Contacts of the helix formed by residues 120 - 133 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B LYS* 4.2 20.6 - - + -
115B PRO* 3.6 4.7 + - + +
116B TYR* 3.3 48.4 + - + +
119B SER* 1.3 86.3 - - - +
121B LEU* 1.3 66.2 + - - +
122B PRO* 3.4 1.4 - - - -
123B GLY* 3.4 5.0 + - - -
124B GLU* 3.4 27.7 + - + +
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Residues in contact with LEU 121 (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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97B LEU* 4.2 13.5 - - + -
116B TYR* 2.9 29.7 + - + +
117B ILE* 4.0 11.9 - - - +
120B ILE* 1.3 77.1 - - - +
122B PRO* 1.3 69.2 - - + +
124B GLU* 3.1 4.5 + - - +
125B LEU* 2.9 46.8 + - + +
161B HIS* 3.3 40.2 - - + +
164B LEU* 5.1 2.2 - - + -
165B ASP* 4.8 7.4 - - + +
168B CYS* 3.8 27.6 - - + -
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Residues in contact with PRO 122 (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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117B ILE 3.3 19.7 - - - +
118B LYS* 3.6 23.1 - - - +
119B SER 4.4 1.1 - - - -
120B ILE 3.5 3.8 - - - +
121B LEU* 1.3 90.6 - - + +
123B GLY* 1.3 56.1 + - - +
125B LEU* 3.3 2.1 + - + -
126B ALA* 3.0 26.6 + - - +
171B LYS* 3.8 34.3 - - - +
172B PHE* 3.4 13.2 - - + -
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Residues in contact with GLY 123 (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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119B SER 5.4 1.8 + - - -
120B ILE 3.4 6.2 + - - -
121B LEU 3.3 0.4 - - - -
122B PRO* 1.3 78.7 - - - +
124B GLU* 1.3 66.3 + - - +
126B ALA* 3.5 14.0 + - - +
127B LYS* 3.5 20.4 + - - +
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Residues in contact with GLU 124 (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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47A PHE* 5.9 0.5 - - - -
96B ASP* 6.1 0.3 - - - +
97B LEU* 3.9 32.1 - - + +
100B LYS* 4.1 26.2 + - + -
120B ILE* 3.4 26.1 + - + +
121B LEU 3.1 7.2 + - - +
123B GLY* 1.3 75.2 - - - +
125B LEU* 1.3 65.4 + - - +
127B LYS* 3.0 47.9 + - - +
128B PHE* 3.2 22.4 - - + -
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Residues in contact with LEU 125 (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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97B LEU* 4.2 14.1 - - + -
121B LEU* 2.9 48.1 + - + +
122B PRO* 4.9 0.7 - - + -
124B GLU* 1.3 75.0 - - - +
126B ALA* 1.3 63.5 + - - +
128B PHE* 3.0 12.4 + - + +
129B GLU* 3.0 18.9 + - - +
158B LEU* 3.9 27.4 - - + -
161B HIS* 5.5 4.7 - - + -
168B CYS* 3.5 30.7 - - + +
169B LEU* 3.9 11.2 - - + -
172B PHE* 3.5 20.0 - - + -
175B LEU* 3.5 10.8 - - + +
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Residues in contact with ALA 126 (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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122B PRO 3.0 16.8 + - - +
123B GLY* 3.6 10.3 - - - +
124B GLU 3.2 0.4 - - - -
125B LEU* 1.3 77.4 - - - +
127B LYS* 1.3 61.0 + - - +
129B GLU* 3.4 3.3 + - - +
130B LYS* 3.1 24.3 + - - +
172B PHE* 3.6 20.6 - - + -
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Residues in contact with LYS 127 (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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42A LYS* 5.2 8.1 - - - +
46A GLN 3.7 21.5 - - - +
47A PHE* 2.7 49.7 + - + +
48A GLY* 4.3 4.2 - - - +
49A GLN* 5.3 3.0 - - - +
100B LYS* 5.9 0.2 - - - +
123B GLY 3.5 16.1 + - - +
124B GLU* 3.0 44.0 + - - +
125B LEU 3.2 0.4 - - - -
126B ALA* 1.3 79.2 - - - +
128B PHE* 1.3 57.7 + - + +
130B LYS* 3.6 5.3 + - - +
131B LEU* 3.1 27.8 + - - +
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Residues in contact with PHE 128 (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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47A PHE* 3.7 26.0 - + - -
90B PHE* 3.6 25.4 - + + -
93B GLY 3.4 23.8 - - - -
94B VAL* 3.7 29.8 - - + -
97B LEU* 4.0 26.2 - - + -
124B GLU* 3.2 30.1 - - + -
125B LEU* 3.0 15.7 + - + +
127B LYS* 1.3 77.2 - - + +
129B GLU* 1.3 57.0 + - - +
131B LEU* 3.8 3.5 - - + +
132B LEU* 2.7 37.1 + - - +
154B LEU* 4.5 7.9 - - + -
158B LEU* 6.1 0.2 - - + -
175B LEU* 3.9 18.8 - - + -
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Residues in contact with GLU 129 (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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125B LEU 3.0 11.7 + - - +
126B ALA* 3.4 8.9 + - - +
128B PHE* 1.3 76.9 - - - +
130B LYS* 1.3 61.0 + - - +
132B LEU* 4.0 2.3 - - - +
133B ALA* 3.6 14.0 + - - +
171B LYS 5.3 0.7 - - - +
172B PHE* 3.3 31.6 - - + +
173B PRO* 3.2 15.3 - - + +
174B LEU* 3.0 46.0 + - + +
175B LEU* 3.0 39.0 + - + +
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Residues in contact with LYS 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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43A SER 4.7 11.3 + - - -
126B ALA 3.1 16.1 + - - +
127B LYS* 3.8 5.6 - - - +
129B GLU* 1.3 76.0 - - - +
131B LEU* 1.3 65.4 + - + +
133B ALA* 3.4 16.7 + - - +
134B THR* 3.9 9.2 - - + +
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Residues in contact with LEU 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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46A GLN* 3.9 29.2 - - + +
47A PHE* 3.6 34.5 - - + -
86B TYR* 2.9 26.6 + - + +
89B MET* 4.3 12.6 - - + -
90B PHE* 3.6 24.9 - - + -
127B LYS 3.1 17.2 + - - +
128B PHE* 3.2 4.5 + - + +
130B LYS* 1.3 74.2 - - + +
132B LEU* 1.3 64.5 + - - +
134B THR* 2.8 38.8 + - + -
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B TYR* 4.6 1.5 + - - -
90B PHE* 3.9 11.1 - - + -
128B PHE 2.7 22.5 + - - +
129B GLU 4.0 4.5 - - - +
131B LEU* 1.3 72.4 - - - +
133B ALA* 1.3 61.1 + - - +
134B THR 3.2 1.4 + - - -
135B ARG 3.6 8.0 + - - +
138B GLY* 3.0 33.8 + - - +
141B LEU 4.2 5.6 - - - +
142B ILE* 4.0 42.2 - - + +
154B LEU* 4.7 2.5 - - + -
174B LEU* 3.7 32.3 - - + +
175B LEU* 4.1 13.0 - - + -
178B PHE* 3.9 21.8 - - + -
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Residues in contact with ALA 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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129B GLU 3.6 4.9 + - - +
130B LYS* 3.4 14.0 + - - +
131B LEU 3.1 1.2 + - - -
132B LEU* 1.3 77.5 - - - +
134B THR* 1.3 62.0 + - - +
135B ARG 3.3 0.9 - - - -
137B ASN* 3.3 24.0 + - - +
138B GLY* 3.6 11.4 - - - +
174B LEU* 3.8 20.6 - - + +
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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