Contacts of the helix formed by residues 129 - 139 (chain C) in PDB entry 1YF9
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 ASN 129 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C LEU* 4.2 9.7 - - - +
82C HIS 3.3 29.4 + - - +
83C PRO* 3.1 12.9 + - - +
85C VAL 3.6 7.4 + - - +
87C GLU* 3.4 33.0 + - + +
127C PRO* 3.8 4.2 - - - +
128C LEU* 1.3 76.8 - - - +
130C VAL* 1.3 60.3 + - - +
131C GLN* 3.1 15.7 + - - +
132C ALA* 2.9 29.3 + - - +
133C ALA 3.3 14.4 + - - -
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Residues in contact with VAL 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C PRO* 3.8 33.9 - - + +
128C LEU 3.7 3.4 + - - +
129C ASN* 1.3 69.4 + - - +
131C GLN* 1.3 66.1 + - + +
133C ALA* 3.4 1.1 + - - +
134C HIS* 3.0 46.3 + - + +
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Residues in contact with GLN 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C GLU* 3.8 20.6 + - - -
129C ASN* 3.1 6.6 + - - +
130C VAL* 1.3 78.0 - - + +
132C ALA* 1.3 63.2 + - - +
134C HIS* 3.2 6.3 + - - +
135C LEU* 3.0 35.6 + - + +
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Residues in contact with ALA 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU* 4.9 1.8 - - + -
82C HIS 4.0 3.6 - - - +
83C PRO* 3.8 19.1 - - + -
129C ASN* 2.9 33.2 + - - +
131C GLN* 1.3 75.9 - - - +
133C ALA* 1.3 63.2 + - - +
135C LEU* 3.5 1.2 + - - +
136C LEU* 3.0 26.9 + - - +
143C PHE* 3.8 30.8 - - + -
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Residues in contact with ALA 133 (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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83C PRO* 4.0 14.1 - - + +
127C PRO* 3.8 33.2 - - + -
129C ASN 3.3 3.6 + - - +
130C VAL 3.7 7.4 - - - +
131C GLN 3.2 0.4 - - - -
132C ALA* 1.3 80.4 - - - +
134C HIS* 1.3 67.1 + - + +
136C LEU* 3.6 3.2 + - - +
137C HIS* 3.1 38.0 + - + +
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Residues in contact with HIS 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C PRO* 5.9 0.7 - - + -
130C VAL* 3.0 47.9 + - + +
131C GLN* 3.2 4.9 + - - +
133C ALA* 1.3 79.9 - - + +
135C LEU* 1.3 61.0 + - + +
137C HIS* 3.3 4.4 + - - +
138C ALA* 2.9 31.5 + - - +
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Residues in contact with LEU 135 (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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131C GLN* 3.0 28.1 + - + +
132C ALA* 3.9 0.9 - - - +
134C HIS* 1.3 75.5 - - + +
136C LEU* 1.3 62.9 + - - +
138C ALA* 4.7 4.3 - - + -
139C ASP* 3.0 34.4 + - + +
143C PHE* 3.5 34.8 - - + -
146C LEU* 4.0 22.4 - - + -
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Residues in contact with LEU 136 (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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83C PRO* 4.4 6.7 - - + -
121C TYR* 4.0 29.4 + - + +
122C PRO* 3.3 37.7 - - + -
132C ALA 3.0 17.2 + - - +
133C ALA* 3.7 4.9 - - - +
135C LEU* 1.3 79.5 - - - +
137C HIS* 1.3 72.6 + - + +
140C ARG* 3.7 44.7 + - + +
143C PHE* 3.9 28.0 - - + -
144C ASP* 5.2 1.8 - - - +
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Residues in contact with HIS 137 (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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18A GLU* 4.0 19.0 + - - -
121C TYR* 3.7 22.8 + + - -
122C PRO* 5.9 1.3 - - + -
133C ALA* 3.1 30.3 + - + +
134C HIS* 4.3 2.9 - - - +
135C LEU 3.3 0.2 - - - -
136C LEU* 1.3 92.2 - - + +
138C ALA* 1.3 61.8 + - - +
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Residues in contact with ALA 138 (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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134C HIS 2.9 18.2 + - - +
135C LEU* 4.2 6.3 - - + +
137C HIS* 1.3 78.4 - - - +
139C ASP* 1.3 64.5 + - + +
140C ARG 4.2 0.4 - - - -
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Residues in contact with ASP 139 (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* 3.0 19.3 + - + +
138C ALA* 1.3 82.8 - - + +
140C ARG* 1.3 65.3 + - - +
141C VAL* 3.7 8.7 + - - +
142C GLY* 3.3 21.6 + - - -
143C PHE 3.0 17.5 + - - -
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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