Contacts of the helix formed by residues 121 - 132 (chain A) in PDB entry 3TGX
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 SER 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A PRO* 5.0 4.5 - - - -
105A PHE* 3.7 9.6 - - - -
119A TRP* 5.7 0.4 - - - -
120A ARG* 1.3 76.5 - - - +
122A ASP* 1.3 61.4 + - - +
123A TYR* 2.9 36.5 + - - +
124A GLU* 2.9 36.8 + - - +
125A ASP 4.4 0.5 + - - -
137A TYR* 4.4 18.1 + - - -
162A ARG* 4.3 8.7 - - - -
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Residues in contact with ASP 122 (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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11A LEU* 4.3 21.2 - - + +
102A ALA* 3.6 22.7 + - + +
103A PRO* 4.5 7.4 + - - +
105A PHE* 3.5 21.9 - - - -
121A SER* 1.3 72.8 + - - +
123A TYR* 1.3 60.0 + - + +
124A GLU 3.1 2.0 - - - -
125A ASP* 3.2 25.9 - - - +
128A PHE* 3.6 13.0 - - + +
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Residues in contact with TYR 123 (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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9A ASP 2.3 31.5 + - - -
10A TYR* 3.3 3.7 + - + -
11A LEU* 3.6 25.8 - - + -
101A PRO* 3.4 4.5 - - - +
102A ALA* 3.0 31.9 + - + +
121A SER* 2.9 22.5 + - - +
122A ASP* 1.3 76.1 - - - +
124A GLU* 1.3 58.6 + - - +
125A ASP 3.1 12.5 + - - +
128A PHE 3.4 25.1 - - - +
129A TYR* 4.1 2.3 - - - -
130A MET* 6.0 0.4 - - + -
131A LEU* 3.7 35.2 - - + +
132A LYS* 3.8 38.1 - - - +
135A LEU* 3.9 23.1 - - + -
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Residues in contact with GLU 124 (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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105A PHE* 5.1 0.9 - - - -
120A ARG* 3.4 21.4 + - - +
121A SER* 2.9 30.9 + - - +
122A ASP 3.1 0.8 - - - -
123A TYR* 1.3 76.7 - - - +
125A ASP* 1.3 62.3 + - - +
126A PRO* 3.4 9.7 - - - +
132A LYS* 5.3 5.5 - - - +
162A ARG* 3.0 57.6 + - - +
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Residues in contact with ASP 125 (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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121A SER 4.4 0.8 + - - -
122A ASP* 3.2 18.2 + - - +
123A TYR 3.6 2.1 - - - +
124A GLU* 1.3 77.8 - - - +
126A PRO* 1.3 64.9 - - - +
127A ALA* 3.0 22.4 + - - +
128A PHE* 2.8 53.7 + - + -
129A TYR* 3.6 1.0 + - - +
66B ILE* 5.5 0.2 - - - +
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Residues in contact with PRO 126 (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 GLU 3.4 9.4 - - - +
125A ASP* 1.3 92.9 - - - +
127A ALA* 1.3 58.6 + - - +
128A PHE 3.2 0.4 + - - -
129A TYR* 3.6 22.6 - - + +
19B GLN* 4.3 1.6 - - - +
23B TYR* 3.4 26.0 + - - +
66B ILE* 3.9 14.9 - - + +
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Residues in contact with ALA 127 (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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67A PHE* 3.7 11.8 - - + -
125A ASP* 3.0 13.7 + - - +
126A PRO* 1.3 78.8 - - - +
128A PHE* 1.3 77.4 + - + +
129A TYR* 3.5 2.7 - - - -
130A MET* 3.5 20.4 - - - +
65B ARG* 6.2 2.0 - - - +
66B ILE* 3.7 27.8 - - + +
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Residues in contact with PHE 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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11A LEU* 3.3 41.1 - - + -
12A GLN* 4.3 18.6 - - - -
67A PHE* 3.8 42.0 - + + -
122A ASP* 3.6 25.4 - - + +
123A TYR* 3.4 24.4 - - - -
125A ASP* 2.8 25.5 + - + +
127A ALA* 1.3 91.9 - - + +
129A TYR* 1.3 61.2 + - - +
130A MET* 3.2 10.6 + - - -
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Residues in contact with TYR 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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123A TYR 4.1 10.3 - - - +
125A ASP 3.6 1.5 + - - +
126A PRO* 3.6 19.3 - - + +
127A ALA* 4.3 2.5 - - - -
128A PHE* 1.3 75.3 - - - +
130A MET* 1.3 96.6 + - + +
131A LEU 3.2 0.7 - - - -
132A LYS* 2.9 30.2 + - + +
15B ASP* 3.7 20.0 - - + -
16B ILE* 3.5 25.6 - - + +
19B GLN* 3.3 55.5 + - + +
66B ILE* 5.4 3.1 - - + -
69B VAL* 6.1 1.7 - - + +
70B SER* 3.5 6.8 + - - -
73B LYS* 4.7 6.1 + - - -
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Residues in contact with MET 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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10A TYR* 3.6 43.5 - - + +
11A LEU* 6.2 0.2 - - - -
67A PHE* 3.2 40.6 - - + +
123A TYR* 6.0 0.7 - - + -
127A ALA 3.5 18.6 - - - +
128A PHE* 3.2 10.0 - - - +
129A TYR* 1.3 114.1 - - + +
131A LEU* 1.3 60.8 + - + +
132A LYS 3.4 0.4 + - - -
134A LYS* 3.3 23.2 + - - +
191A TYR* 4.1 4.3 + - - -
12B GLN* 4.9 7.5 + - - +
15B ASP* 5.4 1.4 - - - +
69B VAL* 5.1 4.7 - - + -
73B LYS* 3.7 13.0 - - - +
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Residues in contact with LEU 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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10A TYR* 3.7 28.3 - - + +
99A ILE* 3.7 28.3 - - + -
123A TYR* 3.7 44.3 - - + +
129A TYR 3.2 0.6 - - - -
130A MET* 1.3 76.1 - - - +
132A LYS* 1.3 64.1 + - - +
133A GLY 3.6 1.8 - - - -
134A LYS* 3.4 17.0 + - + -
135A LEU* 3.6 27.5 - - + +
191A TYR* 3.7 46.9 - - + -
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Residues in contact with LYS 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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123A TYR* 3.8 28.6 - - - +
124A GLU* 5.3 4.5 - - - +
129A TYR* 2.9 27.6 + - + +
130A MET 3.4 1.4 + - - -
131A LEU* 1.3 77.5 - - - +
133A GLY* 1.3 60.3 + - - +
134A LYS* 4.6 0.2 - - - +
135A LEU* 5.8 0.2 - - - +
137A TYR* 4.9 2.3 + - - -
160A ASP* 2.8 21.1 - - - +
162A ARG* 4.0 25.4 + - - +
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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