Contacts of the helix formed by residues 54 - 68 (chain A) in PDB entry 4UQJ
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 ASN 54 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLU* 3.0 21.4 + - + +
53A ALA* 1.3 75.8 - - - +
55A SER* 1.3 63.7 + - - +
56A PHE* 3.0 9.3 + - - +
57A ALA* 3.8 19.9 - - + +
58A VAL* 3.1 25.9 + - - +
87B SER* 2.6 29.3 + - - -
91B THR* 4.3 12.8 + - - -
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Residues in contact with SER 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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53A ALA 3.1 5.2 + - - -
54A ASN* 1.3 71.6 + - - +
56A PHE* 1.3 65.0 + - - +
58A VAL* 3.3 3.8 + - - +
59A THR* 2.8 28.0 + - - -
80A LYS* 3.4 27.9 + - - +
81A SER* 4.3 8.5 - - - -
84A THR* 4.1 14.9 + - - -
83B ASN* 3.6 19.3 + - - +
84B THR* 4.4 4.0 - - - -
87B SER* 3.3 18.8 + - - -
88B PHE* 4.8 1.1 - - - -
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Residues in contact with PHE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ASN* 3.0 7.2 + - - +
55A SER* 1.3 74.0 - - - +
57A ALA* 1.3 69.9 + - + +
59A THR* 3.0 14.9 + - - -
60A ASN* 3.1 39.5 + - - +
87B SER* 2.7 25.2 + - - +
88B PHE* 3.3 46.9 - + + -
91B THR* 3.4 41.7 - - + +
92B LEU* 4.3 5.8 - - + -
315B CYS 3.8 15.7 - - - -
320B ALA* 3.8 22.0 - - + -
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Residues in contact with ALA 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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50A LEU* 3.3 30.7 - - + +
51A GLU* 4.5 8.5 - - + +
54A ASN* 3.5 27.5 + - + +
55A SER 3.4 0.4 - - - -
56A PHE* 1.3 86.9 - - + +
58A VAL* 1.3 58.7 + - - +
60A ASN* 3.2 6.2 + - - +
61A ALA 2.9 24.1 + - - -
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Residues in contact with VAL 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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17A LEU* 4.6 10.8 - - + +
50A LEU* 5.1 2.9 - - + -
51A GLU 4.3 1.8 - - - +
52A VAL* 3.4 32.3 - - + +
54A ASN 3.1 16.6 + - - +
55A SER 3.6 7.9 - - - +
57A ALA* 1.3 74.9 - - - +
59A THR* 1.3 62.1 + - - +
61A ALA* 3.5 6.6 + - - +
62A PHE* 3.1 22.7 + - - +
76A PHE 5.7 3.6 - - - +
77A TYR* 6.2 0.2 - - + -
81A SER* 3.9 13.9 - - - +
84A THR* 4.6 7.9 - - + -
85A ILE* 3.5 33.4 - - + -
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Residues in contact with THR 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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55A SER 2.8 19.4 + - - -
56A PHE 3.0 8.8 + - - -
58A VAL* 1.3 78.3 - - - +
60A ASN* 1.3 57.0 + - - +
62A PHE* 3.4 4.5 + - - +
63A CYS* 3.0 38.2 + - - -
84A THR* 3.5 17.0 + - - +
88A PHE* 3.8 29.3 - - + -
316A LEU* 5.8 0.4 - - + -
59B THR* 4.3 2.9 - - + +
88B PHE* 3.6 29.9 - - + -
316B LEU* 4.2 12.3 - - + -
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Residues in contact with ASN 60 (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 LEU* 5.4 2.9 - - + -
56A PHE* 3.1 38.1 + - - +
57A ALA* 3.2 8.9 + - - +
59A THR* 1.3 74.9 - - - +
61A ALA* 1.3 56.4 + - - +
63A CYS* 3.2 4.4 + - - +
64A SER* 2.7 38.5 + - - -
316B LEU* 3.4 44.3 + - - +
317B ALA 4.3 3.0 + - - -
318B ASN* 3.9 25.6 - - - +
320B ALA* 5.4 0.4 - - - +
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.2 25.6 - - + +
48A ASP* 4.0 12.5 - - - +
50A LEU* 3.7 27.5 - - + +
57A ALA 2.9 16.3 + - - +
58A VAL* 3.9 6.5 - - - +
60A ASN* 1.3 76.6 - - - +
62A PHE* 1.3 60.3 + - - +
64A SER* 3.9 6.4 - - - -
65A GLN* 3.2 24.4 + - - +
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Residues in contact with PHE 62 (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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17A LEU* 5.0 4.5 - - + -
58A VAL 3.1 18.4 + - - +
59A THR* 3.6 5.6 - - - +
61A ALA* 1.3 76.4 - - - +
63A CYS* 1.3 66.2 + - - +
64A SER 3.2 0.2 - - - -
65A GLN* 3.4 5.1 + - - +
66A PHE* 2.9 32.3 + - + +
73A ILE* 3.6 29.6 - - + +
84A THR* 6.2 1.6 - - + -
85A ILE* 4.6 16.8 - - + -
88A PHE* 3.4 41.7 - + + -
89A CYS* 3.5 26.9 - - - -
92A LEU* 3.4 33.2 - - + -
94A VAL* 4.2 14.6 - - + -
96A PHE* 5.5 0.4 - + - -
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Residues in contact with CYS 63 (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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59A THR* 3.0 24.6 + - - +
60A ASN* 3.9 4.0 - - - +
62A PHE* 1.3 77.4 - - - +
64A SER* 1.3 60.2 + - - +
66A PHE* 3.6 6.8 - - - +
67A SER* 2.9 35.1 + - - +
88A PHE* 4.2 13.7 - - - -
314A ASP* 5.0 1.8 - - - +
315A CYS* 2.0 45.1 - - - +
316B LEU* 3.8 19.5 - - + -
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Residues in contact with SER 64 (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 HIS* 5.2 7.2 - - - -
48A ASP* 4.7 7.9 + - - -
60A ASN 2.7 22.9 + - - -
61A ALA* 3.9 7.6 - - - -
63A CYS* 1.3 74.2 - - - +
65A GLN* 1.3 62.7 + - - +
67A SER* 3.4 6.5 + - - -
68A ARG* 3.1 22.7 + - - +
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Residues in contact with GLN 65 (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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15A GLY* 4.6 13.5 - - - -
17A LEU* 5.1 4.5 - - + -
46A HIS* 5.5 8.3 - - + +
48A ASP* 4.8 8.7 + - - +
61A ALA 3.2 17.1 + - - +
62A PHE* 3.9 3.6 - - - +
64A SER* 1.3 78.6 + - - +
66A PHE* 1.3 59.8 + - - +
68A ARG* 3.7 6.8 + - - +
69A GLY 3.6 2.9 + - - -
70A VAL* 3.1 47.1 + - + +
73A ILE* 4.6 8.1 - - + -
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Residues in contact with PHE 66 (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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62A PHE* 2.9 23.5 + + + +
63A CYS* 3.6 8.1 - - - +
64A SER 3.1 0.2 - - - -
65A GLN* 1.3 77.4 - - - +
67A SER* 1.3 60.4 + - - +
68A ARG 3.2 0.2 - - - -
69A GLY* 3.1 18.2 + - - -
70A VAL* 4.6 10.8 - - + -
73A ILE* 5.8 0.9 - - + -
92A LEU* 4.1 28.9 - - + -
94A VAL* 3.9 31.4 - - + -
312A ALA* 3.5 36.7 - - + +
313A GLY 3.6 23.1 - - - -
314A ASP 4.7 1.1 - - - -
315A CYS* 4.0 20.6 - - + -
323A TRP* 4.6 15.3 - + - -
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Residues in contact with SER 67 (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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63A CYS* 2.9 20.2 + - - +
64A SER* 3.9 5.8 - - - -
66A PHE* 1.3 72.6 - - - +
68A ARG* 1.3 58.2 + - - +
69A GLY* 2.9 10.2 + - - -
311A ASN* 5.0 10.4 - - - +
312A ALA* 4.8 8.2 + - - -
313A GLY 3.7 22.6 + - - +
314A ASP* 4.7 5.0 + - - -
315A CYS 5.3 0.7 + - - -
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Residues in contact with ARG 68 (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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13A GLN* 5.4 3.3 - - - +
46A HIS* 5.7 14.1 - - + +
64A SER 3.1 16.8 + - - +
65A GLN* 3.9 10.3 - - - +
66A PHE 3.2 0.2 - - - -
67A SER* 1.3 74.6 - - - +
69A GLY* 1.3 64.0 + - - +
70A VAL* 4.9 5.7 - - + +
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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