Contacts of the helix formed by residues 34 - 38 (chain O) in PDB entry 3EQL
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 34 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30O LEU 2.6 22.0 - - - +
31O LEU 3.6 8.7 - - - -
32O ARG 3.1 5.0 - - - -
33O HIS* 1.3 78.4 - - - +
35O PHE* 1.3 56.0 + - - -
36O LYS 3.5 1.6 - - - -
37O ASN* 2.6 17.8 - - - +
93O TYR* 5.4 0.9 - - - -
95O VAL* 3.3 22.0 - - - -
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Residues in contact with PHE 35 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30O LEU* 3.0 28.1 - - + +
31O LEU* 3.4 34.1 + - + -
34O GLY* 1.3 70.0 - - - +
36O LYS* 1.3 59.9 + - + +
37O ASN* 3.0 11.7 + - - +
38O THR 3.8 5.4 + - - -
55O PHE 5.4 0.2 - - - -
56O ASP* 3.1 26.9 - - - +
57O ASP* 4.3 25.6 - - + +
59O ASN 4.2 3.6 - - - -
60O ALA* 3.6 27.1 - - + -
63O TRP* 3.4 49.3 - + - -
95O VAL* 5.5 3.2 - - - +
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Residues in contact with LYS 36 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34O GLY 3.5 1.2 - - - -
35O PHE* 1.3 75.7 - - + +
37O ASN* 1.3 56.9 + - - +
38O THR* 2.8 28.2 + - + +
41O GLU* 4.7 20.7 + - + +
45O ARG* 5.3 20.2 - - - +
55O PHE 5.7 4.0 - - - +
56O ASP* 6.1 1.8 - - - -
63O TRP* 5.4 2.2 - - + -
93O TYR* 3.8 13.4 - - + -
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Residues in contact with ASN 37 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1488N ASP* 4.4 6.0 + - - +
26O ARG* 3.2 16.8 + - - +
29O GLN* 4.2 2.2 - - - +
30O LEU* 4.3 15.3 - - + -
33O HIS* 3.0 41.0 - - - +
34O GLY* 2.6 35.2 + - - +
35O PHE 3.0 1.6 + - - -
36O LYS* 1.3 75.4 - - - +
38O THR* 1.3 63.8 + - - +
39O VAL* 4.4 2.6 - - - +
89O MET* 3.9 6.5 - - - +
93O TYR* 3.3 46.4 + - + +
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Residues in contact with THR 38 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1490N LYS* 4.5 6.9 - - - -
26O ARG* 3.7 10.7 - - - +
30O LEU* 4.5 2.1 - - - +
35O PHE 3.8 2.2 + - - -
36O LYS* 2.8 17.3 + - + +
37O ASN* 1.3 83.7 - - - +
39O VAL* 1.3 66.7 + - - +
40O LEU* 3.1 32.4 - - + +
41O GLU* 4.0 17.9 - - + +
45O ARG* 4.7 1.8 - - - +
63O TRP* 3.5 37.4 - - + -
67O GLU* 3.9 10.0 + - - +
93O TYR* 4.8 1.2 + - - -
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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