Contacts of the helix formed by residues 48 - 65 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B T 2.7 30.0 + - - -
16B T 4.1 16.2 + - - -
7C A 4.8 3.9 + - - -
8C A 3.6 19.7 + - - -
46D PRO 3.8 0.6 + - - -
47D THR* 1.3 83.3 + - - +
49D ALA* 1.3 67.8 + - - +
50D TYR* 3.3 10.8 + - - +
51D PHE* 3.0 15.0 + - - +
52D LEU* 3.2 10.3 + - - +
96D ARG* 4.0 9.9 + - - +
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Residues in contact with ALA 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D THR 3.8 1.2 + - - -
48D SER* 1.3 74.6 + - - +
50D TYR* 1.3 65.1 + - - +
52D LEU* 3.1 18.9 + - - +
53D TYR 3.3 7.4 + - - -
81D TRP* 3.8 18.3 - - + -
92D TYR* 3.9 3.3 - - - +
93D ILE* 3.9 23.6 - - + +
96D ARG* 3.6 39.7 - - + +
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Residues in contact with TYR 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B A 3.8 25.1 + + + +
15B T 3.5 29.6 - + - +
48D SER* 3.4 9.2 + - - +
49D ALA* 1.3 78.1 - - - +
51D PHE* 1.3 67.0 + + - +
53D TYR* 2.9 13.6 + + - +
54D LEU* 2.7 60.5 + - + +
74D SER* 3.8 2.8 + - - -
77D ALA* 3.4 23.5 - - + +
78D GLY* 3.2 24.8 + - - -
81D TRP* 3.2 53.9 - + + +
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Residues in contact with PHE 51 (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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14B A 3.8 17.3 - + - -
15B T 3.7 19.1 - + - -
8C A 3.0 67.8 - + + -
9C T 3.5 46.0 - + - -
47D THR* 3.2 20.6 - - - +
48D SER* 3.0 6.6 + - - +
50D TYR* 1.3 91.2 - + - +
52D LEU* 1.3 55.5 + - - +
54D LEU* 3.5 19.1 - - + +
55D GLN* 2.9 29.1 + - - +
58D ARG* 5.1 0.2 - - - -
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Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D THR* 3.7 24.7 - - + +
48D SER 3.2 7.0 + - - +
49D ALA* 3.1 13.3 + - - +
51D PHE* 1.3 76.9 - - - +
53D TYR* 1.3 62.0 + - - +
55D GLN* 3.3 13.2 + - + +
56D ASP* 3.1 23.1 - - - +
92D TYR* 3.8 16.4 - - + +
95D GLU* 3.6 26.9 - - + +
96D ARG* 4.5 10.5 - - + +
99D LEU* 3.6 29.8 - - + -
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Residues in contact with TYR 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ALA 3.3 2.0 + - - -
50D TYR* 2.9 13.9 + + - +
52D LEU* 1.3 78.5 - - - +
54D LEU* 1.3 65.0 + - - +
56D ASP 3.4 0.7 + - - -
57D HIS* 3.2 62.1 + + + +
77D ALA* 4.8 3.4 - - + -
80D LYS* 3.7 37.1 + - + +
81D TRP* 3.3 40.8 - + + -
84D LEU* 3.2 39.3 - - + +
88D ILE* 5.6 1.8 - - + -
92D TYR* 3.2 31.7 - + + -
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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
----------------------------------------------------------
14B A 4.6 6.7 - - + +
9C T 4.2 3.1 - - - +
50D TYR* 2.7 45.7 + - + +
51D PHE* 3.2 35.4 + - + +
53D TYR* 1.3 76.7 - - - +
55D GLN* 1.3 56.0 + - - +
56D ASP 3.3 0.2 + - - -
57D HIS* 3.3 2.2 + - - -
58D ARG* 2.7 80.2 + - + +
61D PHE* 6.3 1.3 - - + -
73D ILE* 5.4 9.0 - - + -
74D SER* 5.3 4.5 - - - +
77D ALA* 4.6 13.0 - - + -
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Residues in contact with GLN 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C T 3.7 22.8 - - - +
10C A 4.8 9.3 + - - -
51D PHE 2.9 16.4 + - - +
52D LEU* 3.7 10.1 - - + +
53D TYR 3.3 0.2 - - - -
54D LEU* 1.3 78.3 - - - +
56D ASP* 1.3 64.1 + - - +
57D HIS 3.5 0.2 + - - -
58D ARG* 3.3 37.7 + - - +
59D SER* 4.5 3.8 + - - -
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Residues in contact with ASP 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LEU* 3.1 14.5 + - - +
53D TYR 3.8 0.2 - - - +
54D LEU 3.2 0.8 - - - -
55D GLN* 1.3 84.0 - - - +
57D HIS* 1.3 76.1 + - + +
58D ARG 3.8 0.3 + - - -
59D SER* 4.1 11.1 + - - -
60D GLN* 4.2 11.6 + - - +
92D TYR* 2.3 36.6 + - - +
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Residues in contact with HIS 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D TYR* 3.2 52.3 + + + +
54D LEU* 3.3 5.6 + - - +
56D ASP* 1.3 83.4 - - + +
58D ARG* 1.3 55.4 + - - +
59D SER 3.4 1.3 - - - -
60D GLN* 4.1 25.5 + - + -
61D PHE* 2.7 36.6 + - - +
80D LYS* 4.5 13.8 + - - +
84D LEU* 5.8 0.2 - - - +
88D ILE* 5.9 3.5 - - + +
92D TYR* 3.5 19.5 - + - -
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Residues in contact with ARG 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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9C T 3.2 26.2 + - - -
10C A 2.5 62.4 + - - -
51D PHE* 5.1 0.4 - - - -
54D LEU* 2.7 56.7 + - + +
55D GLN* 3.3 35.1 + - - +
56D ASP 3.4 0.8 - - - -
57D HIS* 1.3 76.1 - - - +
59D SER* 1.3 64.1 + - - +
61D PHE* 3.2 5.6 + - - +
62D VAL* 2.8 39.6 + - + +
73D ILE* 5.5 9.6 - - - +
74D SER* 6.0 0.2 + - - -
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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
----------------------------------------------------------
55D GLN 4.5 3.1 + - - -
56D ASP 4.1 9.7 + - - -
58D ARG* 1.3 78.7 - - - +
60D GLN* 1.3 75.7 + - - +
62D VAL* 3.1 8.8 + - - +
63D LYS* 2.8 32.2 + - - +
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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
----------------------------------------------------------
56D ASP 4.2 13.9 + - - +
57D HIS* 3.9 25.3 + - + +
58D ARG 3.5 0.2 - - - -
59D SER* 1.3 85.4 + - - +
61D PHE* 1.3 51.6 + - - +
63D LYS* 2.8 17.4 + - + +
64D GLU* 2.5 51.6 + - - +
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Residues in contact with PHE 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D LEU* 6.3 1.1 - - + -
57D HIS 2.7 25.7 + - - +
58D ARG* 3.6 5.4 - - - +
59D SER 3.2 0.4 - - - -
60D GLN* 1.3 74.5 - - - +
62D VAL* 1.3 58.9 + - - +
64D GLU* 3.0 18.5 + - + +
65D ASN* 2.9 39.8 + - + +
68D LEU* 5.9 1.8 - - + -
73D ILE* 3.3 63.0 - - + -
76D ILE* 3.7 29.2 - - + -
77D ALA* 4.4 5.8 - - + -
80D LYS* 3.1 37.4 - - - +
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Residues in contact with VAL 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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10C A 5.4 3.6 - - - +
11C T 5.0 17.0 - - - +
58D ARG* 2.8 26.4 + - + +
59D SER* 3.5 9.9 - - - +
61D PHE* 1.3 75.0 - - - +
63D LYS* 1.3 65.3 + - + +
65D ASN 3.0 28.4 - - - +
66D PRO* 3.5 14.1 - - + +
73D ILE* 3.8 23.8 - - + -
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Residues in contact with LYS 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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59D SER* 2.8 22.5 + - - +
60D GLN* 3.2 17.3 - - + +
62D VAL* 1.3 77.9 - - + +
64D GLU* 1.3 61.5 + - - +
66D PRO* 4.5 6.9 - - - +
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Residues in contact with GLU 64 (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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60D GLN* 2.5 42.0 + - + +
61D PHE* 3.0 28.0 + - + +
63D LYS* 1.3 74.6 - - - +
65D ASN* 1.3 74.8 + - - +
66D PRO* 4.4 1.9 - - - +
80D LYS* 5.1 4.9 - - - +
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Residues in contact with ASN 65 (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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61D PHE* 2.9 29.0 + - + +
62D VAL* 3.0 13.6 + - - +
64D GLU* 1.3 94.9 - - + +
66D PRO* 1.4 64.8 - - - +
67D THR* 4.3 13.6 + - - +
68D LEU* 4.7 20.9 + - + +
73D ILE* 4.9 9.2 - - - +
76D ILE* 4.9 11.1 - - - +
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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