Contacts of the strand formed by residues 181 - 189 (chain A) in PDB entry 4DKT
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 SER 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A ILE 3.0 26.1 + - - -
150A LEU* 3.6 17.0 - - - +
179A ASP 4.5 1.2 + - - -
180A MET* 1.3 74.2 - - - +
182A LEU* 1.3 62.2 + - - +
183A MET 3.8 0.3 + - - -
250A TYR* 3.4 5.4 - - - -
251A VAL* 2.9 37.7 + - - +
291A PHE* 4.4 15.0 - - - -
361A HIS* 3.3 19.0 - - - -
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Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ALA* 3.9 9.5 - - - +
120A ASP* 4.6 1.9 + - - +
127A VAL* 3.4 36.8 - - + +
180A MET 4.0 1.6 + - - +
181A SER* 1.3 73.2 - - - +
183A MET* 1.3 61.7 + - - +
184A THR* 4.1 13.2 - - + -
248A ASP* 4.1 19.7 - - + +
249A PHE 3.5 10.8 - - - +
250A TYR* 3.4 41.5 - - + +
291A PHE* 5.4 0.6 - - - -
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Residues in contact with MET 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.6 28.3 - - + -
118A CYS 3.3 17.9 - - - +
119A ALA* 4.5 2.9 - - + -
181A SER 3.8 0.4 + - - -
182A LEU* 1.3 75.2 - - - +
184A THR* 1.3 59.8 + - - +
201A LEU* 4.3 14.8 - - + -
213A VAL* 4.7 1.1 - - + -
249A PHE* 2.8 69.3 + - + +
251A VAL* 4.2 8.3 - - + -
267A LEU* 3.6 28.9 - - + -
289A VAL* 3.8 24.7 - - + -
291A PHE* 4.2 12.3 - - + -
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Residues in contact with THR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A SER 3.6 1.6 - - - +
117A LEU* 3.6 6.7 - - - +
118A CYS* 2.9 52.0 + - - +
127A VAL* 3.7 11.0 - - + +
182A LEU* 4.1 19.7 - - + -
183A MET* 1.3 77.6 - - - +
185A LEU* 1.3 62.2 + - - +
186A SER* 4.6 6.3 + - - -
246A ASN* 6.0 2.9 - - - -
247A MET 3.3 7.9 - - - -
248A ASP* 3.2 26.5 - - - +
249A PHE* 4.8 0.4 - - - -
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ILE* 4.1 19.7 - - + -
116A SER 3.5 22.2 - - - +
117A LEU* 4.3 10.1 - - + +
184A THR* 1.3 74.2 - - - +
186A SER* 1.3 63.3 + - - +
187A THR* 4.0 8.7 + - + +
199A LEU* 3.8 18.8 - - + -
238A LEU* 3.5 32.1 - - + -
240A VAL* 5.1 2.5 - - + -
245A HIS 3.7 1.4 - - - +
246A ASN* 3.4 4.5 - - - -
247A MET* 2.9 41.3 + - + +
249A PHE* 3.8 17.2 - - + -
269A ILE* 4.1 13.5 - - + -
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Residues in contact with SER 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A GLU* 3.0 22.4 - - - +
115A ILE* 3.6 1.0 - - - -
116A SER* 2.9 47.2 + - - -
118A CYS* 4.8 5.5 - - - -
184A THR* 4.1 9.6 + - - -
185A LEU* 1.3 73.0 - - - +
187A THR* 1.3 60.7 + - - +
246A ASN* 2.7 23.9 + - - -
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Residues in contact with THR 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A GLU* 3.0 4.7 - - - -
115A ILE* 3.4 28.9 - - + -
185A LEU* 4.4 12.8 + - + +
186A SER* 1.3 78.1 - - - +
188A LYS* 1.3 58.7 + - - +
189A THR* 4.7 2.7 - - - -
194A PHE* 4.6 9.2 - - + -
199A LEU* 4.0 21.1 - - + -
240A VAL* 3.6 22.2 - - + +
243A GLY 3.8 2.9 + - - -
244A LYS* 3.4 4.9 - - - +
245A HIS* 2.9 44.8 + - - +
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Residues in contact with LYS 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ALA* 3.5 24.0 - - + +
84A SER 5.7 2.5 - - - -
85A GLY* 6.5 0.4 - - - -
113A VAL* 3.4 4.5 - - - -
114A GLU* 2.9 58.9 + - + +
187A THR* 1.3 73.2 - - - +
189A THR* 1.3 68.2 + - - +
243A GLY* 3.3 6.3 - - - -
244A LYS* 3.3 56.7 - - + +
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Residues in contact with THR 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A SER 4.0 5.8 - - - -
85A GLY* 5.6 0.3 - - - -
113A VAL* 3.6 20.2 - - + -
115A ILE* 4.5 7.6 - - + -
187A THR* 4.7 1.6 - - - -
188A LYS* 1.3 90.3 + - - +
190A PRO* 1.3 75.5 + - - +
191A LYS 3.7 0.2 + - - -
193A PHE* 3.8 21.5 - - + -
194A PHE* 3.4 24.4 - - + -
243A GLY* 2.8 46.3 + - - -
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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