Contacts of the strand formed by residues 38 - 42 (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 ARG 38 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ALA 5.0 1.1 - - - +
37C SER* 1.3 76.3 - - - +
39C VAL* 1.3 63.7 + - - +
61C LYS* 4.2 23.8 - - + +
62C GLY* 3.3 17.5 - - - +
64C THR* 3.9 18.8 + - - -
107C ASP* 5.6 3.5 + - - -
109C LYS* 3.8 30.9 - - - +
125C GLN* 3.2 55.2 + - - +
126C PHE* 4.2 7.9 - - + -
127C ASP* 2.8 34.8 + - - +
128C ALA 3.6 4.3 + - - -
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Residues in contact with VAL 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ARG* 1.3 79.5 - - - +
40C LEU* 1.3 75.9 + - - +
41C LEU* 5.1 0.7 - - + -
55C LEU* 3.9 23.8 - - + -
60C VAL* 4.5 10.8 - - + -
62C GLY 2.9 9.3 + - - +
63C LEU* 3.3 14.3 - - + +
64C THR 2.8 25.5 + - - -
126C PHE* 3.7 6.6 - - - -
128C ALA* 3.5 20.6 - - + +
130C CYS* 5.0 6.5 - - + -
314C ILE* 4.4 7.6 - - + -
318C LEU* 3.8 28.5 - - + -
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Residues in contact with LEU 40 (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* 1.3 80.5 - - - +
41C LEU* 1.3 81.2 + - - +
42C VAL* 4.0 12.6 - - + -
64C THR* 3.4 17.7 - - + +
66C LEU* 4.1 17.7 - - + -
115C ILE* 4.5 1.3 - - + -
122C PHE* 4.2 10.3 - - + -
123C PHE* 4.1 23.8 - - + -
126C PHE* 3.5 32.3 - - + -
128C ALA 3.0 9.2 + - - +
129C VAL* 3.8 25.1 - - + -
130C CYS* 2.8 28.1 + - - -
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Residues in contact with LEU 41 (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* 4.1 1.1 + - + -
40C LEU* 1.3 74.5 - - - +
42C VAL* 1.3 68.6 + - - +
43C GLY 4.1 5.5 + - - +
44C LEU* 4.3 10.9 - - + +
48C GLY* 3.2 32.8 - - - +
51C ILE* 4.2 19.3 - - + -
52C ALA* 3.7 25.8 - - + +
55C LEU* 6.0 0.2 - - + -
63C LEU* 3.9 18.4 - - + -
64C THR 2.8 11.7 + - - +
65C MET* 3.6 2.4 - - + -
66C LEU 2.9 25.8 + - - +
130C CYS* 3.5 31.2 - - + +
132C THR* 4.8 1.8 - - - +
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Residues in contact with VAL 42 (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* 4.0 16.6 - - + -
41C LEU* 1.3 77.4 - - - +
43C GLY* 1.3 65.2 + - - +
66C LEU* 3.5 20.4 - - + +
67C ASP* 5.9 0.2 - - - -
115C ILE* 4.0 30.7 - - + -
130C CYS 2.8 14.8 + - - +
131C LEU* 3.9 22.8 - - + -
132C THR* 2.8 33.2 + - - +
134C CYS* 3.8 24.9 - - - -
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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