Contacts of the helix formed by residues 118 - 127 (chain C) in PDB entry 3U53
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 118 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C ASN* 3.7 24.8 + - - -
24C ILE 3.6 15.7 - - - -
25C GLU* 3.8 4.2 + - - +
26C PHE* 4.6 0.9 - - - -
117C LEU* 1.3 76.5 - - - +
119C LEU* 1.3 67.0 + - - -
120C GLU 3.3 2.8 + - - -
121C GLU* 3.3 11.2 + - - +
122C ALA* 3.0 19.5 + - - +
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Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ASN* 4.6 3.8 - - - +
24C ILE 4.4 2.4 + - - -
26C PHE* 3.8 24.9 - - + -
118C GLY* 1.3 71.2 - - - -
120C GLU* 1.3 65.5 + - + +
122C ALA* 3.8 0.8 - - - -
123C CYS* 2.8 40.0 + - - +
135C LEU* 3.4 37.5 - - + +
136C GLN* 3.7 20.6 - - + +
139C HIS* 4.0 31.6 - - + +
157C SO4 5.1 4.9 + - - +
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Residues in contact with GLU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ASN* 5.6 2.1 - - - +
118C GLY 3.3 1.4 + - - -
119C LEU* 1.3 79.5 - - + +
121C GLU* 1.3 77.7 + - - +
123C CYS* 3.2 5.8 + - - +
124C GLN* 3.1 21.2 + - - +
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Residues in contact with GLU 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ASN* 4.5 10.5 + - - +
117C LEU* 4.1 23.8 - - + -
118C GLY* 3.3 22.2 - - - +
120C GLU* 1.3 87.7 + - - +
122C ALA* 1.3 68.8 + - - +
124C GLN* 2.9 18.9 + - - +
125C LEU* 3.0 16.2 + - + +
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Residues in contact with ALA 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C PHE* 4.4 12.1 - - + -
28C LEU* 3.7 20.8 - - + +
117C LEU* 3.8 24.8 - - + +
118C GLY 3.0 20.2 + - - +
119C LEU* 3.8 5.4 - - + +
121C GLU* 1.3 77.1 - - - +
123C CYS* 1.3 62.6 + - - +
125C LEU 3.4 0.7 + - - +
126C ALA* 3.1 20.4 + - - +
135C LEU* 4.0 13.1 - - + +
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Residues in contact with CYS 123 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119C LEU* 2.8 37.0 + - - +
120C GLU* 3.5 6.5 - - - +
122C ALA* 1.3 78.9 - - - +
124C GLN* 1.3 61.3 + - - +
126C ALA 3.4 0.6 + - - +
127C GLN 3.1 19.1 + - - -
132C LYS* 3.2 44.3 - - + +
135C LEU* 4.4 6.1 - - - -
136C GLN* 3.5 28.0 - - - +
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Residues in contact with GLN 124 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120C GLU 3.1 11.8 + - - +
121C GLU* 2.9 13.1 + - - +
123C CYS* 1.3 78.0 - - - +
125C LEU* 1.3 67.6 + - + +
127C GLN* 3.7 11.4 + - - +
132C LYS* 5.1 2.9 - - - +
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Residues in contact with LEU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C LEU* 4.4 3.6 - - + -
36C HIS 5.4 1.9 - - - +
38C TRP* 3.3 69.6 + - + +
115C ARG* 5.3 2.9 - - + -
117C LEU* 3.9 22.4 - - + -
121C GLU* 3.0 15.2 + - + +
122C ALA 3.8 6.5 - - - +
124C GLN* 1.3 80.6 - - + +
126C ALA* 1.3 68.6 + - - +
127C GLN* 3.1 6.2 + - - +
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Residues in contact with ALA 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C LEU* 4.7 3.1 - - + +
37C HIS* 6.1 0.7 - - - -
38C TRP* 4.1 17.2 + - - +
122C ALA 3.1 16.4 + - - +
123C CYS 3.4 4.2 + - - +
125C LEU* 1.3 76.9 - - - +
127C GLN* 1.3 57.2 + - - +
128C PHE* 2.5 25.2 + - - +
131C MET* 3.7 33.2 - - + +
132C LYS* 4.3 6.3 - - + -
135C LEU* 4.2 11.0 - - + -
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Residues in contact with GLN 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C CYS 3.1 7.4 + - - -
124C GLN 4.0 9.0 - - - +
125C LEU 3.1 7.9 - - - +
126C ALA* 1.3 81.1 - - - +
128C PHE* 1.3 58.3 + - + +
129C LYS* 3.3 5.2 + - - +
132C LYS* 2.6 36.0 + - - +
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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