Contacts of the strand formed by residues 130 - 139 (chain D) in PDB entry 4A12
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 130 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105C LYS* 3.5 21.1 - - - +
106C THR* 3.9 17.9 - - + -
128D GLN* 4.3 0.5 - - - +
129D PRO* 1.3 73.7 - - - +
131D VAL* 1.3 63.5 + - - +
132D LEU* 4.4 7.9 - - + -
185D PHE* 3.8 6.1 - - - +
186D TYR* 3.4 6.8 - - - +
187D ASP* 3.0 59.6 + - - +
189D ARG 4.0 11.1 + - - +
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Residues in contact with VAL 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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103C PHE* 4.2 14.2 - - - -
123D VAL* 4.3 23.0 - - + +
126D ILE* 3.7 48.5 - - + +
128D GLN* 3.7 17.7 - - + +
129D PRO 4.2 0.8 + - - -
130D THR* 1.3 77.4 - - - +
132D LEU* 1.3 73.1 + - - +
184D MSE 3.7 29.8 - - + -
185D PHE 3.4 8.7 - - - +
186D TYR* 5.0 0.7 - - + -
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Residues in contact with LEU 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C PHE* 4.3 20.2 - - + -
106C THR* 5.2 3.4 - - + +
108C ILE* 4.2 29.8 - - + -
109C ALA 5.4 0.7 - - - +
143C LYS* 4.1 35.4 - - + +
123D VAL* 6.2 0.4 - - - -
130D THR* 5.3 6.3 - - + -
131D VAL* 1.3 83.3 - - - +
133D THR* 1.3 61.8 + - - +
134D HIS* 3.5 10.7 + - + +
184D MSE 3.6 6.0 - - - -
185D PHE* 2.7 65.6 + - + +
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Residues in contact with THR 133 (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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111C GLY* 4.4 8.0 + - - +
140C PHE* 3.3 41.4 - - + +
115D PHE* 5.1 0.4 - - + -
119D ASN* 2.7 34.4 + - - +
123D VAL* 4.8 1.2 - - - +
132D LEU* 1.3 72.5 - - - +
134D HIS* 1.3 65.5 + - - +
135D GLU 3.9 14.8 - - - +
136D SER* 4.7 1.1 - - - -
182D PHE* 4.0 9.4 - - + -
183D LYS 3.9 2.9 - - - -
184D MSE 3.4 26.5 - - - +
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Residues in contact with HIS 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C GLN* 4.5 0.2 - - - +
140C PHE* 2.8 46.9 + - + +
143C LYS* 6.1 3.6 - - - +
132D LEU* 3.5 11.5 + - + +
133D THR* 1.3 80.4 - - - +
135D GLU* 1.3 62.7 + - + +
163D HIS* 3.1 26.7 + + + +
183D LYS* 2.8 23.8 + - + +
185D PHE* 3.4 41.7 - + + +
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Residues in contact with GLU 135 (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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138C ILE 3.5 7.0 - - - +
139C GLN* 3.7 35.7 + - + -
140C PHE* 4.6 1.8 - - - -
133D THR* 3.9 6.5 - - - +
134D HIS* 1.3 83.3 - - + +
136D SER* 1.3 64.7 + - - +
182D PHE* 3.7 1.0 - - - -
183D LYS* 2.9 65.8 + - + +
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Residues in contact with SER 136 (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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136C SER 4.0 0.7 - - - +
137C SER* 3.6 2.6 + - - -
138C ILE* 2.8 55.7 + - - +
115D PHE* 3.4 16.7 - - - -
133D THR* 4.7 2.5 - - - -
135D GLU* 1.3 77.0 - - - +
137D SER* 1.3 57.8 + - - +
138D ILE* 3.4 9.3 - - - +
181D ASN 3.0 16.8 + - - -
182D PHE* 3.4 21.8 - - - -
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Residues in contact with SER 137 (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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136C SER 3.5 6.5 + - - -
137C SER* 4.4 12.5 + - - +
136D SER* 1.3 71.9 - - - +
138D ILE* 1.3 60.8 + - - +
139D GLN* 5.7 2.2 - - - +
179D LYS 4.2 0.3 - - - +
180D GLY* 3.4 1.4 - - - -
181D ASN* 2.8 46.8 + - - +
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Residues in contact with ILE 138 (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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115C PHE* 3.6 32.3 - - + -
135C GLU* 3.6 3.3 - - - +
136C SER* 2.8 46.6 + - - +
138C ILE* 6.0 1.3 - - + -
115D PHE* 3.7 20.6 - - + -
136D SER* 3.4 23.6 - - - +
137D SER* 1.3 75.2 + - - +
139D GLN* 1.3 68.8 + - - +
140D PHE* 3.6 25.4 - - + -
178D PHE* 3.5 25.8 - - + -
179D LYS 3.4 3.6 - - - -
180D GLY* 3.9 6.7 - - - -
182D PHE* 4.3 2.0 - - + -
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Residues in contact with GLN 139 (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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134C HIS 3.8 5.6 - - - +
135C GLU* 3.7 27.3 + - + -
137D SER* 5.7 2.0 - - - +
138D ILE* 1.3 80.7 - - - +
140D PHE* 1.3 63.0 + - - +
141D ILE* 3.6 16.7 + - + +
178D PHE* 3.3 9.6 - - - -
179D LYS* 2.7 70.5 + - + +
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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