Contacts of the helix formed by residues 127 - 135 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ALA* 3.6 17.2 - - - +
125B ALA 3.6 0.2 + - - -
126B PRO* 1.3 72.9 - - - +
128B VAL* 1.3 62.8 + - - +
129B ALA* 3.3 3.9 - - - +
130B GLU* 3.4 16.1 + - - +
131B PHE* 3.1 18.2 + - - +
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 4.3 23.1 - - + +
86B SER* 3.8 9.6 - - - +
87B ALA* 3.8 25.1 - - - +
114B VAL 4.0 4.0 - - - +
115B MET* 5.5 0.4 - - - -
124B VAL* 3.5 24.0 - - + -
125B ALA* 3.2 26.2 + - + +
126B PRO 3.3 0.6 - - - -
127B GLY* 1.3 77.2 - - - +
129B ALA* 1.3 62.9 + - - +
131B PHE* 3.3 6.7 + - - +
132B HIS* 3.2 42.0 + - + +
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B MET* 3.9 37.8 - - + +
116B GLY 5.9 0.7 - - - +
124B VAL* 5.5 0.8 - - - +
125B ALA 4.9 0.8 + - - -
127B GLY* 3.3 2.0 - - - +
128B VAL* 1.3 75.4 - - - +
130B GLU* 1.3 69.4 + - + +
132B HIS* 3.0 5.1 + - - +
133B VAL* 3.0 27.5 + - - +
152B ILE* 4.8 9.4 - - + -
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B GLY* 3.4 15.9 + - - +
129B ALA* 1.3 79.1 - - + +
131B PHE* 1.3 57.7 + - - +
133B VAL* 3.7 14.2 - - - +
134B ARG* 2.9 72.6 + - - +
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Residues in contact with PHE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LEU* 4.2 11.7 - - + -
87B ALA* 4.4 8.3 - - + +
90B GLY* 3.2 46.0 - - - -
91B GLU* 3.1 24.9 - - - +
93B ILE* 5.4 1.1 - - + -
94B LEU* 3.7 29.6 - - + -
109B TYR* 4.8 7.6 - - - -
127B GLY 3.1 13.4 + - - +
128B VAL* 3.3 12.8 - - - +
129B ALA 3.1 0.4 - - - -
130B GLU* 1.3 77.4 - - - +
132B HIS* 1.3 83.0 + + - +
134B ARG* 4.5 4.7 - - - +
135B HIS* 2.8 35.8 + + + -
136B GLY* 2.9 20.1 + - - -
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Residues in contact with HIS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B SER* 5.3 2.8 + - - -
82B GLY 4.5 4.9 + - - -
84B LEU* 4.3 9.0 - - + +
109B TYR* 5.6 0.2 - - - -
111B CYS* 3.6 27.2 - - - -
112B ASP 4.1 4.8 + - - -
113B PRO* 3.5 39.3 + - + +
114B VAL 3.7 6.1 - - - -
115B MET* 4.0 18.3 - - + +
128B VAL* 3.2 37.2 + - + +
129B ALA 3.0 6.5 + - - +
131B PHE* 1.3 97.0 - + - +
133B VAL* 1.3 63.8 + - - +
136B GLY* 3.4 3.1 + - - +
137B LEU* 2.7 30.9 + - - +
143B ILE* 6.1 0.2 - - + -
153B LEU* 3.9 3.8 - - + +
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B MET* 4.4 0.2 - - + -
129B ALA 3.0 18.0 + - - +
130B GLU* 3.7 16.8 - - - +
132B HIS* 1.3 78.5 - - - +
134B ARG* 1.3 62.9 + - + +
137B LEU* 3.8 8.9 - - - +
138B PRO* 3.8 10.7 - - - +
152B ILE* 3.5 42.0 - - + +
153B LEU* 3.7 24.7 - - + +
155B GLU* 4.6 16.8 - - - +
174B GLN* 5.3 2.1 + - - +
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Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU* 2.9 65.3 + - - +
133B VAL* 1.3 76.7 - - + +
135B HIS* 1.3 96.1 + - + +
138B PRO* 3.4 13.3 - - - +
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Residues in contact with HIS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B GLU* 4.0 28.0 + - - -
94B LEU* 3.7 24.1 - - + +
131B PHE* 2.8 25.1 + + + +
133B VAL 3.6 0.6 - - - -
134B ARG* 1.3 114.0 + - + +
136B GLY* 1.3 65.7 + - - +
137B LEU 3.5 0.9 - - - -
138B PRO* 3.2 14.5 - - - +
139B ALA* 3.3 15.1 + - - +
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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