Contacts of the strand formed by residues 126 - 131 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51I LEU* 3.6 30.3 - - + -
70I VAL* 4.1 26.0 - - + -
71I TRP 3.9 3.6 - - - -
72I GLN* 3.0 37.0 - - + +
106I LEU* 5.1 0.9 - - + -
108I THR* 4.2 4.3 - - + -
111I PRO* 4.1 9.4 - - + -
125I HIS* 1.3 80.3 - - - +
127I ASN* 1.3 63.0 + - - +
128I ILE* 3.9 9.9 + - + +
142I ARG* 3.3 4.5 - - - -
143I LEU* 2.9 42.0 + - + +
145I PHE* 4.2 17.9 - - + -
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Residues in contact with ASN 127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69I GLU 3.8 0.2 - - - +
70I VAL* 3.1 7.3 - - - +
71I TRP* 2.9 52.5 + - + +
72I GLN* 4.7 0.2 - - - +
79I TYR* 3.1 24.7 + - - -
125I HIS* 3.7 7.2 - - - -
126I ILE* 1.3 72.9 - - - +
128I ILE* 1.3 61.2 + - - +
141I THR 3.8 5.8 - - - +
142I ARG* 3.6 24.5 + - - +
344J SER* 3.5 20.2 + - - +
345J GLU* 4.0 4.7 - - - +
470J ILE* 4.1 20.4 - - + +
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Residues in contact with ILE 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I LEU* 4.0 28.3 - - + -
69I GLU 3.3 8.3 - - - +
70I VAL* 4.0 15.7 - - + -
104I TRP* 5.0 4.9 - - + -
106I LEU* 6.4 0.2 - - + -
126I ILE* 4.1 11.0 - - + +
127I ASN* 1.3 80.8 - - - +
129I SER* 1.4 71.3 + - - +
130I LEU* 4.8 2.0 - - + +
139I LEU 3.6 0.3 - - - +
140I HIS* 3.3 5.6 + - - +
141I THR* 2.8 52.3 + - + +
143I LEU* 4.0 19.1 - - + +
185I PHE* 3.9 30.1 - - + -
187I ILE* 4.8 4.9 - - + -
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Residues in contact with SER 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67I PHE 4.0 0.3 - - - +
68I LEU* 3.3 6.6 - - - +
69I GLU* 2.9 38.4 + - - +
128I ILE* 1.4 76.2 - - - +
130I LEU* 1.3 62.6 + - - +
131I PHE* 3.8 21.1 - - - -
138I HIS* 3.9 13.7 + - - -
139I LEU 3.2 4.5 - - - -
140I HIS* 3.4 23.0 + - - -
470J ILE* 5.2 12.1 + - - +
473J LYS* 5.8 2.8 - - - +
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Residues in contact with LEU 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I VAL* 4.3 16.2 - - + -
66I SER* 3.6 31.0 - - - -
67I PHE 3.7 6.3 - - - +
68I LEU* 4.1 17.0 - - + +
128I ILE* 5.1 4.9 - - + -
129I SER* 1.3 77.1 - - - +
131I PHE* 1.3 65.8 + - - +
135I ILE* 4.1 22.7 - - + +
138I HIS* 3.4 5.2 - - - +
139I LEU* 2.7 49.0 + - + +
141I THR* 6.1 1.1 - - + -
187I ILE* 4.1 29.6 - - + -
189I ILE* 4.5 6.3 - - + -
197I PHE* 4.8 2.9 - - + -
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Residues in contact with PHE 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I GLN 6.1 0.4 - - - -
13I ALA* 4.1 14.8 - - + -
66I SER* 3.4 2.4 - - - -
67I PHE* 2.9 59.9 + + + +
69I GLU* 4.2 16.8 - - + -
129I SER* 3.8 23.3 - - - -
130I LEU* 1.3 74.2 - - - +
132I ALA* 1.4 66.6 + - - +
135I ILE* 4.4 8.5 - - - -
138I HIS* 3.2 47.1 - + + -
473J LYS* 3.8 22.9 - - + -
475J ILE* 3.6 36.1 - - + -
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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