Contacts of the strand formed by residues 126 - 131 (chain K) 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 ILE 126 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51K LEU* 3.3 34.3 - - + -
70K VAL* 4.0 20.2 - - + -
71K TRP 4.1 3.4 - - - +
72K GLN* 3.6 33.7 - - + +
106K LEU* 5.2 1.1 - - + -
108K THR* 4.5 2.5 - - + -
111K PRO* 4.2 10.8 - - + -
125K HIS* 1.3 79.5 - - - +
127K ASN* 1.3 73.4 + - - +
128K ILE* 3.4 12.3 + - + +
142K ARG* 3.4 5.1 - - - -
143K LEU* 2.9 42.8 + - + +
145K PHE* 4.0 19.3 - - + -
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Residues in contact with ASN 127 (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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69K GLU 3.9 0.2 - - - +
70K VAL* 3.1 6.6 - - - +
71K TRP* 2.9 57.6 + - + +
79K TYR* 3.1 24.7 + - - -
125K HIS* 3.7 6.7 + - - -
126K ILE* 1.3 71.3 - - - +
128K ILE* 1.4 61.3 - - - +
141K THR 3.9 4.7 - - - +
142K ARG* 3.6 26.3 + - - +
344L SER* 3.6 15.0 + - - -
345L GLU* 3.8 8.1 - - - +
470L ILE* 4.0 21.5 - - + +
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Residues in contact with ILE 128 (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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68K LEU* 4.0 26.5 - - + -
69K GLU 3.5 6.1 - - - +
70K VAL* 4.0 15.3 - - + -
104K TRP* 5.0 10.1 - - + -
126K ILE* 3.9 11.0 - - + +
127K ASN* 1.4 79.5 - - - +
129K SER* 1.3 72.2 + - - +
130K LEU* 4.5 2.5 - - + +
139K LEU 4.2 0.7 - - - -
140K HIS* 3.3 6.1 + - - +
141K THR* 3.0 47.4 + - + +
143K LEU* 4.0 17.0 - - + +
185K PHE* 3.8 33.2 - - + -
187K ILE* 4.6 6.1 - - + -
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Residues in contact with SER 129 (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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68K LEU* 3.2 7.4 - - - +
69K GLU* 2.9 40.2 + - - -
128K ILE* 1.3 72.1 - - - +
130K LEU* 1.3 59.5 + - - +
131K PHE* 3.6 26.4 - - - -
138K HIS* 4.0 4.2 - - - -
139K LEU 3.2 6.3 - - - -
140K HIS* 3.5 24.6 + - - -
470L ILE* 5.4 9.2 + - - +
473L LYS* 5.9 1.9 - - - +
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Residues in contact with LEU 130 (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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55K VAL* 4.2 11.9 - - + -
63K VAL* 6.0 0.2 - - + -
66K SER* 3.7 30.3 - - - +
67K PHE 3.8 4.7 - - - +
68K LEU* 4.3 15.3 - - + +
128K ILE* 4.9 5.8 - - + -
129K SER* 1.3 72.6 - - - +
131K PHE* 1.3 67.0 + - - +
135K ILE* 4.0 19.9 - - + +
138K HIS* 3.4 6.2 - - - +
139K LEU* 2.9 48.9 + - + +
141K THR* 6.2 1.1 - - + -
187K ILE* 4.1 22.9 - - + -
189K ILE* 4.1 25.6 - - + -
197K PHE* 4.8 1.6 - - + -
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Residues in contact with PHE 131 (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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13K ALA* 4.0 13.9 - - + -
66K SER* 3.5 3.1 - - - -
67K PHE* 2.8 66.1 + + + +
69K GLU* 4.0 15.9 - - + -
129K SER* 3.6 27.8 - - - -
130K LEU* 1.3 75.9 - - - +
132K ALA* 1.3 61.4 - - - +
135K ILE* 4.2 6.1 - - - -
138K HIS* 3.2 44.0 - + + -
473L LYS* 3.6 24.7 - - + -
475L ILE* 3.4 32.8 - - + -
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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