Contacts of the helix formed by residues 44 - 60 (chain A) in PDB entry 1I4A
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 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ARG* 1.3 75.5 - - - +
45A THR* 1.3 65.5 + - - +
46A ALA* 3.5 9.1 + - - +
47A GLN* 2.9 37.8 + - - +
48A ARG* 2.9 24.0 + - - +
276A GLU* 3.5 18.6 - - - -
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Residues in contact with THR 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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44A SER* 1.3 72.1 - - - +
46A ALA* 1.3 63.4 + - - +
48A ARG* 3.2 20.7 + - - +
49A GLN* 3.2 34.0 + - + +
82A MET 4.5 3.3 + - - +
84A THR 4.0 20.2 - - - +
85A PRO* 4.4 1.8 - - + -
86A THR* 4.2 23.5 + - - +
276A GLU* 2.8 30.8 + - - -
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Residues in contact with ALA 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 SER* 3.1 8.8 + - - +
45A THR* 1.3 80.0 - - - +
47A GLN* 1.3 63.3 + - + +
49A GLN* 3.2 17.6 + - - +
50A GLU* 3.3 20.8 + - - +
276A GLU* 5.1 0.4 + - - -
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Residues in contact with GLN 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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13A PHE* 3.5 54.3 - - + +
42A TYR 4.5 0.7 - - - +
43A ARG* 3.3 17.8 - - + +
44A SER* 2.9 36.5 + - - +
46A ALA* 1.3 76.6 - - + +
48A ARG* 1.3 64.3 + - - +
50A GLU* 3.0 10.1 + - - +
51A ILE* 2.9 26.2 + - - +
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Residues in contact with ARG 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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40A LEU* 3.0 30.1 + - + -
41A ALA* 4.5 4.4 + - - +
43A ARG* 3.0 31.3 + - + -
44A SER 2.9 14.9 + - - +
45A THR* 3.2 28.4 + - - +
47A GLN* 1.3 76.2 - - - +
49A GLN* 1.3 63.6 + - - +
51A ILE* 3.2 12.2 + - - +
52A ARG* 3.0 30.8 + - - +
82A MET* 2.9 58.0 + - - +
83A MET* 3.6 23.9 - - + +
272A VAL* 5.9 1.0 - - - +
275A ALA* 6.2 0.8 - - - +
276A GLU* 3.9 6.9 + - - +
313A LEU* 4.6 8.7 - - - +
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Residues in contact with GLN 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 THR* 3.2 31.5 + - + +
46A ALA* 3.5 10.3 - - - +
47A GLN 3.1 0.6 - - - -
48A ARG* 1.3 77.2 - - - +
50A GLU* 1.3 67.0 + - + +
52A ARG* 3.3 31.9 + - - +
53A THR* 3.2 24.4 + - - -
83A MET 2.9 27.4 + - - -
85A PRO* 3.4 25.6 - - + +
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Residues in contact with GLU 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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13A PHE* 3.1 24.8 - - + -
15A ALA* 3.6 14.0 - - + +
46A ALA* 3.3 16.3 + - - +
47A GLN* 3.0 9.8 + - - +
49A GLN* 1.3 73.2 - - + +
51A ILE* 1.3 61.2 + - - +
53A THR* 3.3 8.2 + - - -
54A ALA* 2.9 29.5 + - - +
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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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13A PHE* 4.2 9.6 - - + -
15A ALA* 4.1 7.9 - - - -
18A ASP* 3.5 33.9 - - + +
19A ALA* 4.5 15.7 - - + +
22A LEU* 3.9 25.6 - - + -
39A VAL* 4.2 7.0 - - + -
40A LEU* 4.5 7.9 - - + -
43A ARG* 4.1 18.8 - - + -
47A GLN 2.9 18.0 + - - +
48A ARG* 3.4 14.4 - - - +
49A GLN 3.2 0.2 - - - -
50A GLU* 1.3 75.9 - - - +
52A ARG* 1.3 59.5 + - - +
54A ALA* 3.2 1.7 + - - +
55A TYR* 2.8 29.3 + - + +
63A LEU* 3.9 7.9 - - + -
83A MET* 5.4 0.4 - - + -
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Residues in contact with ARG 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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48A ARG 3.0 10.0 + - - +
49A GLN* 3.3 34.1 + - - +
51A ILE* 1.3 75.7 - - - +
53A THR* 1.3 63.8 + - - +
55A TYR* 3.4 2.1 + - - +
56A LYS* 3.1 24.4 + - - +
62A ASP* 5.4 4.4 + - - -
63A LEU* 3.9 21.8 + - + +
64A MET* 3.4 34.8 - - - +
83A MET* 3.4 45.4 + - + -
85A PRO* 3.7 13.9 - - - +
88A LEU* 6.0 1.4 - - - +
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Residues in contact with THR 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 GLN 3.2 11.6 + - - -
50A GLU* 3.5 10.9 - - - -
51A ILE 3.2 0.2 - - - -
52A ARG* 1.3 80.3 - - - +
54A ALA* 1.3 63.3 + - - +
56A LYS* 3.4 4.9 + - - +
57A THR* 3.0 33.7 + - - +
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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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15A ALA* 3.6 36.6 - - + +
16A ALA* 3.7 9.6 - - + +
19A ALA* 4.1 2.0 - - - -
50A GLU 2.9 18.4 + - - +
51A ILE 3.8 1.3 - - - +
53A THR* 1.3 77.8 - - - +
55A TYR* 1.3 56.8 + - - +
57A THR* 3.6 6.2 - - - -
58A THR* 2.8 36.7 + - - +
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Residues in contact with TYR 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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19A ALA* 3.7 27.1 - - + +
22A LEU* 4.6 2.0 - - + -
23A ARG* 3.6 38.2 + - + -
26A MET* 3.3 22.0 - - + +
51A ILE* 2.8 17.1 + - + +
52A ARG 3.6 4.5 - - - +
54A ALA* 1.3 78.0 - - - +
56A LYS* 1.3 54.4 + - - +
59A ILE* 2.7 46.8 + - + +
61A ARG* 3.4 22.4 - - + -
63A LEU* 3.4 47.8 - - + -
66A ASP* 2.5 30.6 + - - -
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Residues in contact with LYS 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 ARG 3.1 13.7 + - - +
53A THR* 3.9 5.4 - - - +
55A TYR* 1.3 78.6 - - - +
57A THR* 1.3 59.9 + - - +
60A GLY* 2.8 28.9 + - - -
61A ARG 3.1 17.6 + - - +
62A ASP* 2.7 45.3 + - - +
63A LEU 5.3 0.4 - - - +
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Residues in contact with THR 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 THR* 3.0 25.7 + - - +
54A ALA* 3.6 6.9 - - - -
56A LYS* 1.3 79.6 - - - +
58A THR* 1.3 64.1 - - - +
60A GLY* 4.3 2.4 + - - -
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Residues in contact with THR 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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16A ALA* 4.3 12.5 - - - +
20A GLN* 2.7 42.7 + - - +
54A ALA* 2.8 23.8 + - - +
55A TYR* 4.2 1.3 - - - -
57A THR* 1.3 81.0 - - - +
59A ILE* 1.3 67.5 + - + +
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Residues in contact with ILE 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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19A ALA 4.8 0.7 - - - +
20A GLN* 4.2 10.5 - - - +
23A ARG* 3.9 36.6 - - + +
55A TYR* 2.7 47.9 + - + +
58A THR* 1.3 96.3 - - + +
60A GLY* 1.3 58.7 + - - +
61A ARG* 3.7 32.6 - - + +
450A SO4 4.1 11.0 - - - +
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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 LYS* 2.8 23.2 + - - -
57A THR 4.3 1.5 + - - -
58A THR 3.7 0.8 - - - -
59A ILE* 1.3 78.8 - - - +
61A ARG* 1.3 62.3 + - - +
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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