Contacts of the strand formed by residues 172 - 179 (chain B) in PDB entry 3WOO
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 172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128B ASP* 3.7 15.9 - - - -
166B CYS 4.8 5.6 - - - +
167B GLU* 3.4 20.6 - - - +
169B GLU* 3.4 48.1 + - + +
170B ALA 3.5 13.3 - - - -
171B GLY* 1.3 81.8 + - - +
173B ARG* 1.3 60.9 + - - +
174B CYS* 4.8 1.1 - - - -
189B LYS* 3.4 28.7 - - + -
190B ASN 3.1 20.4 - - - +
191B LEU* 3.6 20.6 - - + -
192B GLU* 4.5 4.8 - - - +
237B LYS* 4.9 3.1 - - + -
802B GOL 3.3 28.0 - - - -
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Residues in contact with ARG 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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125B PHE* 4.1 19.6 - - + -
167B GLU* 3.4 12.7 + - - +
172B PHE* 1.3 74.8 - - - +
174B CYS* 1.3 67.3 + - - +
190B ASN* 2.7 39.0 + - - +
192B GLU* 3.6 42.1 + - + +
432B ARG* 3.0 56.6 + - - +
433B ASP* 3.3 21.6 + - - +
804B GOL 4.1 9.5 + - - +
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Residues in contact with CYS 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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163B ILE* 4.1 11.1 - - + +
166B CYS* 2.1 62.6 - - + -
167B GLU* 2.9 16.1 + - + +
172B PHE* 4.8 0.7 - - - -
173B ARG* 1.3 83.2 + - - +
175B ARG* 1.3 63.4 + - - +
187B LEU* 4.3 7.0 - - + -
188B PHE 3.1 8.1 - - - +
189B LYS* 3.8 13.7 - - - -
432B ARG* 3.1 22.7 + - - -
804B GOL 4.4 2.1 + - - -
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Residues in contact with ARG 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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163B ILE* 4.5 4.0 - - - -
174B CYS* 1.3 78.1 - - - +
176B LEU* 1.3 67.8 + - - +
177B TYR* 3.5 41.9 - - + -
187B LEU* 3.5 6.3 - - - +
188B PHE* 2.9 33.5 + - + +
576B ASN 5.2 1.0 + - - -
577B LEU* 3.6 30.9 - - - +
804B GOL 2.7 55.3 + - - +
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Residues in contact with LEU 176 (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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133B VAL* 3.8 26.0 - - + -
155B LEU* 4.5 7.4 - - + -
158B PHE* 4.3 15.7 - - + -
159B GLU* 3.7 52.0 + - + +
162B LEU* 4.3 7.2 - - + -
163B ILE* 4.3 6.1 - - + +
175B ARG* 1.3 82.5 + - - +
177B TYR* 1.3 67.1 + - - +
178B SER 4.3 0.5 + - - -
185B TYR* 4.1 19.7 - - + -
186B ARG 3.5 18.2 - - - +
187B LEU* 4.3 6.2 - - + +
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Residues in contact with TYR 177 (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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175B ARG* 3.5 43.1 - - + -
176B LEU* 1.3 76.4 - - - +
178B SER* 1.3 60.1 + - - +
179B PHE* 3.7 16.5 - - + -
185B TYR* 3.2 9.8 - - - +
186B ARG 2.8 40.1 + - - +
188B PHE* 3.4 50.9 - + + -
190B ASN* 5.5 0.2 + - - -
272B TYR* 4.9 2.9 - - - -
576B ASN* 3.3 32.5 - - + +
577B LEU* 3.1 27.0 + - + +
578B SER* 3.7 10.9 - - - -
804B GOL 4.2 13.5 - - - -
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Residues in contact with SER 178 (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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176B LEU* 4.3 0.8 + - - +
177B TYR* 1.3 73.1 - - - +
179B PHE* 1.3 60.4 + - - +
181B GLY* 4.3 1.6 + - - -
182B GLY* 3.4 28.2 + - - -
184B THR 3.5 5.4 - - - -
185B TYR* 3.8 19.0 + - - -
576B ASN* 3.1 18.4 + - - +
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Residues in contact with PHE 179 (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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30B VAL* 3.8 19.7 - - + -
177B TYR* 3.7 30.3 - - + -
178B SER* 1.3 74.5 - - - +
180B SER* 1.3 76.2 + - - +
181B GLY 3.3 2.5 - - - -
182B GLY 3.0 10.4 + - - -
183B ASN 3.2 10.4 + - - -
184B THR* 2.7 26.3 + - - +
186B ARG* 3.4 49.6 - - + +
188B PHE* 4.5 6.5 - + - -
573B PRO* 4.2 7.0 - - + -
574B ASP 5.8 0.9 - - - -
576B ASN* 3.4 14.1 - - - +
578B SER* 3.3 30.5 - - - -
580B ARG* 3.8 9.6 - - - -
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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