Contacts of the helix formed by residues 52 - 60 (chain A) in PDB entry 1UES
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 ASP 52 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.6 12.6 - - + -
3A HIS* 4.3 0.4 - - - -
50A ASN 4.0 0.6 + - - -
51A ALA* 1.3 77.0 - - - +
53A LEU* 1.3 67.8 + - - +
54A ASN* 3.5 20.0 - - - +
55A THR* 2.4 43.3 + - - -
56A ILE* 3.1 11.0 + - - +
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Residues in contact with LEU 53 (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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1A MET* 5.1 2.2 - - + +
3A HIS* 3.8 20.8 - - + +
39A LEU* 3.8 27.4 - - + -
52A ASP* 1.3 73.6 - - - +
54A ASN* 1.3 63.9 + - - +
56A ILE* 3.1 7.1 + - + +
57A VAL* 3.0 25.9 + - + +
68A ALA* 3.8 25.1 - - + +
71A THR* 3.7 24.7 - - + -
72A LEU* 3.8 26.9 - - + +
75A ASN* 3.7 15.3 - - - +
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Residues in contact with ASN 54 (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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52A ASP* 3.2 14.4 + - - +
53A LEU* 1.3 78.1 - - - +
55A THR* 1.3 60.7 + - - +
57A VAL* 3.3 6.2 + - - +
58A GLN* 2.8 51.0 + - - +
72A LEU* 4.1 27.8 - - - +
146A VAL* 4.4 13.9 - - - +
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Residues in contact with THR 55 (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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48A PHE* 4.9 2.2 - - + -
51A ALA* 4.1 15.3 - - + -
52A ASP* 2.4 33.2 + - - -
54A ASN* 1.3 74.5 - - - +
56A ILE* 1.3 66.7 + - - +
58A GLN* 3.2 14.5 + - - +
59A LYS* 3.0 57.1 + - + +
776D LYS* 5.2 3.1 - - - +
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Residues in contact with ILE 56 (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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3A HIS* 3.7 30.1 - - + +
39A LEU* 4.6 6.7 - - + -
43A ILE* 4.4 8.5 - - + -
48A PHE* 3.7 37.2 - - + +
51A ALA* 3.8 15.5 - - + +
52A ASP 3.1 8.5 + - - +
53A LEU* 3.1 7.0 + - - +
55A THR* 1.3 77.9 - - - +
57A VAL* 1.3 55.1 + - - +
60A SER* 2.7 48.5 + - - +
64A ILE* 3.7 17.5 - - + -
68A ALA* 3.6 22.2 - - + -
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Residues in contact with VAL 57 (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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53A LEU* 3.0 21.6 + - + +
54A ASN 3.9 2.5 - - - +
56A ILE* 1.3 76.3 - - - +
58A GLN* 1.3 61.8 + - - +
59A LYS 3.5 0.2 + - - -
60A SER 4.5 0.3 + - - -
65A PHE* 3.4 36.4 - - + -
68A ALA* 3.6 33.4 - - + +
69A GLY* 4.4 2.2 - - - -
72A LEU* 3.9 22.2 - - + -
144A ASN* 4.2 11.0 - - + -
146A VAL* 3.2 28.7 - - + -
147A ARG* 3.7 9.3 + - - +
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Residues in contact with GLN 58 (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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54A ASN* 2.8 35.5 + - - +
55A THR* 3.2 24.5 + - - +
57A VAL* 1.3 79.4 - - - +
59A LYS* 1.3 68.2 + - + +
60A SER 5.3 0.2 - - - -
146A VAL* 4.2 27.9 - - + +
147A ARG* 4.5 12.7 + - - +
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Residues in contact with LYS 59 (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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47A GLU* 5.2 2.5 - - - +
48A PHE* 3.8 13.8 - - + -
55A THR* 3.0 40.1 + - + +
58A GLN* 1.3 92.5 - - + +
60A SER* 1.3 68.1 + - - +
61A GLU* 4.4 5.7 - - - +
776D LYS* 4.0 28.9 - - - +
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Residues in contact with SER 60 (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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48A PHE* 3.5 28.6 - - - -
56A ILE* 2.7 32.5 + - - +
57A VAL 4.8 0.2 - - - +
58A GLN 4.0 0.2 - - - -
59A LYS* 1.3 79.0 - - - +
61A GLU* 1.3 64.2 + - - +
64A ILE* 3.5 16.4 - - - -
65A PHE* 3.1 28.1 + - - +
147A ARG* 3.1 19.9 + - - -
709D GLU* 6.6 0.2 - - - -
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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