Contacts of the helix formed by residues 118 - 127 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ASN* 3.2 30.0 + - - -
24A ILE 3.8 7.4 - - - -
25A GLU* 4.0 4.4 - - - +
117A LEU* 1.3 77.4 - - - +
119A LEU* 1.3 66.9 + - - -
120A GLU 3.2 3.2 + - - -
121A GLU* 3.3 12.7 + - - -
122A ALA* 3.1 16.5 + - - +
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Residues in contact with LEU 119 (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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22A ASN* 4.0 5.7 - - - +
24A ILE 4.4 2.2 + - - -
26A PHE* 3.8 26.3 - - + -
117A LEU 3.9 0.4 + - - -
118A GLY* 1.3 71.3 - - - +
120A GLU* 1.3 64.0 + - - +
122A ALA* 3.4 1.0 + - - +
123A CYS* 3.1 46.8 + - - -
135A LEU* 3.8 26.9 - - + +
136A GLN* 3.8 13.7 - - + +
139A HIS* 3.2 43.1 - - + +
156A SO4 4.9 4.6 + - - +
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Residues in contact with GLU 120 (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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22A ASN* 5.3 1.2 - - - +
118A GLY 3.2 1.2 + - - -
119A LEU* 1.3 79.9 - - - +
121A GLU* 1.3 77.8 + - - +
123A CYS* 3.3 6.7 + - + +
124A GLN* 3.0 29.2 + - + +
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Residues in contact with GLU 121 (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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21A ASN* 6.1 0.7 - - - -
22A ASN* 4.5 6.0 + - - +
117A LEU* 3.9 21.7 - - + +
118A GLY* 3.3 21.2 - - - +
120A GLU* 1.3 92.3 + - - +
122A ALA* 1.3 57.5 + - - +
124A GLN* 3.1 10.0 + - - +
125A LEU* 2.8 31.4 + - - +
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Residues in contact with ALA 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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26A PHE* 4.2 21.5 - - + -
28A LEU* 3.5 13.4 - - + +
117A LEU* 3.6 22.3 - - + +
118A GLY 3.1 17.3 + - - +
119A LEU* 3.5 5.6 - - + +
121A GLU* 1.3 77.6 - - - +
123A CYS* 1.3 57.3 + - - +
125A LEU 3.3 0.5 + - - -
126A ALA* 2.8 30.8 + - - +
135A LEU* 4.2 11.7 - - + -
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Residues in contact with CYS 123 (chain A).
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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119A LEU* 3.1 36.8 + - - -
120A GLU* 3.7 8.5 - - + +
122A ALA* 1.3 77.3 - - - +
124A GLN* 1.3 64.0 + - + +
126A ALA 4.5 0.2 - - - +
127A GLN* 3.1 19.4 + - - -
132A LYS* 3.4 46.7 - - + +
135A LEU* 4.3 7.6 - - - -
136A GLN* 3.8 26.0 - - - +
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Residues in contact with GLN 124 (chain A).
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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120A GLU* 3.0 23.8 + - + +
121A GLU* 3.3 12.3 - - - +
123A CYS* 1.3 78.3 - - - +
125A LEU* 1.3 59.9 + - - +
127A GLN* 3.8 10.6 + - - +
132A LYS* 4.8 7.6 - - - +
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Residues in contact with LEU 125 (chain A).
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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28A LEU* 3.9 6.5 - - + -
36A HIS 5.3 1.4 - - - +
38A TRP* 3.6 65.7 + - + +
115A ARG* 4.7 11.4 - - + +
117A LEU* 3.8 20.2 - - + -
121A GLU 2.8 14.8 + - - +
122A ALA 3.7 3.8 - - - +
124A GLN* 1.3 75.5 - - - +
126A ALA* 1.3 66.2 + - - +
127A GLN* 3.2 6.5 + - - +
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Residues in contact with ALA 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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28A LEU* 4.2 4.4 - - + +
37A HIS* 5.6 4.0 + - - -
38A TRP 3.9 21.7 + - - +
122A ALA 2.8 21.0 + - - +
123A CYS* 4.0 3.8 - - - +
125A LEU* 1.3 73.8 - - - +
127A GLN* 1.3 56.1 + - - +
128A PHE* 2.8 20.8 + - - +
131A MET* 3.7 32.0 - - + +
132A LYS* 4.7 2.9 - - + -
135A LEU* 4.3 8.5 - - + -
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Residues in contact with GLN 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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36A HIS* 5.4 11.7 - - + +
123A CYS 3.1 14.6 + - - -
124A GLN 4.1 8.3 - - - +
125A LEU 3.2 6.8 - - - +
126A ALA* 1.3 77.0 - - - +
128A PHE* 1.3 61.9 + - - +
129A LYS* 3.6 1.4 + - - -
132A LYS* 3.4 16.8 + - - +
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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