Contacts of the helix formed by residues 51 - 63 (chain D) 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 LEU 51 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A GLN* 3.9 19.1 - - + -
90C LEU* 3.8 26.9 - - + -
94C ILE* 4.5 23.1 - - + -
28D PHE* 4.8 9.4 - - + +
29D ASN* 5.5 0.4 - - + -
31D ASP* 4.1 15.5 - - + +
33D LEU* 3.9 27.1 - - + +
47D GLU* 3.5 13.8 + - - +
49D GLY 3.3 1.2 - - - -
50D VAL* 1.3 82.3 - - + +
52D ASN* 1.3 63.2 + - - +
53D SER 3.3 2.0 - - - -
54D LEU* 3.2 24.5 + - + +
55D ALA* 2.9 20.6 + - - +
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Residues in contact with ASN 52 (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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45D PRO* 4.6 0.7 - - - +
47D GLU* 3.1 30.1 - - - +
48D PHE* 3.4 24.8 - - - -
49D GLY 3.3 17.6 + - - +
50D VAL 3.2 1.4 - - - -
51D LEU* 1.3 77.5 - - - +
53D SER* 1.3 63.1 + - - +
55D ALA* 2.8 19.7 + - - +
56D ASN* 3.1 32.8 + - - +
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Residues in contact with SER 53 (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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50D VAL 4.3 7.6 + - - -
51D LEU 3.3 0.6 - - - -
52D ASN* 1.3 86.7 - - - +
54D LEU* 1.3 61.6 + - - +
56D ASN* 3.3 14.5 + - - +
57D VAL* 3.3 22.7 + - - +
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Residues in contact with LEU 54 (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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86C ILE* 4.2 40.8 - - + -
90C LEU* 4.3 9.2 - - + -
28D PHE* 5.2 2.5 - - + -
33D LEU* 3.6 27.1 - - + -
51D LEU* 3.2 31.9 + - + +
52D ASN 3.2 0.4 - - - -
53D SER* 1.3 75.4 - - - +
55D ALA* 1.3 64.2 + - - +
57D VAL* 3.2 14.1 + - + +
58D LEU* 3.0 31.4 + - + +
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Residues in contact with ALA 55 (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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33D LEU* 3.5 39.7 - - + +
34D THR* 4.2 2.8 - - - -
45D PRO* 4.2 11.9 - - + -
47D GLU* 4.2 4.3 - - + +
51D LEU 2.9 12.7 + - - +
52D ASN* 2.8 17.6 + - - +
54D LEU* 1.3 76.8 - - - +
56D ASN* 1.3 56.9 + - - +
58D LEU* 4.2 3.0 - - - +
59D SER* 2.8 31.9 + - - -
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Residues in contact with ASN 56 (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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45D PRO* 3.0 26.6 - - + +
52D ASN* 3.1 30.9 + - - +
53D SER* 3.7 9.5 + - - +
54D LEU 3.2 0.2 - - - -
55D ALA* 1.3 78.7 - - - +
57D VAL* 1.3 58.6 + - + +
59D SER* 3.4 5.8 + - - -
60D GLN* 3.0 52.5 + - - +
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Residues in contact with VAL 57 (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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81C TRP* 5.8 1.8 - - + -
53D SER* 3.3 19.7 - - - +
54D LEU* 3.2 15.2 + - + +
56D ASN* 1.3 75.2 - - + +
58D LEU* 1.3 69.8 + - + +
60D GLN* 3.6 9.1 + - - +
61D HIS* 3.3 37.8 + - + +
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Residues in contact with LEU 58 (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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78C PHE* 4.5 10.8 - - + -
81C TRP* 3.6 33.2 - - + -
82C MET* 4.0 23.3 - - - -
86C ILE* 3.9 14.6 - - + -
26D ILE* 4.1 10.1 - - + -
33D LEU* 3.7 29.4 - - + -
34D THR* 4.5 8.3 - - + -
54D LEU* 3.0 26.9 + - + +
55D ALA* 4.2 3.8 - - - +
57D VAL* 1.3 77.1 - - + +
59D SER* 1.3 66.2 + - - +
60D GLN 3.2 0.3 + - - -
61D HIS* 3.2 5.6 + - - +
62D LEU* 3.2 31.4 + - + +
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Residues in contact with SER 59 (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 THR* 2.8 26.5 + - - +
43D MET* 3.2 25.9 + - - +
45D PRO* 3.9 9.6 - - - +
55D ALA 2.8 21.0 + - - -
56D ASN* 3.5 9.2 - - - -
57D VAL 3.3 0.2 - - - -
58D LEU* 1.3 79.6 - - - +
60D GLN* 1.3 54.5 + - - +
62D LEU* 3.6 3.0 + - - +
63D ASN* 2.7 40.0 + - - +
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Residues in contact with GLN 60 (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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56D ASN* 3.0 37.1 + - - +
57D VAL* 4.2 7.0 - - - +
58D LEU 3.2 0.2 - - - -
59D SER* 1.3 76.4 - - - +
61D HIS* 1.3 66.3 + - - +
62D LEU 3.2 1.5 + - - -
63D ASN* 3.4 15.1 + - + +
64D GLN* 3.4 32.4 - - - +
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Residues in contact with HIS 61 (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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78C PHE* 5.6 4.7 - - + -
81C TRP* 3.8 35.3 - + + -
57D VAL* 3.3 25.7 + - + +
58D LEU* 3.2 10.8 + - - +
60D GLN* 1.3 76.4 - - - +
62D LEU* 1.3 64.9 + - + +
64D GLN* 3.9 13.7 + - - +
65D LYS* 3.3 28.1 - - - +
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Residues in contact with LEU 62 (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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74C PHE* 4.3 10.3 - - + -
78C PHE* 3.6 47.6 - - + -
24D TYR* 5.6 0.9 - - - +
26D ILE* 4.1 21.8 - - + -
34D THR* 4.6 7.4 - - + -
43D MET* 4.1 20.0 - - + -
58D LEU* 3.2 22.7 + - + +
59D SER 4.0 2.2 - - - +
61D HIS* 1.3 73.9 - - + +
63D ASN* 1.3 58.0 + - - +
64D GLN 3.0 10.6 + - - -
65D LYS* 3.3 22.1 + - - +
68D LEU* 4.0 23.4 - - + +
69D MET* 3.2 16.0 - - - +
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Residues in contact with ASN 63 (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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42D LYS* 3.2 25.0 - - - +
43D MET* 2.9 38.6 + - - +
59D SER* 2.7 32.1 + - - +
60D GLN* 3.9 15.9 - - + +
61D HIS 3.4 0.8 - - - -
62D LEU* 1.3 76.6 - - - +
64D GLN* 1.3 60.8 + - + +
65D LYS 3.5 0.9 - - - -
69D MET* 3.4 21.6 - - - +
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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