Contacts of the strand formed by residues 130 - 139 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A GLN* 4.3 0.7 - - - +
129A PRO* 1.3 77.9 - - + +
131A VAL* 1.3 64.6 + - - +
132A LEU* 5.3 8.1 - - + -
185A PHE* 3.8 5.4 - - - +
186A TYR* 3.4 6.2 - - - +
187A ASP* 3.0 51.7 + - - +
189A ARG 5.1 0.4 - - - +
190A GLY 3.1 19.5 + - - +
105B LYS* 6.3 1.1 - - - -
106B THR* 3.7 30.5 - - + -
108B ILE* 6.2 0.2 - - + -
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A VAL* 4.3 22.2 - - + +
126A ILE* 3.7 44.4 - - + +
128A GLN* 3.7 20.4 - - + +
129A PRO 4.2 1.0 + - - -
130A THR* 1.3 78.3 - - - +
132A LEU* 1.3 74.1 + - - +
184A MSE 3.9 29.2 - - + -
185A PHE 3.4 8.5 - - - +
186A TYR* 5.0 0.2 - - + -
103B PHE* 4.2 14.7 - - - -
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A VAL* 6.2 0.7 - - - -
130A THR* 5.3 6.3 - - - -
131A VAL* 1.3 84.0 - - - +
133A THR* 1.3 62.5 + - - +
134A HIS* 4.5 10.3 - - + +
184A MSE 3.5 5.2 - - - -
185A PHE* 2.7 64.2 + - + +
103B PHE* 4.3 18.8 - - + -
106B THR* 5.2 2.9 - - + +
108B ILE* 4.1 31.6 - - + -
109B ALA 5.3 1.1 - - - +
143B LYS* 4.0 36.6 - - + -
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Residues in contact with THR 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A PHE* 5.1 0.4 - - + -
119A ASN* 2.7 34.7 + - - +
123A VAL* 4.9 1.6 - - - +
132A LEU* 1.3 72.4 - - - +
134A HIS* 1.3 63.2 + - - +
135A GLU 3.9 15.7 - - - +
136A SER* 4.7 1.3 - - - -
182A PHE* 4.0 9.2 - - + -
183A LYS 3.9 2.7 - - - -
184A MSE 3.4 27.0 - - - +
111B GLY* 4.5 6.8 - - - -
140B PHE* 3.3 43.9 - - + +
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Residues in contact with HIS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LEU* 3.5 11.9 + - + +
133A THR* 1.3 80.4 - - - +
135A GLU* 1.3 61.7 - - + +
163A HIS* 3.1 26.1 + + + +
183A LYS* 2.8 22.3 + - + +
185A PHE* 3.4 42.4 - + + +
139B GLN* 3.5 0.9 - - - +
140B PHE* 2.8 45.1 + - - +
143B LYS* 6.0 3.4 - - - +
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Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A THR* 3.9 6.6 - - - +
134A HIS* 1.3 83.7 - - + +
136A SER* 1.3 62.1 + - - +
182A PHE* 3.7 0.9 - - - -
183A LYS* 2.9 65.1 + - + +
138B ILE 3.5 7.6 - - - +
139B GLN* 3.8 28.3 - - + +
140B PHE* 4.8 1.6 - - - -
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Residues in contact with SER 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A PHE* 3.4 16.3 - - - -
133A THR* 4.7 2.2 - - - -
135A GLU* 1.3 77.0 - - - +
137A SER* 1.3 59.8 + - - +
138A ILE* 3.4 9.2 - - - +
181A ASN 3.2 13.3 + - - -
182A PHE* 3.4 23.7 - - - -
136B SER 3.9 0.5 - - - +
137B SER* 3.5 2.4 - - - -
138B ILE* 2.8 56.7 + - - +
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Residues in contact with SER 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A SER* 1.3 71.7 + - - +
138A ILE* 1.3 60.3 + - - +
139A GLN* 5.8 2.0 - - - +
179A LYS 4.2 0.3 - - - +
180A GLY* 3.4 1.7 - - - -
181A ASN* 2.8 53.2 + - - -
136B SER 3.6 4.6 + - - -
137B SER* 4.0 14.4 + - - +
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Residues in contact with ILE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A PHE* 3.7 19.1 - - + -
136A SER* 3.4 23.8 - - - +
137A SER* 1.3 75.4 + - - +
139A GLN* 1.3 66.8 + - - +
140A PHE* 3.6 33.2 - - + -
178A PHE* 3.5 25.1 - - + -
179A LYS 3.4 2.5 - - - -
180A GLY* 3.9 7.4 - - - -
182A PHE* 4.3 2.0 - - + -
115B PHE* 3.6 25.4 - - + -
135B GLU* 3.5 4.3 - - - +
136B SER* 2.8 51.6 + - - +
138B ILE* 6.0 1.1 - - + -
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Residues in contact with GLN 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A SER* 5.8 2.7 - - - +
138A ILE* 1.3 78.9 - - - +
140A PHE* 1.3 63.5 + - - +
141A ILE* 3.6 18.7 + - + +
178A PHE* 3.3 9.1 - - - -
179A LYS* 2.7 67.2 + - + +
181A ASN* 5.3 3.1 + - - -
134B HIS 3.7 5.6 - - - +
135B GLU* 3.9 25.2 + - + -
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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