Contacts of the helix formed by residues 127 - 135 (chain A) in PDB entry 1TD2
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 GLY 127 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA* 3.8 15.3 - - - +
125A ALA 3.6 0.2 + - - -
126A PRO* 1.3 72.9 - - - +
128A VAL* 1.3 59.0 + - - +
129A ALA* 3.3 4.3 - - - +
130A GLU* 3.4 20.1 + - - +
131A PHE* 3.0 26.3 + - - +
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Residues in contact with VAL 128 (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 LEU* 4.3 21.8 - - + +
86A SER 3.9 30.5 - - - +
87A ALA* 4.0 2.0 - - - +
114A VAL 3.9 6.5 - - - +
115A MET* 5.3 0.4 - - - -
124A VAL* 3.7 25.4 - - + -
125A ALA* 3.3 23.3 + - + +
126A PRO 3.3 1.0 - - - -
127A GLY* 1.3 74.3 - - - +
129A ALA* 1.3 67.0 + - - +
131A PHE* 2.9 18.7 + - - +
132A HIS* 3.0 36.4 + - + +
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Residues in contact with ALA 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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115A MET* 3.9 39.4 - - + +
125A ALA 4.9 0.2 + - - -
127A GLY 4.6 2.0 - - - +
128A VAL* 1.3 78.0 - - - +
130A GLU* 1.3 64.2 + - - +
132A HIS* 3.0 14.1 + - - +
133A VAL* 3.2 19.5 + - - +
152A ILE* 5.4 5.8 - - + -
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Residues in contact with GLU 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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127A GLY* 3.4 18.9 + - - +
128A VAL 3.2 0.2 - - - -
129A ALA* 1.3 79.3 - - - +
131A PHE* 1.3 65.2 + - - +
133A VAL* 3.6 11.0 - - + +
134A ARG* 3.1 36.5 + - + +
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Residues in contact with PHE 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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84A LEU* 4.3 8.3 - - + -
87A ALA* 4.4 10.3 - - + +
90A GLY* 3.1 47.6 - - - -
91A GLU* 3.5 20.9 - - - +
93A ILE* 5.2 1.6 - - + -
94A LEU* 3.7 35.0 - - + -
109A TYR* 4.6 6.1 - - - -
127A GLY 3.0 12.5 + - - +
128A VAL* 2.9 12.3 + - - +
130A GLU* 1.3 76.6 - - - +
132A HIS* 1.3 87.1 + + - +
134A ARG* 4.7 2.9 - - - -
135A HIS* 2.8 34.2 + - + -
136A GLY* 3.1 16.3 + - - -
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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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81A SER* 5.0 4.5 - - - -
82A GLY 4.7 5.3 + - - -
84A LEU* 4.4 9.5 - - + +
111A CYS* 3.6 22.8 - - - -
112A ASP 4.3 4.0 - - - -
113A PRO* 3.7 39.3 - - + +
114A VAL 3.9 5.0 + - - -
115A MET* 3.9 14.4 - - + -
128A VAL* 3.0 44.5 + - + +
129A ALA* 3.0 9.6 + - - +
131A PHE* 1.3 99.0 - + - +
133A VAL* 1.3 60.4 + - - +
136A GLY* 3.3 4.3 + - - +
137A LEU* 2.8 31.5 + - - +
143A ILE* 6.2 0.2 - - + -
153A LEU* 4.0 3.8 - - + -
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Residues in contact with VAL 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 MET* 4.4 1.1 - - + -
129A ALA 3.2 14.4 + - - +
130A GLU* 3.6 17.0 - - + +
132A HIS* 1.3 76.1 - - - +
134A ARG* 1.3 79.5 + - + +
137A LEU* 4.0 15.9 - - - +
138A PRO* 4.1 2.4 - - - +
152A ILE* 3.6 37.5 - - + +
153A LEU* 3.7 24.5 - - + +
155A GLU* 5.6 7.6 - - + +
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Residues in contact with ARG 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 GLU* 3.1 22.5 + - + +
131A PHE* 4.1 1.3 - - - +
133A VAL* 1.3 96.4 + - + +
135A HIS* 1.3 84.5 + - + +
138A PRO* 3.3 16.0 - - - +
155A GLU* 5.8 2.2 + - - -
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Residues in contact with HIS 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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91A GLU* 3.2 34.0 + - - -
94A LEU* 3.3 24.6 - - + +
131A PHE* 2.8 22.6 + + + +
133A VAL 3.7 0.2 - - - -
134A ARG* 1.3 100.3 + - + +
136A GLY* 1.3 66.5 + - - +
137A LEU 3.2 2.0 - - - -
138A PRO* 3.2 6.4 - - - +
139A ALA* 3.0 26.0 + - - +
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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