Contacts of the strand formed by residues 129 - 131 (chain B) in PDB entry 1YK1
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 LEU 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B ALA* 6.3 0.2 - - + -
99B ALA* 4.7 11.2 - - + +
109B MET* 3.5 45.3 - - + +
111B SER* 4.9 7.0 - - - -
114B ALA* 4.5 7.4 - - + -
119B PHE* 3.9 41.5 - - + +
122B LYS* 2.9 26.6 + - - -
126B TYR* 2.9 20.8 + - + +
127B SER 3.4 2.0 + - - -
128B HIS* 1.3 77.2 - - - +
130B THR* 1.3 69.0 + - - +
131B ARG* 4.2 18.2 - - + -
348B TRP* 3.7 7.8 - - - -
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Residues in contact with THR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B MET 3.1 5.5 + - - +
110B LEU* 2.8 28.4 - - - +
111B SER 3.3 22.7 + - - +
129B LEU* 1.3 77.2 - - - +
131B ARG* 1.3 63.8 + - - +
132B VAL* 3.8 2.0 + - - +
322B LEU* 4.4 7.1 - - - +
344B ILE* 3.6 17.3 - - + -
347B THR* 3.1 22.3 + - - +
348B TRP* 2.8 32.3 - - - +
361B ILE* 5.8 2.9 - - - -
365B GLY* 3.4 7.6 - - - -
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Residues in contact with ARG 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B SER* 3.5 7.2 - - - +
113B GLY 4.0 10.1 - - - +
114B ALA* 2.6 39.2 + - + -
115B LEU* 3.6 7.3 - - + +
116B ALA 2.9 24.5 + - - -
117B ALA* 5.5 0.2 - - - +
119B PHE* 3.7 14.8 + - - +
120B GLN* 4.0 21.2 - - - +
122B LYS* 4.5 1.3 - - - +
129B LEU* 4.2 23.1 - - + -
130B THR* 1.3 74.5 - - - +
132B VAL* 1.3 60.3 + - - +
133B ALA 3.2 10.9 + - - +
135B ALA* 3.8 19.1 - - + +
137B ALA* 6.1 1.4 - - - +
361B ILE* 4.9 3.0 - - - +
365B GLY 2.8 10.9 + - - +
366B ASP* 3.0 39.3 + - + +
367B ARG* 3.0 28.4 + - - +
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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
------------------------------------------------------------
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