Contacts of the strand formed by residues 130 - 139 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128C GLN* 4.3 0.7 - - - +
129C PRO* 1.3 77.3 - - - +
131C VAL* 1.3 63.0 + - - +
132C LEU* 4.3 7.9 - - + -
185C PHE* 3.8 7.1 - - - +
186C TYR* 3.4 6.8 - - - +
187C ASP* 3.0 54.8 + - - +
190C GLY 3.2 19.8 + - - +
105D LYS* 6.0 0.4 - - - +
106D THR* 4.2 24.0 - - + -
108D ILE* 6.4 0.4 - - + -
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Residues in contact with VAL 131 (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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123C VAL* 4.3 25.0 - - + +
126C ILE* 3.7 45.3 - - + +
128C GLN* 3.7 20.4 - - + +
129C PRO 4.2 1.4 + - - +
130C THR* 1.3 77.7 - - - +
132C LEU* 1.3 74.1 + - - +
184C MSE 3.7 29.2 - - + -
185C PHE 3.4 7.9 - - - +
186C TYR* 5.0 0.7 - - + -
103D PHE* 4.5 10.4 - - - -
105D LYS* 6.1 1.8 - - - +
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Residues in contact with LEU 132 (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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123C VAL* 6.3 0.2 - - - -
130C THR* 5.3 6.5 - - + -
131C VAL* 1.3 83.4 - - - +
133C THR* 1.3 62.3 + - - +
134C HIS* 3.5 10.9 + - + +
184C MSE 3.6 5.7 - - - -
185C PHE* 2.7 65.7 + - + +
103D PHE* 4.7 15.0 - - + -
106D THR* 5.2 3.8 - - + +
108D ILE* 4.0 32.1 - - + -
109D ALA 5.6 0.7 - - - +
143D LYS* 4.0 37.0 - - + +
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Residues in contact with THR 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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115C PHE* 5.2 0.4 - - + -
119C ASN* 2.7 33.6 + - - +
123C VAL* 4.8 1.2 - - - +
132C LEU* 1.3 72.2 - - - +
134C HIS* 1.3 66.3 + - - +
135C GLU 3.9 15.7 - - - +
136C SER* 4.7 0.9 - - - -
182C PHE* 4.0 9.6 - - + -
184C MSE 3.4 30.5 - - - +
111D GLY* 4.6 7.3 + - - -
140D PHE* 3.4 40.6 - - + +
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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
----------------------------------------------------------
132C LEU* 3.5 11.7 + - + +
133C THR* 1.3 79.8 - - - +
135C GLU* 1.3 63.5 + - + +
163C HIS* 3.1 26.7 + + + +
183C LYS* 2.8 23.2 + - + +
185C PHE* 3.4 42.7 - + + +
139D GLN* 3.8 0.3 - - - +
140D PHE* 2.9 41.7 + - - +
143D LYS* 6.2 2.0 - - - +
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Residues in contact with GLU 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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133C THR* 3.9 6.4 - - - +
134C HIS* 1.3 83.2 - - + +
136C SER* 1.3 64.4 + - - +
181C ASN 4.6 0.2 - - - -
182C PHE* 3.7 0.9 - - - -
183C LYS* 2.9 67.1 + - + +
138D ILE 3.6 5.6 - - - +
139D GLN* 3.7 33.9 + - + -
140D PHE* 4.8 1.8 - - - -
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Residues in contact with SER 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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115C PHE* 3.4 17.3 - - - -
133C THR* 4.7 2.5 - - - -
135C GLU* 1.3 76.0 - - - +
137C SER* 1.3 60.1 + - - +
138C ILE* 3.4 8.9 - - - +
181C ASN 3.2 13.5 + - - -
182C PHE* 3.4 23.7 - - - -
136D SER 4.0 0.7 - - - +
137D SER* 3.5 3.0 + - - -
138D ILE* 2.8 55.5 + - - +
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Residues in contact with SER 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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136C SER* 1.3 71.6 + - - +
138C ILE* 1.3 60.7 + - - +
139C GLN* 5.8 2.4 - - - +
179C LYS 4.2 0.2 - - - +
180C GLY* 3.3 2.1 - - - -
181C ASN* 2.8 51.7 + - - -
136D SER 3.6 6.4 + - - -
137D SER* 4.4 12.1 + - - +
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Residues in contact with ILE 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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115C PHE* 3.7 20.4 - - + -
136C SER* 3.4 23.8 - - - +
137C SER* 1.3 75.6 + - - +
139C GLN* 1.3 66.5 + - - +
140C PHE* 3.6 24.9 - - + -
178C PHE* 3.5 26.0 - - + -
179C LYS 3.4 2.5 - - - -
180C GLY* 3.9 6.5 - - - -
182C PHE* 4.3 2.2 - - + -
115D PHE* 3.6 33.0 - - + -
135D GLU* 3.5 4.6 - - - +
136D SER* 2.8 49.8 + - - +
138D ILE* 6.0 1.1 - - + -
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Residues in contact with GLN 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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137C SER* 5.8 2.5 - - - +
138C ILE* 1.3 79.3 - - - +
140C PHE* 1.3 62.9 + - - +
141C ILE* 3.6 17.7 + - + +
178C PHE* 3.3 9.3 - - - -
179C LYS* 2.7 68.1 + - + +
181C ASN* 5.7 0.9 + - - -
134D HIS 3.7 5.2 - - - -
135D GLU* 3.7 29.4 + - + +
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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