Contacts of the strand formed by residues 180 - 184 (chain E) in PDB entry 1YKN
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 180 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48E HIS* 3.8 40.7 + - - +
49E ILE* 4.1 14.0 + - - +
50E LEU* 4.4 12.3 - - + +
107E HIS* 4.5 18.6 + - - +
108E THR 5.4 0.4 + - - +
176E GLU* 3.2 5.6 - - - -
177E VAL 2.8 39.5 + - - +
178E ASP* 2.8 10.5 + - + +
179E GLY* 1.4 73.7 - - - +
181E THR* 1.3 75.2 + - - +
182E ALA* 3.4 1.2 + - - +
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Residues in contact with THR 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E GLU* 3.9 14.8 + - - +
48E HIS 4.3 13.8 + - - -
49E ILE* 3.3 6.3 - - + -
50E LEU* 2.8 24.4 + - - +
174E ARG* 3.8 31.6 + - - +
175E CYS 3.9 7.0 - - - +
176E GLU* 4.8 5.6 - - + +
179E GLY 4.3 1.2 + - - -
180E LYS* 1.3 75.0 - - - +
182E ALA* 1.3 60.1 + - - +
183E TYR* 4.1 18.4 - - + -
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Residues in contact with ALA 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E LEU* 2.8 31.4 - - + +
52E LEU* 4.1 13.9 - - + -
174E ARG* 3.6 1.9 - - - +
175E CYS* 3.0 41.4 + - - +
177E VAL* 4.3 7.6 - - + -
180E LYS 3.4 6.3 + - - +
181E THR* 1.3 76.9 - - - +
183E TYR* 1.3 67.4 + - - +
184E ARG 4.2 0.2 - - - -
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Residues in contact with TYR 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E GLU* 4.8 4.0 + - - -
49E ILE* 3.8 32.8 - - + -
50E LEU 2.8 7.5 + - - +
51E LEU* 3.4 15.2 - - + +
52E LEU* 2.9 28.8 + - - +
110E LYS* 3.2 13.9 + - - +
145E PHE* 3.7 32.1 - + + -
146E ASP* 3.9 3.6 - - - -
147E ASP* 2.8 38.0 + - - -
172E ALA* 3.9 20.9 - - + -
173E LYS 3.6 2.7 - - - -
174E ARG* 3.6 43.1 + - + -
181E THR* 4.1 8.0 - - + +
182E ALA* 1.3 76.0 - - - +
184E ARG* 1.4 59.6 + - - +
185E PHE* 4.1 0.9 + - - +
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Residues in contact with ARG 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E LEU* 3.0 35.4 - - + +
53E GLY 4.3 0.4 - - - -
54E GLN* 3.1 35.2 + - - +
56E TYR* 5.0 0.2 + - - -
103E GLU* 3.3 12.3 + - - -
171E ILE 4.8 0.2 - - - +
172E ALA* 3.3 3.6 - - - -
173E LYS* 2.9 44.0 + - + +
175E CYS* 4.3 14.9 - - - -
183E TYR* 1.4 73.2 - - - +
185E PHE* 1.3 62.7 + - - +
186E ASP* 3.0 36.5 + - - +
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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