Contacts of the helix formed by residues 52 - 60 (chain B) in PDB entry 4YET
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 THR 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B PHE* 4.2 2.7 - - - -
50B SER 3.8 2.2 + - - +
51B CYS* 1.3 77.2 - - - +
53B ILE* 1.3 65.4 + - - +
54B GLU* 3.6 14.2 + - - +
55B GLU* 2.9 45.8 + - - +
56B LEU* 3.0 20.6 + - - +
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Residues in contact with ILE 53 (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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3B PHE* 3.8 19.9 - - + -
39B LEU* 5.2 2.0 - - + -
52B THR* 1.3 73.6 - - - +
54B GLU* 1.3 79.3 + - - +
56B LEU* 3.2 6.3 + - - +
57B ILE* 3.0 30.3 + - + +
68B ALA* 3.5 34.1 - - + +
71B ILE* 3.5 30.1 - - + -
72B TRP* 3.7 12.6 - - + +
198B TRP* 3.5 45.7 - - + +
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Residues in contact with GLU 54 (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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52B THR* 3.2 12.5 + - - +
53B ILE* 1.3 93.3 - - - +
55B GLU* 1.3 57.0 + - - +
57B ILE* 3.3 8.1 + - - +
58B LEU* 2.9 41.9 + - + +
72B TRP* 2.9 31.2 + - + +
146B LEU* 3.9 16.4 - - + -
196B PHE 4.4 1.7 - - - +
197B LYS* 3.9 9.1 - - - +
198B TRP* 3.1 24.3 + - - +
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Residues in contact with GLU 55 (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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50B SER 4.5 1.6 - - - +
51B CYS* 3.4 19.2 - - + +
52B THR* 2.9 46.3 + - - +
54B GLU* 1.3 77.7 - - + +
56B LEU* 1.3 57.5 + - - +
58B LEU* 3.8 6.0 - - + +
59B GLY* 2.9 28.6 + - - -
60B GLN* 5.0 1.1 + - - +
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Residues in contact with LEU 56 (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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3B PHE* 3.8 34.1 - - + -
39B LEU* 4.0 24.2 - - + -
43B ILE* 4.3 4.9 - - + -
48B MET* 4.0 20.4 - - + +
51B CYS* 3.6 23.3 - - + -
52B THR 3.0 14.0 + - - +
53B ILE* 3.6 6.1 - - - +
55B GLU* 1.3 73.2 - - - +
57B ILE* 1.3 62.5 + - - +
60B GLN* 2.9 55.2 + - + +
64B VAL* 4.3 6.1 - - + -
65B PHE* 4.5 2.6 - - - -
68B ALA* 3.9 13.9 - - + -
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Residues in contact with ILE 57 (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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53B ILE* 3.0 22.4 + - + +
54B GLU* 3.6 7.6 - - - +
56B LEU* 1.3 77.0 - - - +
58B LEU* 1.3 62.6 + - + +
60B GLN 4.2 2.1 - - - +
65B PHE* 3.3 30.7 - - + -
68B ALA* 3.9 6.1 - - + +
69B ALA* 3.8 26.7 - - + +
72B TRP* 3.6 40.6 - - + -
144B SER* 3.6 30.5 - - - +
146B LEU* 4.4 10.3 - - + -
147B LYS* 4.0 13.4 - - + +
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Residues in contact with LEU 58 (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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54B GLU* 2.9 28.2 + - + +
55B GLU* 4.0 5.6 - - + +
57B ILE* 1.3 78.8 - - + +
59B GLY* 1.3 59.8 + - - +
60B GLN 3.8 0.8 - - - +
146B LEU* 3.7 38.8 - - + +
147B LYS* 4.0 8.5 - - - +
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Residues in contact with GLY 59 (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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55B GLU 2.9 15.1 + - - -
58B LEU* 1.3 79.4 - - - +
60B GLN* 1.3 74.5 + - - +
61B THR* 5.4 1.3 - - - +
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Residues in contact with GLN 60 (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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48B MET* 3.6 30.0 - - - +
51B CYS* 5.5 4.0 - - - -
55B GLU 5.4 0.8 + - - -
56B LEU* 2.9 40.5 + - + +
57B ILE 4.2 1.7 - - - +
58B LEU 5.0 0.5 - - - +
59B GLY* 1.3 90.8 + - - +
61B THR* 1.3 71.5 + - - +
64B VAL* 3.9 21.3 - - + +
65B PHE* 3.5 23.3 - - - +
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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