Contacts of the strand formed by residues 126 - 131 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ILE* 5.4 0.4 - - + -
51C LEU* 3.6 29.8 - - + -
70C VAL* 4.0 26.2 - - + -
71C TRP 4.0 6.5 - - - +
72C GLN* 3.3 34.3 - - + +
106C LEU* 5.5 0.9 - - + -
108C THR* 4.6 2.5 - - + -
111C PRO* 4.3 4.3 - - + -
125C HIS* 1.3 81.4 - - - +
127C ASN* 1.3 64.8 + - - +
128C ILE* 3.6 10.4 + - + +
142C ARG* 3.5 4.7 - - - -
143C LEU* 2.9 46.7 + - + -
145C PHE* 4.2 16.8 - - + -
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Residues in contact with ASN 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C GLU 3.8 0.2 - - - +
70C VAL* 3.1 7.1 - - - +
71C TRP* 2.8 55.7 + - + +
72C GLN* 4.6 0.8 - - - +
79C TYR* 3.0 26.7 + - - -
125C HIS* 3.5 18.5 + - - -
126C ILE* 1.3 70.4 - - - +
128C ILE* 1.3 61.0 + - - +
141C THR 3.9 5.1 - - - +
142C ARG* 3.6 12.0 + - - +
344D SER* 3.6 22.9 + - - +
345D GLU* 4.2 3.8 - - - +
470D ILE* 3.8 22.3 - - + +
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Residues in contact with ILE 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU* 4.5 18.4 - - + -
69C GLU 3.5 4.7 - - - +
70C VAL* 4.1 15.5 - - + -
104C TRP* 5.0 8.3 - - + -
126C ILE* 3.9 10.8 - - + +
127C ASN* 1.3 80.3 - - - +
129C SER* 1.3 74.0 + - - +
130C LEU* 4.6 2.2 - - + +
139C LEU 3.7 0.2 - - - +
140C HIS* 3.4 5.5 + - - +
141C THR* 2.9 52.4 + - + +
143C LEU* 3.8 33.0 - - + +
185C PHE* 3.8 20.0 - - + -
187C ILE* 4.8 4.9 - - + -
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Residues in contact with SER 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C PHE 3.9 0.3 - - - +
68C LEU* 3.3 7.8 - - - +
69C GLU* 2.8 42.3 + - - -
128C ILE* 1.3 74.1 - - - +
130C LEU* 1.3 60.2 + - - +
131C PHE* 3.8 22.5 - - - -
138C HIS* 4.0 9.7 - - - -
139C LEU 3.4 4.9 - - - -
140C HIS* 3.4 25.1 + - - -
470D ILE* 5.2 11.1 + - - +
473D LYS* 5.8 2.7 - - - +
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Residues in contact with LEU 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C VAL* 4.4 11.7 - - + -
66C SER* 3.8 27.8 - - - +
67C PHE 3.8 1.1 - - - -
68C LEU* 4.0 20.2 - - + +
128C ILE* 4.2 2.9 - - + -
129C SER* 1.3 73.5 - - - +
131C PHE* 1.4 63.3 + - - +
135C ILE* 4.1 24.1 - - + +
138C HIS* 3.2 7.4 - - - +
139C LEU* 2.9 49.4 + - + +
141C THR* 5.9 0.7 - - + -
187C ILE* 4.2 34.3 - - + -
189C ILE* 4.2 12.6 - - + -
197C PHE* 4.7 2.5 - - + -
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Residues in contact with PHE 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ALA* 4.1 13.7 - - + +
66C SER* 3.5 3.6 - - - -
67C PHE* 3.0 64.3 + + + -
69C GLU* 4.0 16.4 - - - -
129C SER* 3.8 24.7 - - - -
130C LEU* 1.4 73.5 - - - +
132C ALA* 1.4 66.5 + - - +
135C ILE* 4.6 6.3 - - - -
138C HIS* 3.2 48.2 - + + -
473D LYS* 3.8 22.0 - - + -
475D ILE* 3.6 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