Contacts of the helix formed by residues 143 - 150 (chain C) in PDB entry 1YAA
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 HIS 143 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112C LEU* 4.1 12.9 - - + +
135C LEU* 4.3 14.6 - - + +
139C THR* 2.8 32.6 + - + +
140C TRP* 3.0 34.9 + + + +
142C ASN* 1.3 77.9 - - - +
144C MET* 1.3 61.3 - - - +
146C ILE* 3.4 7.1 + - + +
147C PHE* 3.0 34.9 - + - -
187C VAL* 4.0 22.6 - - + +
189C HIS* 3.7 19.5 - + - -
222C ASP* 2.8 32.0 + - - -
907C PLP 3.9 0.2 + - - -
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Residues in contact with MET 144 (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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135C LEU* 4.0 22.6 - - + +
139C THR* 5.5 1.1 - - + +
140C TRP 4.6 0.6 + - - -
141C ALA 4.5 7.0 + - - +
142C ASN 3.3 0.4 - - - -
143C HIS* 1.3 78.9 - - - +
145C ALA* 1.3 63.5 + - - +
146C ILE 3.2 0.3 + - - -
147C PHE* 3.2 4.5 + - - +
148C GLU* 3.0 51.4 + - + +
154C THR* 3.4 22.2 - - - +
155C ALA 5.5 2.9 - - - +
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Residues in contact with ALA 145 (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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141C ALA 5.0 1.9 + - - +
142C ASN* 3.3 23.5 + - - +
144C MET* 1.3 77.6 - - - +
146C ILE* 1.3 56.6 + - - +
148C GLU* 4.6 5.2 - - - +
149C ASN* 2.9 31.8 + - - +
289D LYS* 3.4 35.9 - - - +
293D SER* 3.6 9.5 - - - -
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Residues in contact with ILE 146 (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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109C THR* 3.9 14.8 - - + -
112C LEU* 3.8 46.2 - - + +
113C HIS* 4.0 8.3 - - + +
116C ALA* 3.8 10.9 - - + +
140C TRP* 3.8 29.2 - - + -
142C ASN* 3.1 24.7 - - - +
143C HIS* 3.6 7.2 - - - +
144C MET 3.2 0.8 - - - -
145C ALA* 1.3 79.1 - - - +
147C PHE* 1.3 68.1 + - + +
149C ASN* 3.5 12.0 - - - +
150C GLN* 3.8 3.8 + - - +
293D SER 3.8 22.3 - - - +
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Residues in contact with PHE 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C LEU* 4.4 20.0 - - + -
115C SER* 5.0 0.7 - - - -
116C ALA* 3.9 25.1 - - + -
119C PHE* 5.1 4.0 - + - -
133C VAL* 3.7 23.3 - - + -
135C LEU* 4.3 9.2 - - + -
143C HIS* 3.0 38.1 - + - -
144C MET* 3.2 2.9 + - - +
146C ILE* 1.3 79.7 - - + +
148C GLU* 1.3 61.3 + - - +
150C GLN* 3.2 10.2 + - - +
152C LEU* 3.2 41.5 + - + +
154C THR* 4.0 18.8 - - + -
185C ILE* 5.6 0.2 - - + -
187C VAL* 3.8 27.6 - - + -
220C LEU* 4.4 18.2 - - + -
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Residues in contact with GLU 148 (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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144C MET* 3.0 42.5 + - + +
145C ALA* 4.4 4.7 - - - +
147C PHE* 1.3 72.5 - - - +
149C ASN* 1.3 61.1 + - - +
150C GLN 2.9 5.8 - - - -
151C GLY* 3.0 13.4 + - - +
152C LEU 3.7 18.8 - - - +
153C LYS* 5.6 0.5 - - - -
154C THR* 3.3 23.2 + - + -
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Residues in contact with ASN 149 (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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113C HIS* 4.2 1.0 + - - -
145C ALA 2.9 21.0 + - - +
146C ILE 3.5 7.6 - - - +
147C PHE 3.2 0.4 - - - -
148C GLU* 1.3 76.6 - - - +
150C GLN* 1.3 81.5 + - - +
151C GLY 3.9 0.2 + - - -
117D LYS* 2.9 44.4 + - - +
121D LYS* 3.7 13.6 + - - +
289D LYS* 6.1 0.2 - - - +
290D ILE* 4.9 1.9 - - - -
293D SER* 3.4 20.3 + - - +
294D GLU* 3.2 32.7 + - - +
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Residues in contact with GLN 150 (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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113C HIS* 3.2 23.5 + - + -
116C ALA* 3.4 44.0 - - + +
117C LYS* 3.3 30.9 + - - +
120C SER* 3.3 24.0 + - - -
146C ILE 3.8 3.6 - - - +
147C PHE 3.2 9.3 + - - +
148C GLU 2.9 0.8 - - - -
149C ASN* 1.3 114.7 + - - +
151C GLY* 1.3 58.9 + - - +
152C LEU* 3.4 1.6 - - + -
294C GLU* 5.5 0.2 + - - -
117D LYS* 4.2 7.0 + - - +
294D GLU* 4.3 1.4 + - - -
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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
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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