Contacts of the helix formed by residues 122 - 132 (chain D) in PDB entry 2YIN
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 ASP 122 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118D ASP 4.2 3.6 + - - +
119D LEU* 2.6 37.5 + - + +
121D ASP* 1.3 70.5 - - - +
123D LYS* 1.3 62.7 + - - +
124D ASP* 3.7 15.8 + - - +
125D THR* 2.9 31.6 + - - +
126D ILE* 2.9 31.5 + - - +
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Residues in contact with LYS 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ASP 3.4 12.0 + - - +
122D ASP* 1.3 74.6 + - - +
124D ASP* 1.3 72.0 + - - +
126D ILE* 2.9 11.2 + - + +
127D GLU* 2.9 36.4 + - + +
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Residues in contact with ASP 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D ASP* 3.4 14.8 + - - +
123D LYS* 1.3 82.1 - - - +
125D THR* 1.3 63.6 + - - +
127D GLU* 3.4 16.3 + - - +
128D LYS* 3.2 40.0 + - - +
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Residues in contact with THR 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D VAL* 4.0 35.9 - - + +
119D LEU* 3.9 20.4 - - + +
122D ASP* 2.9 31.3 + - - +
124D ASP* 1.3 79.6 - - - +
126D ILE* 1.3 63.1 + - + +
128D LYS* 3.5 16.4 + - - +
129D LEU* 3.2 28.0 + - + +
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Residues in contact with ILE 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D LEU 4.4 2.0 - - - +
120D ARG 3.2 29.6 - - - +
121D ASP* 4.4 4.0 - - - -
122D ASP 2.9 20.8 + - - +
123D LYS* 3.5 10.8 - - + +
125D THR* 1.3 77.4 - - + +
127D GLU* 1.3 58.2 + - + +
129D LEU* 3.4 7.0 + - - +
130D LYS* 3.0 28.4 + - + +
134D LEU 4.8 0.2 - - - +
135D THR* 6.2 2.2 - - + -
136D PRO* 3.7 26.9 - - + -
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Residues in contact with GLU 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D LYS* 2.9 24.3 + - + +
124D ASP* 3.6 21.3 - - - +
126D ILE* 1.3 76.0 - - + +
128D LYS* 1.3 66.6 + - + +
130D LYS* 3.2 7.9 + - - +
131D GLU* 3.0 35.8 + - - +
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Residues in contact with LYS 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D ASP* 3.2 26.3 + - - +
125D THR* 4.0 17.5 + - - +
127D GLU* 1.3 79.0 - - + +
129D LEU* 1.3 63.9 + - + +
131D GLU* 3.5 18.5 + - - +
132D LYS* 3.1 32.0 + - - +
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Residues in contact with LEU 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D VAL* 3.6 30.7 - - + +
87D PRO* 4.6 4.7 - - + -
125D THR* 3.2 21.6 + - + +
126D ILE* 3.5 8.5 - - - +
127D GLU 3.2 0.4 - - - -
128D LYS* 1.3 80.6 - - + +
130D LYS* 1.3 55.3 + - - +
132D LYS* 3.1 10.3 + - + +
133D LYS 3.1 4.3 + - - -
134D LEU* 2.7 56.9 + - + +
135D THR* 3.9 4.5 - - - +
136D PRO* 3.6 44.6 - - + -
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Residues in contact with LYS 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D ILE* 3.0 18.2 + - + +
127D GLU* 3.2 7.8 + - - +
129D LEU* 1.3 72.4 - - - +
131D GLU* 1.3 58.1 + - + +
132D LYS 2.9 1.6 - - - -
133D LYS* 2.4 28.2 + - - +
134D LEU 3.3 8.5 + - - +
135D THR* 5.9 2.5 - - + -
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Residues in contact with GLU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1601A ARG* 3.4 21.3 + - - +
1604A GLU* 6.1 0.9 - - - -
1608A ASN* 4.3 16.1 + - - +
1612A LYS* 4.8 6.0 + - - -
67C LEU* 3.4 18.3 - - - +
127D GLU* 3.0 28.6 + - + +
128D LYS* 3.6 20.4 - - - +
129D LEU 3.3 0.2 - - - -
130D LYS* 1.3 75.6 - - - +
132D LYS* 1.3 62.8 + - + +
133D LYS* 3.4 1.6 + - - +
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Residues in contact with LYS 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ASP* 2.5 59.2 + - + +
64C TYR* 4.4 21.7 + - + -
66C ARG* 3.4 16.8 - - - +
67C LEU* 3.7 15.2 - - + +
128D LYS* 3.1 20.6 - - - +
129D LEU* 3.1 9.4 + - + +
130D LYS 2.9 1.2 - - - -
131D GLU* 1.3 79.9 - - + +
133D LYS* 1.3 70.6 + - - +
134D LEU* 3.3 19.1 + - + +
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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