Contacts of the helix formed by residues 37 - 44 (chain D) in PDB entry 5A63
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 PHE 37 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D LEU* 4.2 15.7 - - + -
11D LYS* 3.7 27.8 - - + -
14D LEU* 4.2 7.6 - - + -
15D CYS* 3.4 39.3 - - + -
18D TYR* 5.4 0.4 - - + -
33D ASN* 3.0 36.1 + - - +
34D ILE 3.7 0.9 - - - -
36D TRP* 1.3 112.4 - + - +
38D PHE* 1.3 63.0 + - - +
39D ARG 3.2 1.8 - - - +
40D GLU* 4.6 11.2 - - + +
41D ALA* 2.9 30.3 + - - +
53D ILE* 3.6 24.0 - - + -
57D VAL* 3.4 11.0 - - + +
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Residues in contact with PHE 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ILE* 2.8 24.9 + - + +
35D PHE* 3.5 8.9 + - - +
37D PHE* 1.3 78.0 - - - +
39D ARG* 1.3 85.7 + - + +
41D ALA* 4.0 1.1 - - - +
42D PHE* 2.9 47.1 + + + +
57D VAL* 4.5 12.6 - - + -
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Residues in contact with ARG 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D PHE 4.0 11.6 + - - +
36D TRP 6.1 1.1 - - - -
37D PHE* 3.2 0.6 - - - +
38D PHE* 1.3 95.6 - - + +
40D GLU* 1.3 69.1 + - - +
42D PHE* 4.4 0.4 - - - +
43D LEU* 2.6 52.9 + - + +
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Residues in contact with GLU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 2.7 38.2 - - + +
4D GLU* 3.0 25.7 - - - +
11D LYS* 3.8 19.5 - - + +
36D TRP 4.3 2.9 - - - +
37D PHE* 4.0 13.9 - - + +
38D PHE 3.3 0.2 - - - -
39D ARG* 1.3 87.4 - - - +
41D ALA* 1.3 56.5 + - - +
43D LEU* 4.3 9.5 - - + +
44D VAL* 2.4 51.4 + - + +
47D TYR* 4.8 7.4 - - + +
53D ILE* 6.2 0.7 - - + -
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Residues in contact with ALA 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE 2.9 21.9 + - - +
38D PHE* 4.0 1.6 - - - +
39D ARG 3.2 0.6 - - - -
40D GLU* 1.3 82.2 - - - +
42D PHE* 1.3 64.2 + - + +
44D VAL* 4.0 1.3 + - - -
50D GLN* 3.3 33.1 + - - +
53D ILE* 4.1 10.7 - - + +
54D LYS* 3.9 37.5 + - + +
57D VAL* 4.7 1.8 - - + -
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Residues in contact with PHE 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D PHE* 2.9 40.2 + + + +
39D ARG* 5.5 0.2 - - - -
41D ALA* 1.3 79.7 - - + +
43D LEU* 1.3 62.7 - - - +
44D VAL 3.5 7.6 - - - +
54D LYS* 5.0 25.3 + - + +
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D GLU* 6.1 0.4 - - - +
39D ARG* 2.6 38.9 + - + +
40D GLU* 3.8 8.5 - - + +
42D PHE* 1.3 76.6 - - - +
44D VAL* 1.3 68.2 + - + +
45D PRO* 3.2 5.7 - - - +
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Residues in contact with VAL 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D GLU* 2.4 56.9 + - + +
42D PHE 3.4 9.6 - - - +
43D LEU* 1.3 77.2 - - + +
45D PRO* 1.4 75.8 - - + +
46D ALA* 2.7 31.4 - - - +
47D TYR* 2.9 37.7 - - + -
50D GLN* 3.9 24.4 + - + -
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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