Contacts of the strand formed by residues 138 - 143 (chain C) in PDB entry 1YCH
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 SER 138 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C SER* 4.8 7.5 + - - -
132C VAL 3.1 17.5 - - - -
133C SER* 3.9 9.0 - - - -
134C LEU* 4.1 4.0 - - - +
137C ARG* 1.3 74.9 - - - +
139C LEU* 1.3 67.5 + - - +
140C THR* 4.2 0.6 - - - +
157C VAL* 3.6 23.2 - - - +
158C PRO* 3.6 8.4 - - - +
159C GLU* 2.9 29.8 + - - +
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Residues in contact with LEU 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ILE* 3.6 29.8 - - + -
48C ALA* 4.2 15.0 - - + -
50C VAL* 5.1 1.8 - - + -
78C VAL* 3.7 29.6 - - + -
103C LEU* 4.1 11.9 - - + -
131C SER* 3.4 2.4 - - - -
132C VAL* 2.9 33.0 + - + +
134C LEU* 3.6 26.9 - - + -
138C SER* 1.3 73.2 - - - +
140C THR* 1.3 60.9 + - - +
141C PHE* 3.6 19.3 - - + -
155C THR* 4.3 10.5 - - + -
156C TYR 3.5 4.3 - - - -
157C VAL* 3.9 9.9 - - + -
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Residues in contact with THR 140 (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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129C GLY* 4.3 8.3 + - - -
130C THR 3.5 9.8 + - - -
131C SER* 3.7 15.3 - - - -
138C SER* 6.0 0.4 - - - -
139C LEU* 1.3 74.4 - - - +
141C PHE* 1.3 69.7 + - - +
142C ILE* 5.6 1.0 - - - +
155C THR* 3.6 3.6 - - - +
156C TYR* 2.8 56.8 + - + +
158C PRO* 3.5 26.7 - - + -
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Residues in contact with PHE 141 (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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78C VAL* 4.2 8.3 - - + -
103C LEU* 3.9 30.5 - - + -
126C VAL* 3.3 42.2 - - + -
127C LYS 4.3 1.1 - - - +
128C THR* 4.0 1.3 - - - +
129C GLY* 2.9 27.2 + - - -
130C THR* 3.2 15.3 + - - +
131C SER* 4.8 0.2 - - - -
132C VAL* 4.6 8.7 - - + -
139C LEU* 3.6 28.3 - - + -
140C THR* 1.3 78.9 + - - +
142C ILE* 1.3 69.8 + - - +
143C GLU* 6.3 0.2 - - + -
153C MET* 3.6 31.0 - - + -
154C PHE 3.6 3.4 - - - +
155C THR* 3.8 28.3 - - + -
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Residues in contact with ILE 142 (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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128C THR* 3.8 7.9 - - + -
140C THR* 5.4 1.8 - - + +
141C PHE* 1.3 81.4 - - - +
143C GLU* 1.3 71.8 + - - +
153C MET* 3.3 3.0 - - - -
154C PHE* 2.7 57.0 + - + +
156C TYR* 4.8 12.6 - - + -
163C LEU* 4.9 3.1 - - + -
210C LYS* 4.4 13.2 - - + -
213C GLU* 3.7 24.2 - - - +
214C ILE* 4.7 11.7 - - + -
217C ILE* 6.0 5.8 - - + -
219C LEU* 3.7 30.5 - - + -
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Residues in contact with GLU 143 (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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105C THR* 4.3 23.0 - - + -
126C VAL* 4.2 2.6 - - + +
127C LYS* 3.2 37.3 + - - +
128C THR* 2.6 45.7 + - - +
141C PHE* 6.3 0.2 - - + -
142C ILE* 1.3 76.6 - - - +
144C ALA* 1.3 59.7 + - - +
145C PRO* 3.5 16.5 - - + +
152C SER 4.8 1.1 - - - +
153C MET* 3.9 6.3 - - + -
210C LYS* 2.9 23.9 + - - -
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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