Contacts of the helix formed by residues 44 - 60 (chain A) in PDB entry 3SJ5
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 ASP 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET 4.3 1.3 - - - +
42A ASP* 4.0 5.0 + - - -
43A ILE* 1.3 79.0 - - - +
45A ASP* 1.3 74.7 + - - +
46A ASP* 3.2 25.0 + - - +
47A GLU* 3.3 26.2 + - + +
48A VAL* 3.4 12.1 + - - +
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Residues in contact with ASP 45 (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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1A MET* 2.8 40.5 + - - +
43A ILE 3.5 0.4 + - - -
44A ASP* 1.3 79.1 + - - +
46A ASP* 1.3 58.0 + - + +
48A VAL* 3.3 10.4 + - - +
49A ARG* 3.1 24.9 + - - +
135A ARG* 3.1 34.0 + - - +
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Residues in contact with ASP 46 (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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44A ASP* 3.2 16.3 + - - +
45A ASP* 1.3 78.1 - - + +
47A GLU* 1.3 62.7 + - - +
48A VAL 3.3 0.2 - - - -
49A ARG* 3.6 21.3 + - - +
50A ARG* 3.1 35.2 + - - +
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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
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29A VAL* 3.9 26.1 - - + +
31A TRP* 3.6 29.8 + - + -
35A ARG* 5.1 1.9 + - - -
43A ILE* 4.6 9.3 - - + +
44A ASP* 3.3 23.7 + - + +
46A ASP* 1.3 75.9 - - - +
48A VAL* 1.3 65.4 + - - +
50A ARG* 3.3 18.5 + - - +
51A ILE* 3.0 30.5 + - - +
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Residues in contact with VAL 48 (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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1A MET* 5.6 1.8 - - + +
6A VAL* 3.6 34.1 - - + -
9A TRP* 4.0 22.0 - - + -
43A ILE* 4.0 4.9 - - + +
44A ASP 3.4 15.9 - - - +
45A ASP* 3.3 12.5 + - - +
47A GLU* 1.3 74.8 - - - +
49A ARG* 1.3 66.4 + - - +
51A ILE* 3.1 9.4 + - - +
52A PHE* 3.0 46.1 + - + -
67A TRP* 4.0 9.9 - - + -
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Residues in contact with ARG 49 (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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45A ASP 3.1 9.4 + - - +
46A ASP* 3.6 25.9 + - - +
47A GLU 3.3 0.2 - - - -
48A VAL* 1.3 82.0 - - - +
50A ARG* 1.3 87.6 + - - +
52A PHE* 3.4 5.9 + - - +
53A ALA* 2.9 40.8 + - + +
63A VAL* 5.7 0.3 - - - +
67A TRP* 5.9 2.2 - - - +
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Residues in contact with ARG 50 (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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28A SER 3.9 19.6 + - - -
29A VAL* 3.9 33.8 + - + +
46A ASP* 3.1 26.6 + - - +
47A GLU* 3.6 20.8 + - - +
48A VAL 3.2 0.8 - - - -
49A ARG* 1.3 96.4 - - - +
51A ILE* 1.3 63.3 + - - +
53A ALA* 3.3 4.9 + - - +
54A LYS* 3.1 26.2 + - - +
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Residues in contact with ILE 51 (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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6A VAL* 5.2 3.1 - - + -
10A ILE* 4.7 9.9 - - + -
13A LEU* 4.5 14.1 - - + -
22A VAL* 6.1 1.6 - - + -
25A SER* 4.0 5.7 - - - +
26A LEU* 3.6 33.0 - - + -
29A VAL* 3.8 22.4 - - + -
31A TRP* 4.0 30.3 - - + +
47A GLU 3.0 21.9 + - - +
48A VAL* 3.1 11.6 + - - +
50A ARG* 1.3 76.3 - - - +
52A PHE* 1.3 71.4 + - + +
54A LYS* 3.1 6.6 + - - +
55A VAL* 3.0 26.0 + - + +
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Residues in contact with PHE 52 (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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9A TRP* 4.3 16.4 - + + -
10A ILE* 6.1 1.8 - - + -
13A LEU* 4.0 24.7 - - + -
48A VAL* 3.0 28.6 + - + +
49A ARG* 3.9 4.5 - - - +
51A ILE* 1.3 80.1 - - + +
53A ALA* 1.3 62.4 + - - +
55A VAL* 3.3 7.6 + - - +
56A SER* 3.0 24.4 + - - -
63A VAL* 3.7 15.9 - - + +
66A ILE* 3.9 31.4 - - + +
67A TRP* 3.5 65.5 - + + +
70A VAL* 4.0 13.5 - - + -
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Residues in contact with ALA 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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49A ARG* 2.9 36.3 + - + +
50A ARG* 3.5 8.5 - - - +
51A ILE 3.2 0.2 - - - -
52A PHE* 1.3 75.3 - - - +
54A LYS* 1.3 59.2 + - - +
56A SER* 3.5 7.5 - - - -
57A GLU* 3.0 35.8 + - + +
63A VAL* 4.4 5.3 - - - +
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Residues in contact with LYS 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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25A SER* 3.7 14.4 - - - +
28A SER* 3.5 32.2 - - - +
50A ARG 3.1 13.8 + - - +
51A ILE 3.1 7.6 + - - +
53A ALA* 1.3 76.0 - - - +
55A VAL* 1.3 65.0 + - - +
57A GLU* 3.3 31.7 + - - +
58A LYS* 3.0 58.7 + - - +
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Residues in contact with VAL 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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13A LEU* 4.1 25.6 - - + -
17A TYR* 4.0 24.2 - - + -
21A VAL* 4.1 14.8 - - + +
22A VAL* 4.9 7.4 - - + -
25A SER* 3.4 21.1 - - - +
51A ILE* 3.0 14.1 + - + +
52A PHE* 3.8 9.0 - - - +
54A LYS* 1.3 76.5 - - - +
56A SER* 1.3 51.9 + - - +
58A LYS 3.3 0.7 + - - -
59A THR* 2.8 44.6 + - + +
66A ILE* 4.0 16.8 - - + -
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Residues in contact with SER 56 (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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52A PHE 3.0 13.8 + - - -
53A ALA* 3.5 10.5 - - - -
55A VAL* 1.3 73.6 - - - +
57A GLU* 1.3 58.0 + - - +
59A THR* 3.7 2.2 - - - -
60A GLY* 2.7 36.4 + - - -
61A LYS 2.6 26.2 + - - -
62A ASN* 4.0 1.6 - - - -
63A VAL* 3.6 18.9 + - - +
66A ILE* 3.8 8.0 - - - +
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Residues in contact with GLU 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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53A ALA* 3.0 20.1 + - + +
54A LYS* 3.4 37.6 + - - +
56A SER* 1.3 81.3 + - - +
58A LYS* 1.3 66.7 + - + +
59A THR 3.6 0.2 + - - -
60A GLY* 3.7 6.2 + - - -
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Residues in contact with LYS 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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21A VAL* 4.2 27.3 - - + +
24A GLU* 3.1 50.0 + - + +
25A SER* 4.0 9.0 - - - +
54A LYS* 3.0 45.9 + - - +
55A VAL 4.0 2.9 - - - +
56A SER 3.2 0.2 - - - -
57A GLU* 1.3 80.2 + - + +
59A THR* 1.3 61.5 + - - +
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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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17A TYR* 3.9 37.2 - - + -
21A VAL* 4.0 15.3 - - + -
55A VAL* 2.8 26.0 + - + +
56A SER* 3.4 2.1 + - - -
58A LYS* 1.3 80.2 - - - +
60A GLY* 1.3 58.0 + - - +
61A LYS* 3.0 35.2 + - - +
66A ILE* 4.1 2.6 - - - +
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Residues in contact with GLY 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 SER* 2.7 11.8 + - - -
57A GLU 3.7 5.6 + - - -
58A LYS 3.5 1.8 - - - -
59A THR* 1.3 76.9 - - - +
61A LYS* 1.3 61.6 + - - +
62A ASN 3.7 1.7 + - - -
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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