Contacts of the strand formed by residues 134 - 142 (chain A) in PDB entry 2ILU
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 GLU 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A ILE 5.2 0.3 - - - +
129A SER* 2.6 45.3 + - - +
131A ARG* 3.0 42.0 + - + +
133A GLY* 1.3 78.9 - - - +
135A ASN* 1.3 72.5 + - - +
136A ILE* 4.0 6.7 + - - +
476A TYR* 3.7 31.4 - - - +
477A LEU 3.8 15.9 - - - +
478A GLN* 3.5 23.6 - - - +
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Residues in contact with ASN 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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126A ILE* 4.9 9.6 - - + +
127A ILE 5.1 0.4 - - - -
133A GLY 5.0 4.9 + - - -
134A GLU* 1.3 79.3 - - - +
136A ILE* 1.3 61.3 + - - +
137A LEU* 3.7 16.7 + - + -
475A VAL 3.3 1.9 - - - +
476A TYR* 3.7 1.7 - - - -
477A LEU* 2.9 55.2 + - + +
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Residues in contact with ILE 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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125A GLU 3.8 0.3 - - - +
126A ILE* 3.5 5.6 - - - +
127A ILE* 2.9 62.4 + - + +
128A GLN 4.2 3.8 - - - +
129A SER* 3.7 33.9 - - - -
134A GLU* 4.0 7.6 - - - +
135A ASN* 1.3 76.2 - - - +
137A LEU* 1.3 61.1 + - - +
138A LEU 4.0 0.2 + - - -
474A VAL* 3.7 28.9 - - + -
475A VAL 3.4 3.1 - - - +
476A TYR* 4.0 24.9 - - + +
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Residues in contact with LEU 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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125A GLU 3.7 1.8 - - - +
126A ILE* 4.0 33.0 - - + -
135A ASN* 4.6 15.9 - - + +
136A ILE* 1.3 76.6 - - - +
138A LEU* 1.3 60.5 + - - +
139A PHE* 3.3 35.6 - - + -
473A GLN 3.5 1.2 - - - +
474A VAL* 3.4 2.8 - - - +
475A VAL* 2.6 53.2 + - + +
477A LEU* 4.8 19.1 - - + -
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Residues in contact with LEU 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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124A GLY* 2.9 8.7 - - - -
125A GLU* 2.7 70.7 + - - +
127A ILE* 3.8 22.4 - - + -
137A LEU* 1.3 73.9 - - - +
139A PHE* 1.3 58.7 + - - +
140A LYS* 4.0 13.7 - - - -
472A THR* 3.9 30.3 - - + -
473A GLN 3.7 2.2 - - - -
474A VAL* 3.9 24.7 - - + +
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Residues in contact with PHE 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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124A GLY* 4.6 2.2 - - - -
137A LEU* 3.3 40.4 - - + -
138A LEU* 1.3 75.8 - - - +
140A LYS* 1.3 61.3 + - - +
141A ARG* 3.3 43.6 + - - +
472A THR* 3.4 5.5 - - - -
473A GLN* 2.8 44.3 + - + +
475A VAL* 3.6 20.4 - - + -
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Residues in contact with LYS 140 (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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122A TYR* 4.1 16.8 + - + -
123A GLU 3.1 34.1 + - - +
124A GLY* 4.0 4.0 - - - +
125A GLU* 5.0 6.1 + - - -
138A LEU* 4.0 13.0 - - - -
139A PHE* 1.3 73.8 - - - +
141A ARG* 1.3 65.1 + - - +
467A HIS* 3.6 28.8 + - + -
470A LEU* 3.8 36.5 - - + +
471A GLN 3.5 4.3 - - - +
472A THR* 4.0 28.3 - - + -
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Residues in contact with ARG 141 (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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61A GLU* 4.2 9.0 - - - +
139A PHE* 3.3 43.3 - - - +
140A LYS* 1.3 77.8 + - - +
142A ALA* 1.3 66.2 + - - +
470A LEU* 3.3 10.1 - - - +
471A GLN* 2.8 42.1 + - + +
472A THR 5.4 0.2 - - - -
473A GLN* 2.7 43.8 + - + +
475A VAL* 5.8 0.2 - - - +
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Residues in contact with ALA 142 (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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57A GLN* 4.2 2.7 - - - +
61A GLU* 2.9 30.4 + - - +
141A ARG* 1.3 77.9 - - - +
143A LEU* 1.3 62.5 - - - +
144A GLY 3.4 0.4 + - - -
169A THR 3.4 21.9 + - - +
170A GLY 3.5 18.6 - - - +
171A ASN* 3.6 9.2 - - - +
469A TYR 4.1 5.2 - - - -
470A LEU* 4.3 0.4 - - - +
471A GLN* 3.1 15.8 + - - -
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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