Contacts of the strand formed by residues 168 - 173 (chain B) in PDB entry 4A04
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 LYS 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ASP* 3.4 20.7 + - + +
167B ASP* 1.4 85.4 - - - +
169B ARG* 1.3 60.7 + - - +
170B TYR* 3.7 29.9 - - + +
181B VAL* 3.7 33.3 - - + +
183B GLY 3.7 8.5 - - - +
184B LYS* 5.2 4.5 - - + +
185B ALA* 3.6 6.6 - - - +
235B HIS* 4.1 15.1 - - - -
236B ARG 4.9 0.2 + - - -
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Residues in contact with ARG 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LYS* 1.3 72.5 - - - +
170B TYR* 1.3 60.2 + - - +
181B VAL* 3.5 6.1 - - - -
182B ALA* 2.7 41.9 + - - +
183B GLY* 2.9 31.3 + - - +
184B LYS* 3.1 31.4 + - - +
185B ALA 3.9 1.0 - - - +
186B ASP* 3.4 24.4 + - - -
233B SER 5.4 0.4 - - - -
234B MET* 3.9 14.6 - - + +
235B HIS* 3.6 25.4 - - + +
3E T 5.9 2.7 - - - -
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Residues in contact with TYR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ASP* 2.8 42.4 + - - -
168B LYS* 3.7 25.2 - - + +
169B ARG* 1.3 75.7 - - - +
171B ARG* 1.3 60.3 + - - +
179B TRP* 3.6 21.5 - - + -
180B LEU* 3.4 21.8 - - - -
181B VAL* 3.7 21.4 - - + +
182B ALA* 4.1 4.1 - - - +
234B MET* 2.7 43.6 + - - +
236B ARG* 3.5 53.3 + - + -
271B THR* 5.0 2.5 - - + -
3E T 4.2 4.7 + - - -
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Residues in contact with ARG 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B TYR* 1.3 74.4 - - - +
172B TYR* 1.3 67.1 + - - +
173B ALA* 3.9 7.8 + - - +
179B TRP* 3.5 6.8 - - - -
180B LEU* 2.8 63.1 + - - +
181B VAL 3.8 19.2 + - - -
182B ALA* 3.8 18.9 - - + +
234B MET* 5.6 0.7 - - - -
2E A 4.8 9.4 - - - -
3E T 3.6 25.8 - - - +
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Residues in contact with TYR 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ARG* 1.3 80.5 + - - +
173B ALA* 1.3 66.3 + - - +
174B PHE* 3.7 40.2 + + - -
177B SER* 3.4 29.3 + - - -
178B SER* 3.8 22.0 - - - -
179B TRP* 3.7 33.2 - + + -
234B MET* 5.9 0.4 - - - -
277B GLN* 3.6 51.7 + - + +
278B ASN* 3.5 39.6 + - + -
3E T 4.8 5.0 + - - -
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Residues in contact with ALA 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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171B ARG* 3.9 8.6 + - - +
172B TYR* 1.3 71.1 - - - +
174B PHE* 1.3 54.6 + - - +
175B HIS* 3.3 4.0 + - + +
176B SER* 3.6 19.3 - - - +
177B SER* 2.8 34.7 + - - -
178B SER 3.0 10.3 + - - +
180B LEU* 3.8 24.7 - - + -
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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