Contacts of the strand formed by residues 128 - 132 (chain C) in PDB entry 1Y8Q
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 ALA 128 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C ARG 3.6 1.8 + - - -
39C VAL* 3.5 18.0 - - + -
40C LEU 3.0 23.6 + - - -
126C PHE* 3.5 3.9 - - - +
127C ASP* 1.3 83.3 - - - +
129C VAL* 1.3 66.2 + - - +
151C ILE* 4.0 0.7 - - - -
152C LYS* 3.2 17.9 - - + +
154C PHE* 4.5 11.9 - - + -
314C ILE* 4.5 4.5 - - + -
318C LEU* 4.0 20.2 - - + -
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Residues in contact with VAL 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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40C LEU* 3.5 28.9 - - + -
123C PHE* 4.1 13.9 - - + -
126C PHE* 4.4 7.2 - - + -
128C ALA* 1.3 79.9 - - - +
130C CYS* 1.3 65.1 + - - +
131C LEU* 3.5 25.1 - - + -
142C VAL* 3.8 13.7 - - + -
146C CYS* 3.8 25.8 - - - -
151C ILE* 4.0 8.7 - - + -
152C LYS 2.9 6.8 + - - +
153C PHE* 3.6 2.7 - - + -
154C PHE* 2.9 30.3 + - - +
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Residues in contact with CYS 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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39C VAL* 5.0 3.4 - - + -
40C LEU 2.8 14.0 + - - +
41C LEU* 3.5 21.7 - - + +
42C VAL* 2.8 26.7 + - - +
51C ILE* 4.2 6.7 - - + -
129C VAL* 1.3 76.7 - - - +
131C LEU* 1.3 69.1 + - - +
154C PHE* 3.3 9.2 - - + -
310C LEU* 3.8 29.2 - - - -
314C ILE* 3.9 27.4 - - + -
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Residues in contact with LEU 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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42C VAL* 4.0 13.7 - - + -
115C ILE* 5.4 1.1 - - + -
129C VAL* 3.5 28.0 - - + -
130C CYS* 1.3 77.2 - - - +
132C THR* 1.3 63.5 + - - +
134C CYS* 3.8 18.6 - - + -
138C VAL* 4.1 5.8 - - + +
139C ILE* 3.6 35.0 - - + +
142C VAL* 3.9 20.9 - - + -
153C PHE* 3.7 19.1 - - + -
154C PHE 2.9 10.4 + - - +
155C THR* 3.3 14.6 - - - +
156C GLY 3.0 27.4 + - - +
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Residues in contact with THR 132 (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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41C LEU* 4.8 2.6 - - - +
42C VAL* 2.8 27.0 + - - +
43C GLY* 3.4 21.1 - - - +
45C LYS* 5.1 1.3 - - + +
47C LEU* 3.7 21.4 - - + +
48C GLY* 4.2 10.1 + - - +
51C ILE* 4.2 10.4 - - - +
131C LEU* 1.3 77.0 + - - +
133C CYS* 1.3 89.9 + - - +
134C CYS* 3.1 11.7 + - - -
156C GLY 3.6 12.9 + - - -
157C ASP* 4.5 1.6 - - - +
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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