Contacts of the helix formed by residues 117 - 128 (chain B) in PDB entry 4UQJ
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 LEU 117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B PRO 3.3 4.5 + - - +
116B ASP* 1.3 72.1 + - - +
118B LYS* 1.3 67.3 + - - +
119B GLY 3.1 3.4 - - - -
120B ALA* 3.0 12.3 + - + +
121B LEU* 2.9 27.9 + - + +
145B THR* 5.3 7.2 - - + +
223B ALA* 3.5 38.6 - - + +
224B ASN* 3.5 14.4 - - - +
225B LEU* 3.8 23.8 - - + +
245B PHE* 3.6 39.5 - - + -
358B ILE* 4.3 4.9 - - + -
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Residues in contact with LYS 118 (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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116B ASP* 3.3 22.8 + - - +
117B LEU* 1.3 77.8 - - - +
119B GLY* 1.3 60.2 + - - +
121B LEU* 3.6 5.8 + - - +
122B LEU* 3.3 31.7 + - + +
144B SER* 5.5 3.6 - - - +
145B THR* 4.5 21.5 - - + +
148B ALA* 4.5 17.9 - - + +
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Residues in contact with GLY 119 (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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116B ASP* 4.2 5.9 + - - -
117B LEU 3.1 1.2 - - - -
118B LYS* 1.3 77.1 - - - +
120B ALA* 1.3 62.8 + - - +
121B LEU 3.3 0.3 + - - -
122B LEU* 3.4 7.9 + - - +
123B SER* 3.1 26.3 + - - -
374B TRP* 3.6 23.5 - - - -
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Residues in contact with ALA 120 (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 LEU* 3.0 18.6 + - + +
119B GLY* 1.3 74.8 - - - +
121B LEU* 1.3 63.1 + - - +
123B SER* 3.6 2.1 + - - -
124B LEU* 3.2 16.8 + - - +
245B PHE* 3.4 28.7 - - + -
358B ILE* 4.2 12.8 - - + -
374B TRP* 3.7 38.4 - - + +
380B MET* 4.4 3.1 - - - +
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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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117B LEU* 2.9 20.0 + - + +
118B LYS* 3.8 5.8 - - - +
120B ALA* 1.3 74.5 - - - +
122B LEU* 1.3 67.4 + - + +
124B LEU* 3.0 13.6 + - + +
125B ILE* 3.1 35.5 + - + +
135B TYR* 4.5 20.4 - - + +
145B THR* 5.1 12.6 - - + -
149B VAL* 4.7 10.8 - - + -
193B ILE* 4.1 14.6 - - + -
221B ILE* 5.0 5.8 - - + -
223B ALA* 3.9 24.5 - - + -
245B PHE* 3.6 22.8 - - + -
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LYS* 3.3 19.1 + - + +
119B GLY* 3.4 6.5 + - - +
121B LEU* 1.3 79.2 - - + +
123B SER* 1.3 61.6 + - - +
125B ILE* 3.4 8.7 + - + +
126B GLU* 3.4 25.9 + - - +
148B ALA* 4.2 13.2 - - + +
149B VAL* 3.9 34.8 - - + +
152B SER* 3.5 30.7 - - - +
158B TRP* 4.3 12.6 - - + -
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Residues in contact with SER 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 GLY 3.1 8.6 + - - -
120B ALA 3.8 1.3 - - - -
121B LEU 3.1 0.8 - - - -
122B LEU* 1.3 75.4 - - - +
124B LEU* 1.3 65.0 + - - +
126B GLU* 3.4 9.8 + - - +
127B TYR* 3.1 21.3 + - - +
374B TRP* 2.8 39.9 + - - -
379B LYS* 4.6 7.1 - - - +
380B MET* 3.9 16.0 - - - +
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Residues in contact with LEU 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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120B ALA 3.2 10.5 + - - +
121B LEU* 3.0 10.0 + - + +
123B SER* 1.3 75.1 - - - +
125B ILE* 1.3 64.8 + - - +
127B TYR* 3.1 17.4 + - + +
128B TYR* 3.2 53.5 + - + -
221B ILE* 3.9 24.2 - - + -
243B SER* 4.4 9.2 - - - -
244B GLY 4.8 5.6 - - - +
245B PHE* 3.6 24.5 - - + -
360B ILE* 3.6 26.7 - - + -
380B MET* 3.6 15.0 - - + +
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Residues in contact with ILE 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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121B LEU* 3.1 35.0 + - + +
122B LEU* 3.6 11.0 - - - +
123B SER 3.3 0.4 - - - -
124B LEU* 1.3 77.1 - - - +
126B GLU* 1.3 57.8 + - - +
128B TYR* 3.4 3.3 + - - -
129B GLN 3.0 20.3 + - - -
130B TRP* 3.1 39.2 + - + +
133B PHE* 3.7 21.3 - - + -
149B VAL* 4.6 7.4 - - + -
158B TRP* 3.7 32.5 - - + -
193B ILE* 3.7 22.0 - - + -
221B ILE* 5.0 7.0 - - + -
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Residues in contact with GLU 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 LEU 3.4 12.1 + - - +
123B SER* 3.4 10.5 + - - +
124B LEU 3.3 0.4 - - - -
125B ILE* 1.3 73.8 - - - +
127B TYR* 1.3 65.0 + - - +
129B GLN* 2.9 22.8 + - - +
130B TRP 5.0 0.4 - - - +
156B LYS* 4.8 8.1 - - - +
158B TRP* 4.1 21.5 - - + -
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Residues in contact with TYR 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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123B SER 3.1 13.6 + - - +
124B LEU* 3.1 14.3 + - + +
126B GLU* 1.3 78.5 - - - +
128B TYR* 1.3 98.6 + + - +
129B GLN* 3.3 10.6 + - - +
362B GLU* 4.3 2.6 + - - -
371B ILE* 4.1 17.4 - - + +
380B MET* 3.8 15.9 - - - -
382B LEU* 3.3 44.2 - - + +
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Residues in contact with TYR 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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124B LEU* 3.2 50.2 + - + +
125B ILE 4.1 0.9 - - - +
127B TYR* 1.3 92.7 - + - +
129B GLN* 1.3 72.3 + - - +
130B TRP* 3.2 27.4 + + + +
191B ARG* 4.5 4.9 + - - -
219B HIS* 3.8 26.0 - + - -
221B ILE* 4.4 8.3 - - + -
241B GLU* 5.2 2.7 - - - -
243B SER* 2.7 27.6 + - - -
360B ILE* 5.0 0.2 - - - +
362B GLU* 2.6 34.6 + - - +
371B ILE* 4.0 4.2 - - - +
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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