Contacts of the strand formed by residues 183 - 187 (chain K) in PDB entry 2WQT
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 MET 183 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106K ALA* 3.6 33.4 - - + +
181K CYS 4.6 1.8 - - - +
182K ALA* 1.3 75.4 - - - +
184K LYS* 1.3 80.8 + - - +
185K MET* 3.8 9.9 - - - -
193K SER* 4.0 7.6 - - - +
194K SER* 3.2 23.2 - - - -
195K GLY 2.8 37.6 + - - +
233K LEU* 3.7 19.7 - - + -
234K GLY* 3.4 37.9 - - - +
247K ALA* 5.0 0.4 - - + -
248K HIS 3.2 11.7 - - - +
249K ILE* 3.9 9.4 - - + -
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Residues in contact with LYS 184 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K ALA* 4.3 2.4 - - + -
183K MET* 1.3 78.8 - - - +
185K MET* 1.3 60.1 + - - +
186K THR* 5.6 4.4 - - + +
191K GLU* 2.8 41.0 + - + +
193K SER 3.8 1.8 - - - -
194K SER* 4.3 10.8 - - - -
246K GLU 3.9 1.0 - - - +
247K ALA* 3.4 0.9 - - - -
248K HIS* 2.9 40.1 + - + +
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Residues in contact with MET 185 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104K ILE* 3.7 38.6 - - + +
105K GLU* 4.4 4.3 - - - -
106K ALA 4.6 8.1 - - - +
137K LEU* 4.0 26.0 - - - -
183K MET* 3.8 11.4 - - - -
184K LYS* 1.3 74.9 - - - +
186K THR* 1.3 71.5 + - - +
191K GLU* 3.6 5.0 - - - +
192K VAL* 2.9 28.9 + - + -
193K SER* 2.9 37.8 + - - +
235K PRO 4.8 0.4 - - - +
237K VAL* 3.9 7.9 - - + -
245K PHE* 4.2 11.7 - - + -
246K GLU 3.3 13.7 - - - +
247K ALA* 4.2 3.8 - - + -
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Residues in contact with THR 186 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184K LYS* 5.6 4.0 - - + +
185K MET* 1.3 77.0 - - - +
187K ARG* 1.3 59.8 + - - +
189K ASN* 4.1 12.2 + - - +
190K GLU* 3.5 31.9 - - - +
191K GLU* 3.9 7.0 - - + +
192K VAL* 3.9 2.7 - - - -
244K ARG 3.6 1.0 - - - +
245K PHE* 3.3 8.9 - - - -
246K GLU* 2.8 54.2 + - - +
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Residues in contact with ARG 187 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186K THR* 1.3 70.3 - - - +
188K ASN* 1.3 85.1 + - - +
189K ASN 3.2 1.1 - - - -
190K GLU* 3.1 28.4 + - - +
192K VAL* 3.6 28.0 - - + +
237K VAL* 4.1 9.1 - - - +
238K ALA* 2.9 28.1 + - - +
240K ASN* 4.0 13.4 + - - -
243K ASP* 3.3 27.1 - - + -
244K ARG 3.4 3.8 - - - +
245K PHE* 3.5 23.3 - - + -
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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