Contacts of the helix formed by residues 120 - 133 (chain D) in PDB entry 1TU8
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 ILE 120 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100D LYS* 4.4 12.3 - - + -
112D GLU* 6.0 1.8 - - - +
115D PRO* 4.2 6.1 - - + +
116D TYR* 3.2 45.5 + - + +
119D SER* 1.3 85.2 - - - +
121D LEU* 1.3 66.1 + - - +
122D PRO* 3.5 0.7 - - - -
123D GLY* 3.5 4.7 + - - -
124D GLU* 3.3 34.5 + - + +
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Residues in contact with LEU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D LEU* 4.2 9.9 - - + -
116D TYR* 2.8 35.6 + - + +
117D ILE* 4.1 12.1 - - - +
120D ILE* 1.3 76.0 - - - +
122D PRO* 1.3 67.6 - - + +
124D GLU* 3.0 5.3 + - - +
125D LEU* 2.9 45.1 + - + +
161D HIS* 3.3 42.2 - - + +
164D LEU* 5.1 2.0 - - + -
165D ASP* 4.9 5.8 - - + +
168D CYS* 3.8 28.7 - - + -
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Residues in contact with PRO 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ILE 3.4 19.1 - - - +
118D LYS* 3.5 23.3 - - - +
119D SER 4.3 1.3 - - - -
120D ILE 3.5 5.8 - - - +
121D LEU* 1.3 91.4 - - + +
123D GLY* 1.3 55.6 + - - +
125D LEU* 4.6 1.3 - - + -
126D ALA* 3.0 26.0 + - - +
171D LYS* 5.3 10.5 - - - +
172D PHE* 3.3 27.6 - - + -
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Residues in contact with GLY 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D SER 5.4 2.3 + - - -
120D ILE 3.5 6.1 + - - -
121D LEU 3.3 0.4 - - - -
122D PRO* 1.3 78.6 - - - +
124D GLU* 1.3 66.9 + - - +
126D ALA* 3.6 8.1 + - - +
127D LYS* 3.6 25.6 + - - +
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Residues in contact with GLU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D LEU* 3.9 31.6 - - + +
100D LYS* 4.2 31.7 + - + -
120D ILE* 3.3 20.3 + - + +
121D LEU* 3.0 8.4 + - - +
123D GLY* 1.3 76.5 - - - +
125D LEU* 1.3 65.1 + - - +
127D LYS* 3.1 51.5 + - - +
128D PHE* 3.3 20.7 - - + -
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Residues in contact with LEU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D LEU* 4.3 13.7 - - + -
121D LEU* 2.9 46.4 + - + +
122D PRO* 4.9 0.7 - - + -
124D GLU* 1.3 73.4 - - - +
126D ALA* 1.3 65.8 + - - +
128D PHE* 3.0 9.3 + - + +
129D GLU* 3.0 18.4 + - - +
158D LEU* 3.9 27.8 - - + -
161D HIS* 5.5 4.3 - - + -
168D CYS* 3.5 29.8 - - + +
169D LEU* 3.8 12.1 - - + -
172D PHE* 3.7 20.4 - - + -
175D LEU* 3.4 13.9 - - + +
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Residues in contact with ALA 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D PRO 3.0 17.4 + - - +
123D GLY* 3.7 9.6 - - - +
124D GLU 3.2 0.2 - - - -
125D LEU* 1.3 76.0 - - - +
127D LYS* 1.3 63.0 + - - +
129D GLU* 3.3 3.0 + - - +
130D LYS* 3.0 24.6 + - - +
172D PHE* 3.6 20.6 - - + -
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Residues in contact with LYS 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LYS* 5.1 9.4 - - - +
46C GLN 3.8 20.0 - - - +
47C PHE* 2.9 48.4 + - + +
48C GLY* 4.6 5.4 - - - +
49C GLN* 5.3 2.4 - - - +
100D LYS* 5.9 0.6 - - - +
123D GLY 3.6 13.9 + - - +
124D GLU* 3.1 45.3 + - - +
125D LEU 3.2 0.4 - - - -
126D ALA* 1.3 79.3 - - - +
128D PHE* 1.3 58.6 + - + +
130D LYS* 3.5 6.3 + - - +
131D LEU* 3.1 27.4 + - - +
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Residues in contact with PHE 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C PHE* 3.7 23.8 - + - -
90D PHE* 3.4 27.2 - + + -
93D GLY 3.4 24.0 - - - -
94D VAL* 3.7 30.3 - - + -
97D LEU* 4.0 26.9 - - + -
124D GLU* 3.3 28.3 - - + -
125D LEU* 3.0 15.1 + - + +
127D LYS* 1.3 75.4 - - + +
129D GLU* 1.3 62.2 + - - +
130D LYS 3.2 0.2 - - - -
131D LEU* 3.9 4.0 - - + +
132D LEU* 2.8 34.3 + - - +
154D LEU* 4.5 8.7 - - + -
158D LEU* 6.0 0.2 - - + -
175D LEU* 3.9 18.8 - - + -
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Residues in contact with GLU 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D LEU 3.0 12.0 + - - +
126D ALA* 3.7 7.6 - - - +
128D PHE* 1.3 77.0 - - - +
130D LYS* 1.3 63.5 + - - +
132D LEU* 3.7 1.7 + - - +
133D ALA* 3.5 14.6 + - - +
171D LYS 5.5 0.2 - - - +
172D PHE* 3.4 30.1 - - + +
173D PRO* 3.2 15.2 - - + +
174D LEU* 3.0 46.2 + - + +
175D LEU* 3.0 37.3 + - + +
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Residues in contact with LYS 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C SER* 4.5 15.0 + - - -
126D ALA 3.0 16.8 + - - +
127D LYS* 3.7 6.3 - - - +
129D GLU* 1.3 79.3 - - - +
131D LEU* 1.3 62.1 + - - +
133D ALA* 3.5 15.8 + - - +
134D THR* 3.7 10.9 - - + +
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Residues in contact with LEU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C GLN* 3.9 29.2 - - + +
47C PHE* 3.6 34.1 - - + -
86D TYR* 2.9 27.6 + - + +
89D MET* 4.2 11.4 - - + -
90D PHE* 3.6 26.7 - - + -
127D LYS 3.1 13.9 + - - +
128D PHE* 3.9 3.8 - - + +
129D GLU 3.4 0.2 - - - -
130D LYS* 1.3 80.1 - - - +
132D LEU* 1.3 63.3 + - - +
134D THR* 2.6 36.8 + - + +
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Residues in contact with LEU 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D TYR* 4.5 1.4 + - - -
90D PHE* 4.0 12.2 - - + -
128D PHE 2.8 18.5 + - - +
129D GLU 4.0 3.8 - - - +
131D LEU* 1.3 76.1 - - - +
133D ALA* 1.3 61.3 + - - +
134D THR 3.2 1.4 + - - -
135D ARG* 3.5 9.9 + - - +
138D GLY* 3.1 34.1 + - - +
140D ASN 5.1 0.7 - - - +
141D LEU 4.1 9.4 - - - +
142D ILE* 4.1 35.2 - - + +
154D LEU* 4.8 2.0 - - + -
174D LEU* 3.8 29.6 - - + +
175D LEU* 3.9 19.7 - - + -
178D PHE* 4.1 18.2 - - + -
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Residues in contact with ALA 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D GLU 3.5 5.3 + - - +
130D LYS* 3.6 13.2 - - - +
131D LEU 3.1 0.8 - - - -
132D LEU* 1.3 79.7 - - - +
134D THR* 1.3 61.3 + - - +
135D ARG 3.2 1.7 + - - -
137D ASN* 3.6 20.1 + - - +
138D GLY* 3.6 12.1 - - - +
174D LEU* 3.7 20.8 - - + +
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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