Contacts of the helix formed by residues 54 - 59 (chain A) in PDB entry 4P5E
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 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A TYR* 3.5 46.7 - - + -
25A PHE* 2.7 41.8 + - - +
43A VAL* 4.9 0.5 - - - +
52A VAL* 3.4 5.2 - - - +
53A LEU* 1.3 82.7 - - + +
55A GLU* 1.3 61.8 + - - +
56A HIS* 2.9 32.7 + - + +
57A VAL* 3.2 15.9 + - - +
83A TRP* 4.2 4.3 - - + -
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Residues in contact with GLU 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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43A VAL* 4.6 14.4 - - + -
47A ARG* 3.2 31.5 + - - +
52A VAL* 4.4 10.1 + - + +
53A LEU 3.7 3.4 + - - +
54A THR* 1.3 74.7 - - - +
56A HIS* 1.3 66.0 + - - +
57A VAL 3.1 0.4 - - - -
58A ALA* 3.1 16.7 + - - +
59A ALA* 3.4 9.6 + - + +
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Residues in contact with HIS 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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29A ILE* 4.2 6.2 - - + +
33A ARG* 3.8 6.9 + - - -
53A LEU 4.7 0.2 + - - -
54A THR* 2.9 29.0 + - + -
55A GLU* 1.3 82.9 + - - +
57A VAL* 1.3 86.6 + - + +
59A ALA* 3.1 24.0 + - + +
80A ASP* 3.4 22.4 - - - -
83A TRP* 3.8 14.6 - + - -
201A N6P 2.9 56.6 + + + +
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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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25A PHE* 3.6 38.4 - - + +
27A GLY* 3.4 35.0 - - - +
28A SER 5.0 0.2 - - - +
29A ILE* 4.2 9.6 - - + +
33A ARG* 3.1 18.0 + - - -
36A ARG* 4.1 1.6 - - - +
39A TYR* 3.7 17.2 - - + -
54A THR 3.5 14.1 - - - +
55A GLU 3.1 0.6 + - - -
56A HIS* 1.3 93.7 - - + +
58A ALA* 1.3 57.4 + - - +
201A N6P 3.7 17.0 - - + +
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Residues in contact with ALA 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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36A ARG* 2.9 34.3 + - - -
39A TYR* 3.9 9.2 - - + +
40A GLU* 3.6 39.2 - - + +
43A VAL* 4.3 11.7 - - + -
54A THR 4.8 0.2 + - - -
55A GLU 3.1 9.8 + - - +
57A VAL* 1.3 78.6 - - - +
59A ALA* 1.3 59.0 + - - +
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Residues in contact with ALA 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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33A ARG* 2.8 33.6 + - - -
36A ARG* 4.1 11.2 - - - -
55A GLU* 3.4 5.7 + - + +
56A HIS* 3.1 23.9 + - + +
58A ALA* 1.3 81.9 - - - +
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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