Contacts of the strand formed by residues 153 - 157 (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 MET 153 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78C VAL* 3.8 7.2 - - + -
79C VAL 3.8 15.0 - - - +
80C ASN* 3.0 49.5 + - - +
103C LEU 3.9 9.9 - - - +
104C CYS* 4.3 1.6 - - - -
105C THR* 3.5 30.7 - - + -
126C VAL* 4.5 6.1 - - - -
141C PHE* 3.6 42.2 - - + -
142C ILE 3.3 13.7 - - - +
143C GLU* 3.9 5.2 - - - -
144C ALA* 3.7 6.3 - - - +
152C SER* 1.3 78.6 - - - +
154C PHE* 1.3 67.7 + - - +
165C PRO 4.3 4.7 - - - +
166C ASN* 4.5 1.4 - - - +
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Residues in contact with PHE 154 (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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80C ASN* 4.1 0.6 + - - -
141C PHE* 3.6 7.6 - - - +
142C ILE* 2.7 47.2 + - + +
144C ALA* 3.6 21.5 - - + -
147C LEU* 4.3 18.2 - - + -
152C SER* 5.9 0.9 - - - -
153C MET* 1.3 80.6 - - - +
155C THR* 1.3 64.3 + - - +
163C LEU* 3.9 22.7 - - + -
164C LEU 3.7 4.5 - - - -
165C PRO* 3.6 33.9 - - + -
168C ALA* 4.1 19.3 - - + -
169C PHE* 5.0 7.2 - + - -
207C ILE* 6.4 0.2 - - + -
210C LYS* 3.9 23.8 - - + -
214C ILE* 4.3 18.2 - - + -
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Residues in contact with THR 155 (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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50C VAL* 4.8 6.3 - - + -
78C VAL* 3.5 11.7 - - + +
80C ASN* 2.9 24.4 + - - -
139C LEU* 4.3 23.1 - - + -
140C THR 3.6 8.1 - - - +
141C PHE* 3.8 15.4 - - + -
154C PHE* 1.3 71.5 - - - +
156C TYR* 1.3 65.9 + - - +
157C VAL* 4.9 0.4 - - + -
162C LEU 4.0 0.3 - - - +
163C LEU* 3.5 4.0 - - - +
164C LEU* 2.8 60.5 + - + +
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Residues in contact with TYR 156 (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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139C LEU* 3.5 2.4 - - - -
140C THR* 2.8 59.1 + - + +
142C ILE* 4.8 11.9 - - + -
155C THR* 1.3 75.2 - - - +
157C VAL* 1.3 61.6 + - - +
158C PRO* 3.3 25.6 + - + +
161C ALA* 3.5 19.0 - - - +
162C LEU 3.3 19.3 - - - -
163C LEU* 4.1 16.2 - - + -
219C LEU* 3.1 36.3 - - + -
220C ALA* 2.4 42.2 + - - +
221C ILE* 4.7 5.2 - - + -
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Residues in contact with VAL 157 (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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11C ILE* 4.7 4.9 - - + -
42C ILE* 3.9 27.4 - - + -
137C ARG* 4.0 24.5 - - + -
138C SER 3.6 17.9 - - - +
139C LEU* 3.9 7.9 - - + -
155C THR* 4.9 0.9 - - + -
156C TYR* 1.3 76.8 - - - +
158C PRO* 1.4 54.1 - - - +
159C GLU* 4.0 7.6 - - - +
160C GLU* 2.9 33.0 + - + +
161C ALA 2.9 11.3 + - - -
162C LEU* 3.0 28.6 + - + +
164C LEU* 4.9 7.0 - - + -
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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