Contacts of the strand formed by residues 179 - 188 (chain L) in PDB entry 4WEB
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 TYR 179 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501H ARF 5.2 1.3 - - - -
111L GLU* 2.7 37.6 + - - +
144L ASN* 3.1 4.3 + - - -
145L PHE* 2.8 55.2 + - + +
146L TYR* 3.8 26.1 - + - -
148L LYS* 3.7 38.2 - - + +
169L TRP* 4.8 5.8 - + + -
170L THR* 3.9 16.6 - - - +
171L ASP* 5.0 0.4 - - - -
172L GLN* 3.6 46.1 + - + -
178L THR* 1.3 74.4 - - - +
180L SER* 1.3 65.7 + - - +
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Residues in contact with SER 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H HIS* 3.2 32.9 + - - -
171H PHE* 3.8 11.2 - - - -
501H ARF 4.9 0.2 + - - -
142L LEU 3.4 5.2 - - - -
143L ASN* 3.3 18.1 - - - -
144L ASN* 3.0 19.9 + - - -
145L PHE* 3.8 1.8 - - - -
169L TRP* 3.5 6.8 - - - +
170L THR* 3.1 32.7 + - - -
179L TYR* 1.3 72.8 + - - +
181L MET* 1.3 66.6 + - - +
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Residues in contact with MET 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171H PHE* 3.4 8.2 - - - -
141L PHE* 3.7 2.3 - - - -
142L LEU* 2.8 62.2 + - + +
145L PHE* 3.7 18.8 - - + -
150L ILE* 4.6 4.7 - - + +
152L VAL* 3.8 18.6 - - + +
167L ASN* 3.3 40.6 - - + +
168L SER 3.4 12.8 - - - +
169L TRP* 3.6 35.0 - - + +
180L SER* 1.3 80.4 - - - +
182L SER* 1.3 65.9 + - - +
183L SER* 4.2 0.7 - - - -
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Residues in contact with SER 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171H PHE* 3.5 31.2 - - - -
183H SER* 2.8 22.5 + - - -
139L VAL* 4.4 1.2 - - - +
140L CYS 3.7 3.2 + - - -
141L PHE* 3.4 12.7 - - - -
166L LEU 3.6 0.9 - - - +
167L ASN* 3.3 5.7 - - - +
168L SER* 2.9 36.3 + - - -
181L MET* 1.3 74.8 - - - +
183L SER* 1.3 61.7 + - - +
184L THR* 4.1 7.8 + - - -
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Residues in contact with SER 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140L CYS* 2.7 50.1 + - - -
142L LEU* 4.5 0.4 - - - -
152L VAL* 3.7 13.6 - - - +
154L TRP* 2.7 34.3 + - - -
165L VAL* 3.7 2.3 - - - +
166L LEU 3.3 3.4 - - - -
167L ASN* 2.7 19.7 + - - -
181L MET* 4.3 8.7 - - - -
182L SER* 1.3 73.5 + - - +
184L THR* 1.3 61.5 + - - +
200L CYS* 6.1 0.2 - - - -
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Residues in contact with THR 184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146H LEU* 4.8 11.9 - - + +
148H LYS* 6.1 0.4 - - - -
181H THR* 5.7 5.2 - - + -
183H SER* 4.7 3.8 + - - -
137L SER* 3.9 10.1 - - - -
138L VAL 3.4 2.9 - - - +
139L VAL* 3.5 30.8 - - + +
154L TRP* 4.7 0.2 - - - -
164L GLY 3.1 7.1 - - - +
165L VAL* 4.1 0.4 - - - -
166L LEU* 2.8 43.5 + - + +
182L SER* 4.1 7.4 + - - -
183L SER* 1.3 76.8 + - - +
185L LEU* 1.3 57.7 + - - +
186L THR* 3.4 19.6 + - - +
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Residues in contact with LEU 185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136L ALA 3.9 0.3 - - - +
137L SER* 3.3 0.7 - - - -
138L VAL* 2.6 61.7 + - + +
154L TRP* 3.8 37.3 - - + +
156L ILE* 3.8 27.8 - - + -
161L ARG* 3.7 27.4 - - + -
163L ASN 4.0 7.9 - - - +
164L GLY 3.6 6.3 - - - -
165L VAL* 4.0 8.1 - - + +
184L THR* 1.3 69.3 - - - +
186L THR* 1.3 61.0 + - - +
187L LEU* 3.8 23.3 - - + -
198L TYR* 4.3 2.5 - - + -
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Residues in contact with THR 186 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H LYS* 4.0 20.4 - - - +
130L GLN* 5.1 1.3 - - - +
136L ALA 3.4 7.4 - - - +
137L SER* 2.6 30.6 + - - +
164L GLY* 3.0 27.0 + - - -
166L LEU* 5.2 5.2 - - - +
184L THR* 3.7 10.0 - - - +
185L LEU* 1.3 73.8 - - - +
187L LEU* 1.3 77.4 + - - +
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Residues in contact with LEU 187 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135L GLY* 4.5 1.9 - - - -
136L ALA 2.8 25.1 + - - +
138L VAL* 5.8 1.8 - - + -
156L ILE* 3.7 27.1 - - + -
161L ARG* 4.8 7.2 - - + +
163L ASN 4.3 9.0 - - - +
185L LEU* 3.8 27.8 + - + -
186L THR* 1.3 90.1 - - - +
188L THR* 1.3 73.1 + - - +
191L GLU* 3.4 34.3 - - + +
192L TYR* 4.6 7.0 - - + +
195L HIS* 6.1 0.4 - - - +
198L TYR* 4.2 15.0 - - + +
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Residues in contact with THR 188 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134L GLY 5.2 0.7 - - - -
135L GLY* 5.5 0.4 - - - -
136L ALA* 4.3 1.3 - - - -
187L LEU* 1.3 79.1 - - - +
189L LYS* 1.3 57.3 + - - +
190L ASP* 3.2 5.4 + - - +
191L GLU* 2.6 47.0 + - + +
192L TYR* 2.8 29.5 + - - +
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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