Contacts of the strand formed by residues 184 - 189 (chain B) in PDB entry 4DY0
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 184 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B GLU 5.9 0.7 - - - +
182B ASN 3.4 8.3 + - - +
183B THR* 1.3 77.7 - - - +
185B LYS* 1.3 67.6 + - - +
186B ARG* 3.5 50.7 + - - +
199B PRO* 4.1 2.7 - - - -
200B MET 3.0 24.3 + - - +
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Residues in contact with LYS 185 (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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184B LYS* 1.3 82.4 - - - +
186B ARG* 1.3 63.6 + - - +
197B GLN* 3.8 38.7 + - + +
198B VAL 3.1 7.2 - - - +
199B PRO* 3.7 28.9 - - + +
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Residues in contact with ARG 186 (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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182B ASN 4.8 2.4 + - - -
184B LYS* 3.5 43.5 + - - +
185B LYS* 1.3 79.8 - - - +
187B THR* 1.3 63.2 + - - +
188B PHE 3.6 0.2 + - - -
196B TYR 3.4 0.7 - - - +
197B GLN* 3.4 9.9 - - - +
198B VAL 2.9 26.6 + - - +
200B MET* 3.9 25.5 + - + +
202B ALA* 4.4 13.9 - - - +
273B ILE* 3.8 46.5 - - - +
351B TRP* 4.5 12.1 - - - -
353B ILE* 6.1 0.9 - - - -
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Residues in contact with THR 187 (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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186B ARG* 1.3 72.9 - - - +
188B PHE* 1.3 62.2 + - - +
189B VAL* 4.1 12.3 - - + -
195B SER* 3.7 27.8 - - - +
196B TYR 3.5 5.2 - - - +
197B GLN* 3.0 19.0 + - - +
200B MET* 3.3 13.0 - - - +
355B ASP* 3.3 16.9 - - - +
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Residues in contact with PHE 188 (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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186B ARG 3.6 0.2 + - - -
187B THR* 1.3 73.6 - - - +
189B VAL* 1.3 76.1 + - - +
190B ALA* 3.8 4.9 + - + -
194B LYS 3.9 0.2 - - - +
195B SER* 3.2 1.4 - - - -
196B TYR* 2.8 42.2 + + + +
198B VAL* 4.4 11.9 - - + -
200B MET* 3.9 8.3 - - + -
275B PRO* 4.2 16.4 - - + -
354B VAL 4.0 7.4 - - - -
355B ASP* 3.5 18.2 - - - -
356B ARG 3.5 35.7 - - - -
357B PRO* 3.7 7.0 - - + -
358B PHE* 4.3 5.2 - + - -
376B ILE 4.2 5.8 - - - -
377B ASN 3.5 23.3 - - - -
378B LYS* 4.7 0.9 - - - -
379B PRO* 3.6 28.0 - - + -
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B THR* 4.1 9.4 - - + -
188B PHE* 1.3 76.5 - - - +
190B ALA* 1.3 71.0 + - - +
193B GLY* 3.7 26.2 - - - +
194B LYS 3.5 4.3 - - - +
195B SER* 4.0 14.6 - - - -
355B ASP* 3.0 14.2 + - - +
356B ARG* 3.7 10.7 - - + +
357B PRO* 3.2 20.3 - - - +
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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