - - -
122B PHE* 3.0 28.1 - - + -
123B TYR 2.5 15.9 + - - +
124B GLU* 4.0 15.5 - - + -
125B LEU* 2.7 29.3 + - - +
164B PHE* 1.3 70.8 - - - +
166B ILE* 1.3 66.5 + - - +
167B ASN* 4.0 8.9 + - - +
189B GLU* 4.3 10.5 - - - +
191B PHE* 3.8 6.6 - - - +
223B ARG* 3.1 31.9 + - - -
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Residues in contact with ILE 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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88B LEU* 4.6 15.5 - - + -
112B THR* 6.0 0.7 - - + -
125B LEU* 3.6 17.5 - - + +
127B ASP* 6.3 0.2 - - + -
143B ILE* 4.8 13.7 - - + -
148B LEU* 5.3 5.6 - - + -
151B THR* 5.1 2.9 - - + -
164B PHE* 3.5 28.9 - - + -
165B ASP* 1.3 80.5 - - - +
167B ASN* 1.3 61.5 + - - +
168B TYR* 3.7 31.1 - - + +
190B LEU* 2.8 45.1 + - + +
191B PHE* 3.9 23.3 + - + -
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Residues in contact with ASN 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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2B SER* 3.4 14.1 - - - +
124B GLU* 2.3 50.0 + - + +
125B LEU 3.3 8.6 + - - +
126B LEU* 4.4 4.7 - - + -
127B ASP* 3.3 20.7 + - - +
165B ASP* 4.0 7.2 + - - +
166B ILE* 1.3 83.3 + - - +
168B TYR* 1.3 74.8 + - - +
187B PHE* 3.4 20.4 - - + -
188B ALA 3.5 6.3 - - - +
189B GLU* 3.4 25.6 - - - +
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Residues in contact with TYR 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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126B LEU* 4.4 2.9 - - - -
127B ASP* 3.1 44.0 - - + +
129B LYS* 4.3 5.4 - - + -
142B ILE* 3.4 44.2 + - + -
143B ILE* 3.4 21.7 - - - +
166B ILE* 3.7 33.5 - - + +
167B ASN* 1.3 75.7 - - - +
169B LEU* 1.3 61.0 + - - +
170B GLU 4.0 0.4 - - - -
186B SER 3.8 0.7 - - - +
187B PHE* 3.5 6.6 - - - -
188B ALA 2.7 39.3 + - - +
189B GLU 5.3 0.2 - - - -
190B LEU* 4.0 15.0 - - + -
210B PHE* 4.1 15.0 - + + -
212B VAL* 3.8 20.3 - - + +
215B LEU* 5.7 0.2 - - + -
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Residues in contact with LEU 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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4B ILE* 5.7 5.4 - - + -
8B TYR* 3.7 16.4 - - + -
11B ILE* 5.1 8.1 - - + -
15B LEU* 4.4 7.4 - - + -
41B VAL* 3.5 43.5 - - + -
126B LEU* 4.1 14.8 - - + +
127B ASP 2.8 14.7 + - - +
128B VAL* 3.3 8.9 - - + +
129B LYS* 2.7 27.4 + - - -
168B TYR* 1.3 73.4 - - - +
170B GLU* 1.3 64.1 + - - +
171B VAL* 3.8 2.8 + - + +
185B THR* 3.4 30.5 - - + -
186B SER 3.4 6.5 - - - +
187B PHE* 4.4 7.0 - - + -
212B VAL* 4.7 0.4 - - - -
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Residues in contact with GLU 170 (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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129B LYS* 3.1 14.1 - - + +
131B ARG* 3.6 29.4 + - + -
168B TYR 4.0 1.2 - - - -
169B LEU* 1.3 72.8 - - - +
171B VAL* 1.3 61.3 + - - +
172B ASP* 2.7 31.0 - - - +
185B THR* 3.2 9.7 - - - +
186B SER* 2.7 39.6 + - - +
211B HIS* 4.8 3.6 - - - -
212B VAL* 3.1 27.2 + - + +
213B ARG* 2.8 35.6 + - - +
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Residues in contact with VAL 171 (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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15B LEU* 4.9 15.7 - - + -
37B PHE* 3.9 34.8 - - + -
41B VAL* 5.4 2.2 - - + -
128B VAL* 3.5 27.8 - - + -
129B LYS 2.7 21.5 + - - +
130B THR* 3.3 13.1 - - + -
131B ARG 3.2 18.5 + - - -
169B LEU* 4.3 4.3 - - + +
170B GLU* 1.3 74.6 - - - +
172B ASP* 1.3 62.2 + - - +
173B TRP* 4.1 1.2 - - - -
182B CYS* 3.9 16.8 - - - -
184B SER 3.9 4.7 - - - +
185B THR* 4.5 4.3 - - + +
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Residues in contact with ASP 172 (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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131B ARG* 3.5 9.1 - - - +
133B ILE* 4.1 20.2 - - + -
170B GLU* 2.7 37.0 - - - +
171B VAL* 1.3 71.6 - - - +
173B TRP* 1.3 60.0 + - - +
182B CYS* 3.1 11.1 - - - -
183B VAL* 2.9 23.6 + - + -
184B SER* 2.6 39.2 + - - +
185B THR* 4.6 1.0 + - - -
186B SER* 4.9 2.3 + - - -
213B ARG* 2.9 25.3 + - - -
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Residues in contact with TRP 173 (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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28B LEU* 3.4 31.2 - - + -
33B ALA* 3.9 14.6 - - + -
34B GLY* 4.1 3.6 - - - -
37B PHE* 3.9 24.5 - + + -
130B THR* 3.6 25.0 + - - -
131B ARG 2.9 33.7 + - - +
132B ASN* 3.7 36.0 - - + -
133B ILE* 2.9 31.7 + - - +
171B VAL 4.1 2.9 - - - -
172B ASP* 1.3 76.5 - - - +
174B GLU* 1.3 84.4 + - - +
175B LEU* 3.8 9.0 - - + -
180B LEU* 3.3 41.1 - - + -
181B VAL 3.4 19.3 - - - +
183B VAL* 4.2 2.5 - - - +
10F C 4.8 3.1 + - - -
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Residues in contact with GLU 174 (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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132B ASN* 4.7 1.1 - - - -
133B ILE* 4.0 15.7 - - + +
134B SER* 4.1 14.6 + - - +
173B TRP* 1.3 85.5 - - - +
175B LEU* 1.3 63.4 + - - +
176B ASN* 3.8 12.6 - - - +
181B VAL* 2.7 41.2 + - + +
183B VAL* 3.8 23.6 - - + +
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Residues in contact with LEU 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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22B ARG* 3.2 32.5 - - - +
28B LEU* 4.4 11.7 - - + -
132B ASN* 5.0 1.2 + - - +
134B SER* 4.8 4.2 + - - +
173B TRP* 3.8 8.0 - - + -
174B GLU* 1.3 75.6 - - - +
176B ASN* 1.3 64.2 + - - +
177B GLY 3.6 22.3 + - - +
178B GLU 3.8 9.4 - - - +
179B ASP 3.3 19.7 - - - +
180B LEU* 3.4 22.2 - - + -
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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