Contacts of the strand formed by residues 181 - 189 (chain B) in PDB entry 4U0Q
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 GLY 181 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B LYS* 4.2 9.0 - - - -
179B ASP 3.1 4.9 + - - -
180B PRO* 1.3 73.0 - - - +
182B GLN* 1.3 63.1 + - - -
183B TYR* 3.3 13.3 - - - -
199B THR* 4.6 1.1 - - - -
200B LEU 2.9 30.3 + - - -
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Residues in contact with GLN 182 (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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141B LYS* 3.8 5.8 - - - +
142B ILE* 2.8 64.2 + - + +
181B GLY* 1.3 73.0 - - - -
183B TYR* 1.3 59.4 + - - +
197B ILE* 3.9 18.8 - - + +
198B ILE 3.7 4.0 - - - -
199B THR* 3.7 23.4 - - + +
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Residues in contact with TYR 183 (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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124B LEU* 3.7 30.3 - - + -
139B TRP* 4.9 5.8 - - + -
140B TYR 3.5 7.2 - - - +
141B LYS* 3.7 24.5 + - + +
142B ILE* 3.7 3.1 - - - -
150B LEU* 3.8 26.9 - - + -
158B PHE* 4.6 11.0 - + - -
169B LEU* 4.0 6.3 - - + -
171B ILE* 4.8 5.5 - - + +
179B ASP* 2.8 47.8 + - - +
181B GLY 3.3 19.3 - - - -
182B GLN* 1.3 74.5 - - - +
184B ARG* 1.3 58.4 + - - +
196B ALA 3.8 0.3 - - - +
197B ILE* 3.3 5.9 - - - +
198B ILE* 2.8 41.5 + - + +
200B LEU* 4.0 15.8 - - + +
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Residues in contact with ARG 184 (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 TRP* 3.4 5.7 - - - -
140B TYR* 2.8 52.3 + - + +
142B ILE* 3.6 31.9 - - + +
147B ASP* 3.0 29.9 + - - +
183B TYR* 1.3 72.8 - - - +
185B CYS* 1.3 61.5 + - - +
186B ASN* 5.9 0.4 - - - -
195B GLN* 3.6 45.8 + - + +
196B ALA 3.4 13.0 - - - +
197B ILE* 3.5 30.4 - - + +
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Residues in contact with CYS 185 (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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107B VAL* 4.6 2.5 - - - -
126B CYS* 2.0 52.0 - - + -
137B TRP* 4.3 11.0 - - + -
138B ALA 3.4 4.7 - - - +
139B TRP* 3.7 25.7 - - + +
184B ARG* 1.3 73.5 - - - +
186B ASN* 1.3 60.5 + - - +
194B ASP 4.1 0.3 - - - +
195B GLN* 3.4 6.9 - - - +
196B ALA* 3.0 39.9 + - - -
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Residues in contact with ASN 186 (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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136B ASP 3.8 1.0 - - - +
137B TRP* 3.3 7.4 - - - -
138B ALA* 2.8 41.7 + - + +
140B TYR* 4.2 18.8 - - + -
184B ARG* 4.3 1.1 - - - -
185B CYS* 1.3 73.4 - - - +
187B GLY* 1.3 59.0 + - - +
188B THR* 3.2 23.6 + - - -
193B SER* 4.4 12.5 + - - -
194B ASP 3.5 8.9 + - - -
195B GLN* 3.4 33.4 - - + +
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Residues in contact with GLY 187 (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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105B PRO* 4.3 2.1 - - - +
107B VAL* 4.1 6.6 - - - +
134B VAL* 3.5 22.2 - - - -
136B ASP 3.7 2.0 - - - -
137B TRP* 3.7 16.8 - - - -
185B CYS 4.1 0.6 - - - -
186B ASN* 1.3 70.7 - - - +
188B THR* 1.3 61.9 + - - -
193B SER* 3.3 4.3 - - - -
194B ASP* 3.1 34.3 + - - +
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Residues in contact with THR 188 (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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134B VAL* 3.3 4.4 - - - +
135B THR* 3.0 23.6 + - - -
136B ASP* 2.8 34.2 + - - +
186B ASN* 3.2 22.5 + - - -
187B GLY* 1.3 71.9 + - - -
189B SER* 1.3 68.6 + - - +
192B GLY 3.6 12.1 - - - +
193B SER* 3.7 10.4 - - - -
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Residues in contact with SER 189 (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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104B PRO 5.0 0.3 - - - -
105B PRO* 3.5 21.9 - - - +
132B PRO* 3.7 15.5 + - - +
133B PRO 3.5 24.7 - - - -
134B VAL* 4.1 3.4 - - - -
135B THR* 4.3 5.2 - - - +
188B THR* 1.3 82.2 - - - +
190B SER* 1.3 62.7 + - - +
191B LYS* 3.3 13.7 + - - +
192B GLY 2.8 22.0 + - - +
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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