Contacts of the helix formed by residues 128 - 138 (chain A) in PDB entry 1TE6
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 PRO 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A LEU* 1.3 95.2 - - + +
129A LEU* 1.3 67.4 + - - +
130A TYR* 3.5 43.1 - - + +
131A ARG* 3.0 24.5 + - + -
132A HIS* 3.1 8.8 + - - +
415A GLU* 3.5 14.8 - - - +
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Residues in contact with LEU 129 (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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118A CYS* 3.8 24.7 - - - +
119A LYS* 3.8 40.2 - - + +
122A ALA* 3.8 11.4 - - + +
127A LEU 3.6 1.8 + - - -
128A PRO* 1.3 70.9 - - - +
130A TYR* 1.3 57.3 + - - +
132A HIS* 3.3 2.6 + - + +
133A ILE* 3.0 36.9 + - + +
379A PHE* 3.7 31.2 - - + -
382A ASP* 3.5 32.6 + - + +
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Residues in contact with TYR 130 (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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128A PRO* 3.5 22.0 - - + +
129A LEU* 1.3 75.7 - - - +
131A ARG* 1.3 74.6 + - + +
133A ILE* 3.6 1.0 + - - -
134A ALA* 3.1 21.7 + - - +
142A LEU* 3.4 18.6 - - + -
382A ASP* 3.1 52.8 + - + +
385A VAL* 4.1 13.0 - - + -
386A GLY* 3.3 12.3 - - - -
412A ILE* 3.6 26.9 - - + -
415A GLU* 2.7 41.2 + - - +
416A LEU* 3.7 36.3 - - + +
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Residues in contact with ARG 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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127A LEU* 3.9 30.7 - - + -
128A PRO* 3.0 27.8 + - + +
130A TYR* 1.3 83.4 - - + +
132A HIS* 1.3 66.3 + - - +
134A ALA* 3.2 6.8 + - - +
135A GLN* 3.0 38.7 + - + +
139A ASN 4.8 2.4 + - - -
140A SER* 3.1 30.5 + - - +
142A LEU* 3.6 26.5 - - - +
416A LEU* 4.1 15.2 - - - +
419A GLU* 5.6 3.8 - - - +
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Residues in contact with HIS 132 (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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83A VAL 4.7 2.0 + - - -
84A VAL* 4.3 15.3 + - - -
86A GLN* 4.9 1.0 + - - +
118A CYS* 3.3 40.1 + - - -
121A GLY* 3.7 17.7 + - - -
122A ALA* 3.4 34.6 + - + -
125A ARG* 4.3 20.3 - - - +
127A LEU* 4.7 6.5 - - + +
128A PRO 3.1 6.1 + - - +
129A LEU* 3.3 4.0 + - + +
131A ARG* 1.3 78.9 - - - +
133A ILE* 1.3 61.3 + - - +
135A GLN* 3.1 12.2 + - - +
136A LEU* 3.0 49.1 + - + +
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Residues in contact with ILE 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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118A CYS* 3.0 36.1 - - - -
129A LEU* 3.0 29.7 + - + +
130A TYR* 3.8 6.7 - - - +
131A ARG 3.3 0.2 - - - -
132A HIS* 1.3 76.4 - - - +
134A ALA* 1.3 61.2 + - - +
136A LEU* 3.1 10.1 + - + +
137A ALA* 2.9 21.5 + - - +
349A VAL* 4.3 10.1 - - + -
353A ILE* 5.2 3.8 - - + +
379A PHE* 3.7 17.7 - - + -
382A ASP 4.5 3.6 - - - +
383A LEU* 3.9 27.1 - - + +
386A GLY* 4.0 17.9 - - - -
387A LEU* 4.2 7.6 - - + -
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Residues in contact with ALA 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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130A TYR 3.1 12.3 + - - +
131A ARG* 3.2 16.3 + - - +
133A ILE* 1.3 77.7 - - - +
135A GLN* 1.3 51.2 + - - +
137A ALA* 3.2 1.7 + - - -
138A GLY 2.7 30.7 + - - -
139A ASN* 2.8 21.3 + - + +
142A LEU* 3.4 33.4 - - + -
386A GLY 3.4 14.6 - - - +
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Residues in contact with GLN 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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125A ARG* 3.6 28.3 + - - +
127A LEU* 3.6 29.0 - - - +
131A ARG* 3.0 26.2 + - - +
132A HIS* 3.6 9.2 + - - +
134A ALA* 1.3 74.7 - - + +
136A LEU* 1.3 64.4 + - + +
138A GLY* 3.2 12.8 + - - +
139A ASN 4.7 4.9 - - - +
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Residues in contact with LEU 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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84A VAL 4.1 14.1 - - - +
86A GLN* 3.7 39.3 - - + +
87A GLU 5.6 0.9 - - - +
118A CYS* 4.0 14.8 - - - -
125A ARG* 5.9 3.4 - - - +
132A HIS* 3.0 41.2 + - + +
133A ILE* 3.1 13.9 + - + +
135A GLN* 1.3 77.0 - - + +
137A ALA* 1.3 58.2 + - - +
349A VAL* 5.2 2.5 - - + -
353A ILE* 4.5 11.6 - - + +
357A LYS* 4.4 9.9 + - - -
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Residues in contact with ALA 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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133A ILE 2.9 15.7 + - - +
134A ALA* 3.7 4.3 - - - +
136A LEU* 1.3 78.9 - - - +
138A GLY* 1.3 59.8 + - - +
139A ASN* 3.9 17.1 + - - +
353A ILE* 4.0 13.7 - - + -
357A LYS* 3.6 23.6 + - + +
386A GLY 4.5 0.2 - - - +
387A LEU* 3.5 27.8 - - + -
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Residues in contact with GLY 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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134A ALA 2.7 11.0 + - - -
135A GLN* 3.2 11.8 + - - -
137A ALA* 1.3 75.9 - - - +
139A ASN* 1.3 65.4 + - - -
140A SER* 5.5 0.2 + - - -
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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