Contacts of the helix formed by residues 46 - 62 (chain A) in PDB entry 4JUA
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 GLN 46 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASN* 5.1 0.4 - - - -
44A ALA 3.4 0.4 - - - -
45A LEU* 1.3 78.6 - - - +
47A GLU* 1.3 76.7 + - - +
48A ALA* 2.8 39.0 + - - +
49A CYS* 3.0 25.7 + - - +
50A VAL* 3.1 14.3 + - - +
77A ASN* 3.7 30.2 + - - +
433A TYR 5.4 3.8 - - - +
436A SER* 4.0 15.2 + - - +
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Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASN* 3.2 29.9 - - + +
46A GLN* 1.3 77.1 + - - +
48A ALA* 1.3 65.4 + - - +
49A CYS 3.1 1.1 - - - -
50A VAL* 3.6 6.0 - - - +
51A VAL* 3.0 28.9 + - - +
69A LEU* 3.8 19.5 - - + -
70A SER* 4.8 6.6 - - - -
74A GLY* 3.3 44.1 - - - +
77A ASN* 2.9 29.4 + - + -
78A ALA* 4.0 7.2 - - + -
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLN* 2.8 17.9 + - - +
47A GLU* 1.3 76.4 - - - +
49A CYS* 1.3 56.8 + - - +
52A GLY* 2.9 25.3 + - - -
77A ASN 3.7 16.4 + - - +
78A ALA* 4.4 0.4 - - - +
81A ALA* 4.0 21.7 - - + +
404A GLY 4.8 2.1 - - - +
408A PRO* 4.3 3.1 - - - +
433A TYR 5.3 3.1 - - - +
434A SER* 4.0 16.5 + - - +
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Residues in contact with CYS 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA* 4.0 13.7 - - + -
45A LEU 4.9 0.4 - - - +
46A GLN* 3.0 21.0 + - - +
48A ALA* 1.3 76.0 - - - +
50A VAL* 1.3 66.0 + - - +
53A ILE* 2.9 30.1 + - - +
408A PRO* 3.6 8.2 - - - +
434A SER* 3.8 25.6 - - - -
436A SER* 3.5 24.5 - - - -
437A ALA* 3.6 25.4 - - + -
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 3.5 36.5 - - + +
22A GLY* 3.6 27.6 - - - +
23A ASN* 3.8 13.5 - - + +
42A ILE 5.5 0.2 - - - +
44A ALA* 3.7 15.5 - - + +
46A GLN 3.1 14.5 + - - +
47A GLU* 3.6 10.3 - - - +
49A CYS* 1.3 75.6 - - - +
51A VAL* 1.3 63.6 + - - +
53A ILE* 3.7 4.2 - - - +
54A ALA* 3.1 21.8 + - - +
67A ILE* 4.0 6.3 - - + -
69A LEU* 3.9 16.2 - - + -
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU 3.0 16.7 + - - +
50A VAL* 1.3 76.8 - - - +
52A GLY* 1.3 57.1 + - - +
54A ALA* 3.3 6.1 + - - +
55A ASP* 2.8 29.8 + - + +
67A ILE* 4.2 24.5 - - + -
69A LEU* 4.3 6.3 - - + -
78A ALA* 3.5 19.5 - - + -
81A ALA* 3.6 26.2 - - + +
82A LEU* 4.0 24.9 - - + -
92A LEU* 4.0 14.8 - - + -
94A VAL* 5.4 0.9 - - + -
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Residues in contact with GLY 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ALA 2.9 18.9 + - - -
49A CYS 3.3 1.1 + - - -
51A VAL* 1.3 76.9 - - - +
53A ILE* 1.3 61.4 + - - +
55A ASP* 3.3 7.1 + - - +
56A GLY 3.0 19.1 + - - -
81A ALA* 4.4 5.1 - - - +
404A GLY 5.4 0.7 - - - -
405A PHE* 4.8 8.5 - - - -
408A PRO* 4.0 10.8 - - - -
409A ALA* 3.2 17.9 - - - +
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Residues in contact with ILE 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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21A PHE* 3.7 25.4 - - + -
42A ILE* 4.7 6.5 - - + -
44A ALA* 3.9 23.3 - - + -
49A CYS 2.9 21.5 + - - +
50A VAL* 3.7 4.3 - - - +
52A GLY* 1.3 75.2 - - - +
54A ALA* 1.3 63.9 + - - +
55A ASP 3.3 0.2 + - - -
57A TYR* 3.0 19.9 + - - +
408A PRO* 3.3 27.6 - - + +
411A ILE* 4.3 11.2 - - + -
412A GLY* 3.3 23.2 - - - +
415A LEU* 5.3 2.0 - - + -
437A ALA* 4.8 5.8 - - + -
440A THR* 3.9 24.7 - - + -
446A ILE* 6.2 0.2 - - + -
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Residues in contact with ALA 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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21A PHE* 3.7 27.8 - - + -
50A VAL 3.1 13.5 + - - +
51A VAL 3.7 1.3 - - - +
53A ILE* 1.3 77.3 - - - +
55A ASP* 1.3 57.5 + - - +
57A TYR* 3.3 0.9 + - - +
58A ALA* 2.8 30.3 + - - +
65A ALA* 3.5 9.4 - - + +
67A ILE* 3.5 38.1 - - + -
92A LEU* 4.0 2.5 - - - -
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Residues in contact with ASP 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 2.8 19.0 + - + +
52A GLY* 3.5 9.8 - - - +
53A ILE 3.2 0.2 - - - -
54A ALA* 1.3 73.6 - - - +
56A GLY* 1.3 65.2 + - - +
58A ALA* 3.2 1.2 + - - +
59A GLN* 2.9 40.2 + - - +
81A ALA 4.5 4.0 - - - +
84A ASN 4.6 0.5 - - - -
85A ALA* 3.8 22.0 + - - +
88A SER* 4.3 0.3 + - - -
90A SER* 2.6 31.1 + - - -
92A LEU* 3.9 16.3 - - + +
405A PHE* 3.6 18.4 - - + -
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Residues in contact with GLY 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLY 3.0 12.3 + - - -
53A ILE 3.8 0.7 - - - -
55A ASP* 1.3 75.1 - - - +
57A TYR* 1.3 62.4 + - - +
59A GLN* 4.0 5.9 - - - +
60A ALA* 3.0 28.4 + - - +
396A TYR* 6.1 0.4 - - - -
405A PHE* 5.3 0.7 - - - -
409A ALA* 3.6 27.7 - - - +
413A VAL* 3.5 16.8 - - - +
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Residues in contact with TYR 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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18A ASP* 4.7 2.7 + - - -
19A THR* 4.5 6.8 + - - -
21A PHE* 3.6 28.5 - + + -
40A ARG* 3.4 20.5 + - - -
53A ILE 3.0 13.5 + - - +
54A ALA 3.5 7.9 - - - +
56A GLY* 1.3 76.8 - - - +
58A ALA* 1.3 53.8 + - - +
60A ALA 3.9 0.2 - - - -
61A SER* 2.7 45.4 + - - -
63A LYS* 3.8 35.0 + - - -
64A PRO 5.3 2.5 - - - -
65A ALA* 4.4 8.3 - - + -
412A GLY* 3.5 21.1 - - - +
415A LEU* 3.9 23.8 - - + -
416A ALA* 3.7 27.9 - - + +
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Residues in contact with ALA 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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54A ALA 2.8 19.9 + - - +
55A ASP 3.7 3.1 - - - +
57A TYR* 1.3 73.6 - - - +
59A GLN* 1.3 58.4 + - - +
61A SER* 3.4 2.4 + - - -
62A ARG* 2.8 29.3 + - - -
63A LYS 3.3 22.9 + - - +
65A ALA* 3.8 9.9 - - + +
90A SER* 5.1 1.3 - - - -
91A PRO* 4.1 16.4 - - + +
92A LEU* 3.8 19.5 - - + -
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Residues in contact with GLN 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 ASP* 2.9 38.3 + - - +
56A GLY* 4.0 3.3 - - - +
58A ALA* 1.3 78.3 - - - +
60A ALA* 1.3 62.3 + - - +
62A ARG* 3.6 9.0 + - - +
88A SER* 3.6 21.2 + - - +
90A SER* 3.4 22.1 + - - +
91A PRO* 5.7 2.7 - - + -
238A PRO* 4.9 1.6 - - - +
239A ARG* 3.0 52.9 + - - +
396A TYR* 3.6 25.8 - - + -
405A PHE* 3.7 21.2 - - - -
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Residues in contact with ALA 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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56A GLY 3.0 17.3 + - - +
59A GLN* 1.3 78.4 - - - +
61A SER* 1.3 61.8 + - - +
62A ARG* 3.5 17.0 + - - -
239A ARG* 4.8 0.2 - - - +
371A ILE* 5.8 0.7 - - + -
396A TYR* 3.5 17.4 + - - +
413A VAL* 4.0 19.5 - - + -
416A ALA* 3.7 20.0 - - + -
417A GLU* 4.2 18.6 - - + +
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Residues in contact with SER 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 2.7 30.1 + - - -
58A ALA* 3.4 6.8 + - - -
60A ALA* 1.3 75.2 - - - +
62A ARG* 1.3 70.4 + - - +
63A LYS* 3.1 40.0 + - - +
416A ALA* 4.1 11.9 - - - +
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Residues in contact with ARG 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ALA 2.8 10.5 + - - -
59A GLN* 3.7 10.8 - - - +
60A ALA 3.3 12.4 + - - +
61A SER* 1.3 79.2 - - - +
63A LYS* 1.3 59.0 + - - +
91A PRO* 5.5 2.5 - - - -
151A GLN* 5.6 5.4 + - - -
212A ASP* 2.9 46.9 + - - -
213A ALA* 3.1 21.3 + - - +
214A ALA 4.6 0.7 - - - -
215A ASN* 3.7 26.4 + - - +
239A ARG* 3.9 7.6 - - - +
392A PRO* 3.7 18.0 - - - +
393A GLY* 3.7 9.1 - - - +
417A GLU* 5.3 4.2 + - - -
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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
------------------------------------------------------------
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