Contacts of the helix formed by residues 48 - 65 (chain A) in PDB entry 5JGH
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 SER 48 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR* 1.3 86.2 + - - +
49A ALA* 1.3 63.6 + - - +
50A TYR* 3.6 5.0 + - - -
51A PHE 3.3 18.5 + - - -
52A LEU* 3.3 16.8 + - - +
96A ARG* 3.7 11.7 - - - +
15E T 2.6 29.3 + - - -
16E T 4.3 21.5 - - - -
7F A 4.4 2.3 + - - -
8F A 3.4 11.9 + - - -
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A SER* 1.3 73.4 - - - +
50A TYR* 1.3 66.9 + - - +
51A PHE 3.2 0.2 + - - -
52A LEU* 3.3 13.8 + - - +
53A TYR* 3.1 21.1 + - - +
81A TRP* 3.9 7.8 - - + -
92A TYR* 3.9 7.7 - - - +
93A ILE* 3.6 46.0 - - + +
96A ARG* 3.5 14.4 - - + +
16E T 6.3 2.4 - - - -
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Residues in contact with TYR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A SER* 3.3 2.7 + - - +
49A ALA* 1.3 79.8 - - - +
51A PHE* 1.3 67.7 + + - +
53A TYR* 3.2 5.7 + + - +
54A LEU* 2.7 50.2 + - + +
74A SER* 3.0 25.3 + - - -
77A ALA* 3.2 21.7 - - + +
78A GLY* 3.7 21.1 - - - -
81A TRP* 3.6 37.1 - + + -
14E A 3.2 35.4 + + + -
15E T 3.1 39.0 - + - +
16E T 6.1 1.8 - - - -
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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
----------------------------------------------------------
47A THR* 3.0 21.8 - - + +
48A SER* 3.3 5.1 + - - +
49A ALA 3.2 0.6 - - - -
50A TYR* 1.3 92.8 - + - +
52A LEU* 1.3 61.1 + - - +
54A LEU* 3.6 9.3 - - + +
55A GLN* 2.8 37.9 + - + +
14E A 3.5 35.0 - + - -
15E T 3.8 7.0 - - - -
8F A 3.2 74.0 - + + -
9F T 3.6 33.9 - + - -
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR* 4.0 13.4 - - + +
48A SER 3.3 18.6 - - - +
49A ALA* 3.3 16.1 + - - +
51A PHE* 1.3 78.6 - - - +
53A TYR* 1.3 61.4 + - - +
55A GLN* 3.5 4.7 + - - +
56A ASP* 3.2 26.3 + - - +
92A TYR* 3.6 33.9 - - + +
95A GLU* 4.1 12.6 - - + +
96A ARG* 3.9 17.0 - - + +
99A LEU* 4.0 22.4 - - + -
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Residues in contact with TYR 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA 3.1 2.8 + - - +
50A TYR* 3.5 8.5 - + - +
52A LEU* 1.3 75.7 - - - +
54A LEU* 1.3 69.3 + - - +
56A ASP 3.3 0.9 + - - -
57A HIS* 3.0 55.1 + + - +
61A PHE* 3.4 32.2 - + - -
77A ALA* 4.1 19.1 - - + -
80A LYS* 3.4 14.0 + - + +
81A TRP* 3.4 44.0 - + + -
84A LEU* 3.5 29.0 - - + +
88A ILE* 5.8 1.6 - - + -
92A TYR* 3.5 30.6 - + + -
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 2.7 44.1 + - + +
51A PHE* 3.6 12.3 - - + +
52A LEU 3.3 0.2 - - - -
53A TYR* 1.3 78.8 - - - +
55A GLN* 1.3 76.7 + - - +
57A HIS* 2.9 3.8 + - - -
58A ARG* 2.8 73.2 + - + +
61A PHE* 4.8 3.1 - - + -
73A ILE* 5.9 0.9 - - + -
74A SER* 5.2 0.9 - - - +
77A ALA* 3.7 26.5 - - + -
14E A 4.0 9.6 - - + -
9F T 4.0 6.1 - - - +
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Residues in contact with GLN 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PHE* 2.8 27.3 + - + +
52A LEU* 4.0 4.7 - - - +
54A LEU* 1.3 90.4 - - - +
56A ASP* 1.3 61.4 + - - +
57A HIS 3.5 0.2 + - - -
58A ARG* 4.0 19.3 + - - +
59A SER 5.5 0.2 + - - -
8F A 5.7 0.9 - - + -
9F T 2.8 59.5 + - - +
10F A 4.0 5.9 - - - +
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Residues in contact with ASP 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU 3.2 10.8 + - - +
53A TYR 3.6 2.5 - - - +
54A LEU 3.0 1.0 - - - -
55A GLN* 1.3 81.2 - - - +
57A HIS* 1.3 78.0 + - + +
58A ARG 3.6 0.4 + - - -
59A SER* 5.5 1.7 + - - -
60A GLN* 4.7 9.0 + - - +
92A TYR* 2.4 31.0 + - - +
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Residues in contact with HIS 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 3.0 40.1 + + - +
54A LEU 2.9 3.9 + - - -
56A ASP* 1.3 84.2 - - + +
58A ARG* 1.3 61.9 + - - +
59A SER 3.6 1.6 - - - -
60A GLN* 3.3 33.6 + - + +
61A PHE* 3.0 46.2 + + + -
88A ILE* 5.1 10.0 - - + +
92A TYR* 3.4 25.6 - + - -
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Residues in contact with ARG 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 2.8 44.6 + - - +
55A GLN* 4.0 16.7 + - - +
56A ASP 3.6 2.4 - - - -
57A HIS* 1.3 72.4 - - - +
59A SER* 1.3 67.1 - - - +
61A PHE* 3.2 16.9 + - - +
62A VAL* 3.3 21.1 + - + +
70A PRO* 4.4 4.0 + - - +
73A ILE* 4.4 13.8 - - - +
74A SER* 3.6 27.9 + - - +
9F T 2.3 42.2 + - - -
10F A 3.7 40.0 + - - -
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Residues in contact with SER 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 GLN 5.5 0.2 + - - -
56A ASP 5.5 1.7 + - - -
58A ARG* 1.3 81.0 + - - +
60A GLN* 1.3 70.9 + - - +
62A VAL* 3.0 25.8 - - - +
63A LYS* 3.2 19.1 + - - +
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Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASP 4.7 6.7 + - - +
57A HIS* 3.5 42.7 - - + +
58A ARG 3.1 1.2 - - - -
59A SER* 1.3 83.8 + - - +
61A PHE* 1.3 65.6 + - + +
63A LYS* 3.4 5.6 + - - +
64A GLU* 3.0 25.5 + - - +
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Residues in contact with PHE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 3.4 28.5 - + - -
54A LEU* 4.8 4.9 - - + -
57A HIS* 3.0 37.0 - + + -
58A ARG* 3.2 9.9 + - - +
60A GLN* 1.3 77.7 - - + +
62A VAL* 1.3 60.3 + - - +
64A GLU* 3.1 13.4 + - - +
65A ASN* 2.7 32.9 + - - +
73A ILE* 3.9 18.4 - - + -
76A ILE* 4.4 12.8 - - + -
77A ALA* 3.8 27.1 - - + -
80A LYS* 3.3 46.0 - - + -
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Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 3.5 18.4 - - + +
59A SER* 3.0 22.9 - - - +
61A PHE* 1.3 75.0 - - - +
63A LYS* 1.3 89.6 + - - +
65A ASN 2.8 26.0 - - - +
66A PRO* 2.9 10.6 - - + +
73A ILE* 3.4 33.0 - - + -
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Residues in contact with LYS 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 SER* 3.2 23.9 + - - +
60A GLN* 3.9 4.9 - - - +
62A VAL* 1.3 106.3 - - - +
64A GLU* 1.3 61.2 + - - +
65A ASN 3.5 0.3 + - - -
66A PRO* 4.0 13.9 - - + +
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Residues in contact with GLU 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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60A GLN* 3.0 17.0 + - - +
61A PHE* 3.4 14.4 - - - +
63A LYS* 1.3 77.7 - - - +
65A ASN* 1.3 70.4 + - - +
66A PRO* 3.7 6.0 - - - +
80A LYS* 3.6 28.5 + - - -
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Residues in contact with ASN 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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61A PHE* 2.7 20.6 + - - +
62A VAL* 2.8 6.4 - - - +
64A GLU* 1.3 96.1 + - - +
66A PRO* 1.3 67.0 - - - +
67A THR* 3.1 6.4 + - - +
68A LEU* 3.2 43.6 + - + +
73A ILE* 3.6 15.9 - - + +
76A ILE* 4.5 20.4 - - - +
80A LYS* 5.5 0.2 - - - +
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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