Contacts of the strand formed by residues 180 - 184 (chain B) in PDB entry 4KAL
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 GLU 180 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LYS 3.1 10.9 + - - +
150B VAL* 3.3 12.6 - - + +
151B THR* 3.0 24.4 + - - -
174B ALA* 4.7 0.8 - - - +
178B GLY 5.4 1.6 - - - +
179B ARG* 1.3 83.6 - - - +
181B MSE 1.3 65.8 + - - +
208B ASP* 3.4 24.0 - - + +
209B ILE* 4.5 8.3 - - + +
238B LYS* 5.4 5.4 - - - +
239B ILE* 5.3 2.1 - - - +
286B TYR* 2.7 40.9 + - - -
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Residues in contact with MSE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B THR* 3.3 33.4 - - + +
153B PHE* 3.6 34.8 - - + -
167B ILE* 4.5 3.1 - - + +
170B CYS* 3.9 4.7 - - + +
171B ALA* 3.7 30.5 - - + +
174B ALA* 3.6 24.5 - - + -
175B HIS* 3.6 16.6 - - + +
180B GLU* 1.3 75.1 - - - +
182B SER* 1.3 61.3 + - - +
206B LYS 3.0 28.5 - - - +
207B VAL* 4.0 2.2 - - - -
208B ASP* 2.8 34.2 + - - +
209B ILE* 3.1 7.8 + - - +
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Residues in contact with SER 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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150B VAL* 3.9 20.6 - - - -
151B THR 2.7 9.6 + - - -
152B TYR* 3.1 12.9 - - - -
153B PHE* 2.9 32.5 + - - -
181B MSE 1.3 76.5 - - - +
183B MSE 1.3 60.9 + - - +
207B VAL* 4.4 1.6 - - - -
209B ILE* 2.8 28.7 + - - +
211B PHE* 3.3 24.9 - - - -
283B LEU* 4.8 1.6 - - - -
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Residues in contact with MSE 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TYR* 4.2 5.4 - - - -
153B PHE* 3.2 31.0 - - + +
155B GLY* 3.6 21.5 - - - +
182B SER* 1.3 76.2 + - - +
184B THR* 1.3 78.9 + - - +
185B LEU* 4.5 7.9 - - + +
198B PHE* 3.7 33.0 - - + +
201B LEU* 3.9 22.7 - - + -
202B MSE 5.2 3.6 - - - -
207B VAL* 3.9 21.4 - - + +
209B ILE 3.0 6.9 + - - +
210B VAL* 3.3 11.2 - - + -
211B PHE* 2.8 26.7 + - - -
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Residues in contact with THR 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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58B SER* 4.7 7.2 - - - +
152B TYR* 3.2 30.2 - - + +
153B PHE 3.1 12.8 + - - +
154B GLU* 3.8 10.8 - - + -
155B GLY* 2.8 31.2 + - - -
183B MSE 1.3 79.9 - - - +
185B LEU* 1.3 61.5 + - - +
186B SER* 3.1 24.3 + - - +
211B PHE* 3.5 17.7 + - - +
216B GLU* 4.6 2.3 + - - -
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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