Contacts of the helix formed by residues 123 - 131 (chain D) in PDB entry 2W93
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 THR 123 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D GLN* 6.1 0.4 - - - +
121D ASP* 2.6 19.7 + - - +
122D PHE* 1.3 83.8 - - + +
124D VAL* 1.3 58.7 + - - +
125D PHE 3.3 3.0 + - - -
126D HIS* 3.3 14.7 + - - +
127D ARG* 2.9 52.1 + - - +
138D MET* 6.2 0.4 - - - -
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Residues in contact with VAL 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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131C ASN* 3.9 34.5 - - + +
117D LEU* 4.1 17.5 - - + -
119D ASN* 6.1 0.4 - - - +
121D ASP* 3.6 31.8 + - + +
122D PHE 3.5 0.4 - - - -
123D THR* 1.3 78.1 + - - +
125D PHE* 1.3 87.2 + - + +
127D ARG* 3.3 21.0 + - - +
128D MET* 3.0 33.0 + - - +
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Residues in contact with PHE 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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132C ILE* 4.7 1.6 - - + -
412C TRP* 3.5 24.0 - + - -
74D PHE* 3.7 27.8 - + + -
75D GLY* 3.6 15.7 - - - -
78D GLU* 3.3 29.7 - - + +
79D LEU* 3.7 36.8 - - + +
115D HIS 3.6 18.4 - - - -
116D THR* 4.7 2.0 - - - -
117D LEU* 4.1 18.4 - - + -
121D ASP 5.3 0.4 - - - -
122D PHE 5.1 0.2 + - - -
123D THR 3.3 0.4 - - - -
124D VAL* 1.3 96.7 - - + +
126D HIS* 1.3 66.7 + - - +
128D MET* 3.1 13.5 + - - +
129D SER* 2.9 25.5 + - - -
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Residues in contact with HIS 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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74D PHE* 6.3 0.4 - - - -
122D PHE 5.2 1.5 + - - +
123D THR* 3.4 17.6 + - - +
125D PHE* 1.3 78.3 - - - +
127D ARG* 1.3 65.3 + - + +
129D SER* 3.2 3.1 + - - -
130D ALA* 3.0 21.9 + - + +
136D THR* 2.8 32.7 + - + +
137D ALA 4.6 0.6 + - - -
138D MET* 3.9 41.5 - - + +
164D TYR* 3.6 42.0 + + + +
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Residues in contact with ARG 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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131C ASN* 2.8 29.2 + - - +
121D ASP* 2.9 28.1 + - - -
123D THR* 2.9 31.7 + - - +
124D VAL* 3.5 21.7 - - - +
126D HIS* 1.3 81.2 - - + +
128D MET* 1.3 61.4 + - - +
130D ALA* 3.4 16.7 + - - +
131D ASN* 3.1 15.0 + - - -
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Residues in contact with MET 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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82C LEU* 3.9 24.9 - - + -
128C MET* 3.4 35.4 - - + +
131C ASN* 3.7 29.6 - - + +
132C ILE* 4.0 23.6 - - + -
79D LEU* 4.0 24.2 - - + -
82D LEU* 4.6 10.3 - - + -
124D VAL* 3.0 20.4 + - - +
125D PHE* 3.1 17.7 + - - +
127D ARG* 1.3 75.7 - - - +
129D SER* 1.3 60.6 + - - +
131D ASN* 3.1 28.0 + - - +
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Residues in contact with SER 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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78D GLU* 4.7 1.6 + - - -
82D LEU* 3.3 29.7 - - - +
85D ILE* 5.6 1.9 - - - +
97D HIS* 4.7 0.9 + - - -
125D PHE 2.9 10.8 + - - -
126D HIS 3.8 2.2 - - - -
128D MET* 1.3 73.4 - - - +
130D ALA* 1.3 60.2 + - - +
131D ASN 3.0 2.9 - - - -
132D ILE* 3.0 20.2 + - - +
133D SER* 2.7 24.7 + - - -
136D THR* 5.0 0.2 - - - -
164D TYR* 3.3 40.6 - - - -
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Residues in contact with ALA 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 HIS* 3.0 15.7 + - + +
127D ARG* 3.7 13.7 - - - +
128D MET 3.3 0.6 - - - -
129D SER* 1.3 75.7 - - - +
131D ASN* 1.3 61.2 - - - +
132D ILE 3.3 0.7 + - - -
133D SER* 3.5 15.9 + - - +
136D THR* 3.9 25.5 - - + +
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Residues in contact with ASN 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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117C LEU* 3.9 13.3 - - - +
124C VAL* 3.8 17.5 - - + +
127C ARG* 2.8 32.3 + - - +
128C MET* 3.6 23.1 - - + +
131C ASN* 5.2 3.0 - - - +
89D TYR* 5.2 3.6 - - - -
127D ARG 3.1 15.5 + - - -
128D MET* 3.1 24.1 + - - +
129D SER 3.0 0.4 - - - -
130D ALA* 1.3 79.0 - - - +
132D ILE* 1.3 60.7 + - - +
133D SER 3.6 0.7 - - - -
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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