Contacts of the helix formed by residues 48 - 56 (chain A) in PDB entry 4FQX
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 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLU 4.3 0.2 - - - -
31A ILE* 3.5 38.6 - - + +
43A TRP* 3.9 5.8 - - + -
44A ARG 4.3 0.2 - - - -
45A LEU* 3.0 42.6 + - + +
47A GLU* 1.3 86.4 - - + +
49A GLY* 1.3 65.3 + - - +
50A ARG 3.4 2.0 - - - -
51A PHE* 3.4 9.2 + - + +
52A ALA* 2.9 23.4 + - + +
88B SER* 4.1 11.2 - - - -
89B PHE* 3.3 39.9 - + + -
93B ARG* 5.7 1.8 - - - -
153B TRP* 3.6 48.0 - + - -
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Residues in contact with GLY 49 (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 TRP* 3.8 26.9 - - - -
46A GLU 2.9 16.7 + - - -
47A GLU 3.3 0.6 - - - -
48A PHE* 1.3 76.4 - - - +
50A ARG* 1.3 62.1 + - - +
52A ALA* 3.3 2.1 + - - +
53A SER* 3.1 27.1 + - - -
30D LYS* 4.4 12.8 - - - +
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Residues in contact with ARG 50 (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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46A GLU 5.8 1.1 - - - -
47A GLU 4.7 11.0 - - - +
48A PHE 3.4 0.6 - - - -
49A GLY* 1.3 71.3 - - - +
51A PHE* 1.3 66.8 + - - +
52A ALA 3.3 0.2 + - - -
53A SER* 3.3 6.8 + - - -
54A PHE* 3.1 23.1 + - - +
154C ASP* 5.4 4.8 + - - -
155C GLY* 4.1 33.2 - - - +
30D LYS* 5.8 3.4 - - - +
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Residues in contact with PHE 51 (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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24A PHE* 4.2 21.8 - + - -
31A ILE* 3.6 28.9 - - + -
32A PHE* 3.5 25.1 - + - -
47A GLU 5.4 1.1 + - - +
48A PHE* 3.4 12.2 + - + +
49A GLY 3.4 0.2 - - - -
50A ARG* 1.3 79.6 - - - +
52A ALA* 1.3 59.8 + - - +
54A PHE* 3.4 6.4 + + + +
55A GLU* 2.9 55.3 + - + +
82B ASN* 4.9 7.9 - - + -
85B VAL* 3.5 33.4 - - + -
86B GLY* 6.0 0.7 - - - +
89B PHE* 3.8 29.2 - + + -
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Residues in contact with ALA 52 (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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32A PHE* 3.6 42.0 - - + -
41A THR* 4.2 9.9 - - + -
43A TRP* 4.0 12.3 - - + -
48A PHE 2.9 18.4 + - - +
49A GLY 3.7 3.8 - - - +
51A PHE* 1.3 75.6 - - + +
53A SER* 1.3 64.8 + - - +
56A ALA* 3.0 31.0 + - - +
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Residues in contact with SER 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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41A THR* 4.8 4.0 - - - +
43A TRP* 4.8 2.1 - - - -
49A GLY 3.1 14.2 + - - -
50A ARG* 3.7 8.1 - - - -
52A ALA* 1.3 78.6 - - - +
54A PHE* 1.3 62.4 + - - +
55A GLU 3.5 0.2 + - - -
56A ALA 3.7 2.9 + - - -
57A GLN* 2.5 33.1 + - - +
97C SER* 3.8 8.3 + - - -
29D ASN 4.4 1.1 - - - -
30D LYS* 3.2 49.0 + - - +
31D ASP* 4.2 4.8 - - - +
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Residues in contact with PHE 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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50A ARG 3.1 10.3 + - - +
51A PHE* 3.5 12.3 - + + +
53A SER* 1.3 80.2 - - - +
55A GLU* 1.3 70.0 + - + +
56A ALA 3.6 0.5 + - - -
57A GLN* 4.3 7.8 + - - +
81B HIS* 6.3 2.2 - + - -
85B VAL* 6.1 9.6 - - + -
31D ASP* 5.1 5.3 - - - +
46D SER 5.9 2.5 - - - -
47D GLU* 3.7 27.1 - - - +
48D PHE 5.3 5.2 - - - -
49D GLY* 5.1 9.4 - - - -
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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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22A PHE* 3.8 19.4 - - - -
24A PHE* 4.1 14.5 - - + -
32A PHE* 3.9 19.1 - - + -
51A PHE* 2.9 49.9 + - + +
52A ALA 3.3 0.6 + - - -
54A PHE* 1.3 87.5 - - + +
56A ALA* 1.3 56.7 + - - +
57A GLN 3.7 0.9 - - - -
58A GLY 5.3 0.7 + - - -
59A ALA 5.6 0.2 + - - -
78B TYR* 6.0 0.2 - - - -
81B HIS* 5.4 2.9 + - - -
82B ASN* 3.7 23.9 + - - +
85B VAL* 5.9 2.4 - - - +
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Residues in contact with ALA 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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32A PHE* 3.5 16.6 - - + -
34A VAL* 3.9 7.0 - - + -
41A THR* 3.5 28.3 - - + +
52A ALA 3.0 17.8 + - - +
53A SER* 4.5 1.3 - - - +
54A PHE 3.4 0.4 - - - -
55A GLU* 1.3 77.7 - - - +
57A GLN* 1.3 66.3 + - - +
58A GLY 3.2 4.1 + - - -
59A ALA* 3.2 17.0 + - - +
95C PRO* 3.3 16.3 - - - +
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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