Contacts of the strand formed by residues 67 - 71 (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 PHE 67 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E VAL* 4.1 25.1 - - + -
18E HIS* 4.4 6.5 - + - +
21E LEU* 3.6 43.5 - - + -
22E ALA* 4.8 2.0 - - + -
36E TRP* 5.0 1.8 - + - -
66E SER* 1.3 75.3 - - - +
68E LEU* 1.3 67.6 + - - +
69E GLU* 3.4 41.3 - - + -
94E ARG* 3.4 32.3 - - + -
95E THR 3.6 13.7 - - - -
96E ALA* 4.4 5.8 - - + +
130E LEU* 3.8 0.9 - - - +
131E PHE* 2.8 57.1 + + + +
475F ILE* 4.6 2.0 - - + -
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Residues in contact with LEU 68 (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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55E VAL* 4.7 2.0 - - + -
66E SER* 3.9 19.5 - - - +
67E PHE* 1.3 84.8 - - - +
69E GLU* 1.3 68.3 + - - +
70E VAL* 5.1 4.9 - - + -
94E ARG* 3.4 3.6 - - - -
95E THR* 3.1 44.6 + - + +
96E ALA* 4.4 5.8 - - - -
104E TRP* 3.8 49.6 - - + +
128E ILE* 4.3 19.3 - - + -
129E SER 3.4 8.5 - - - +
130E LEU* 4.2 12.8 - - + -
187E ILE* 4.6 9.9 - - + -
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Residues in contact with GLU 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E PHE* 3.4 21.3 - - + -
68E LEU* 1.3 75.7 - - - +
70E VAL* 1.3 64.1 + - - +
92E PHE* 3.7 22.7 - - + -
93E GLY 3.3 10.3 - - - +
94E ARG* 2.8 29.6 + - + -
127E ASN 3.8 0.2 - - - +
128E ILE* 3.4 4.9 - - - +
129E SER* 2.9 36.3 + - - +
131E PHE* 4.0 10.8 - - + -
473F LYS* 2.9 46.4 + - - +
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Residues in contact with VAL 70 (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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39E LEU* 4.0 15.0 - - + -
68E LEU* 5.1 7.2 - - + -
69E GLU* 1.3 79.4 - - - +
71E TRP* 1.3 64.5 + - - +
72E GLN* 5.7 0.2 - - - +
91E SER 4.1 0.2 - - - -
92E PHE* 3.4 10.3 - - - -
93E GLY* 3.0 40.5 + - - +
95E THR* 5.5 2.0 - - + -
104E TRP* 6.2 0.7 - - + -
106E LEU* 3.7 34.8 - - + -
126E ILE* 4.0 12.1 - - + -
127E ASN 3.2 6.3 - - - +
128E ILE* 4.3 17.5 - - + -
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Residues in contact with TRP 71 (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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70E VAL* 1.3 76.1 - - - +
72E GLN* 1.3 59.7 + - - +
79E TYR* 3.3 32.5 - + + -
80E GLN 3.9 17.7 - - - -
81E ASP* 3.9 8.7 - - + -
91E SER* 3.2 42.0 - - - -
92E PHE* 3.7 17.0 - - + -
126E ILE* 4.8 0.9 - - - -
127E ASN* 3.0 42.4 + - + -
344F SER 3.4 20.0 + - - -
347F THR* 3.0 29.7 + - - -
348F GLY* 3.4 35.7 - - - -
349F PRO* 3.8 14.8 - - + -
470F ILE* 3.7 32.3 - - + -
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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