Contacts of the helix formed by residues 45 - 54 (chain A) in PDB entry 1GAJ
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 GLY 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ALA* 3.7 17.7 - - - -
23A LEU* 3.2 10.2 - - - +
43A GLY 3.4 2.6 + - - -
44A SER* 1.3 78.7 - - - +
46A LYS* 1.3 59.6 + - - +
47A SER 3.3 2.0 - - - -
48A THR* 3.4 12.7 + - - -
49A LEU* 2.8 27.0 + - - +
226A MET* 3.5 3.8 - - - -
301A SO4 3.2 11.4 + - - -
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Residues in contact with LYS 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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38A ILE* 4.1 15.3 - - + +
39A ILE* 3.4 33.9 - - - +
40A GLY 2.9 22.0 + - - +
41A PRO 4.0 2.0 + - - -
42A ASN* 4.2 0.4 - - - +
44A SER* 3.2 15.4 - - - +
45A GLY* 1.3 77.0 - - - +
47A SER* 1.3 62.1 + - - +
49A LEU* 3.4 4.9 + - - +
50A ILE* 3.1 26.9 + - - +
209A ILE* 3.5 28.0 - - + +
210A GLU 4.8 0.2 - - - -
211A HIS* 3.1 31.4 + - - -
226A MET* 4.0 15.3 - - + -
301A SO4 3.1 25.1 + - - +
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Residues in contact with SER 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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46A LYS* 1.3 71.1 - - - +
48A THR* 1.3 56.0 + - - +
50A ILE* 3.0 4.8 + - - +
51A ASN* 2.8 46.3 + - - -
86A ARG* 6.3 0.2 - - - -
178A ASP* 2.9 25.6 + - - -
209A ILE* 3.8 9.6 - - - +
301A SO4 2.8 23.3 + - - -
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Residues in contact with THR 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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15A LYS* 3.7 16.2 - - + -
17A PHE* 3.7 32.8 - - + -
22A ALA* 4.2 6.0 - - + +
23A LEU* 4.1 12.6 - - + -
45A GLY* 3.4 18.6 + - - -
47A SER* 1.3 76.4 - - - +
49A LEU* 1.3 66.1 + - - +
51A ASN* 3.2 10.6 + - - +
52A VAL* 2.8 28.1 + - + +
57A LEU* 3.7 13.6 - - + +
301A SO4 5.1 1.9 + - - -
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Residues in contact with LEU 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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10A THR* 5.0 4.9 - - + -
13A ILE* 4.3 13.9 - - + -
23A LEU* 3.6 26.2 - - + +
26A VAL* 4.0 23.6 - - + -
28A ILE* 4.2 10.1 - - + -
38A ILE* 4.0 21.3 - - + -
45A GLY 2.8 20.2 + - - +
46A LYS* 3.4 6.3 - - - +
48A THR* 1.3 77.0 - - - +
50A ILE* 1.3 58.5 + - + +
52A VAL* 3.1 3.5 + - + +
53A ILE* 2.9 48.8 + - + +
226A MET* 3.9 20.9 - - - -
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Residues in contact with ILE 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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38A ILE* 4.9 6.3 - - + -
46A LYS 3.1 14.0 + - - +
47A SER* 3.0 8.9 + - - +
49A LEU* 1.3 82.1 - - + +
51A ASN* 1.3 57.2 + - - +
53A ILE* 3.4 4.2 + - + +
54A THR* 3.0 30.8 + - - +
86A ARG* 3.4 24.9 - - + +
176A VAL* 3.3 20.6 - - + -
177A MET 5.8 0.4 - - - +
178A ASP* 4.9 7.0 - - + +
207A LEU* 3.3 42.4 - - + +
209A ILE* 3.3 29.6 - - + -
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Residues in contact with ASN 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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47A SER* 2.8 31.8 + - - -
48A THR* 3.4 10.7 - - - +
50A ILE* 1.3 70.6 - - - +
52A VAL* 1.3 65.6 + - - +
54A THR* 3.4 4.9 + - - -
55A GLY 3.1 2.4 + - - -
56A PHE* 2.7 34.2 + - + +
57A LEU* 2.9 22.5 + - + +
86A ARG* 3.2 22.4 + - - +
600A PEG 3.3 33.4 + - - +
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Residues in contact with VAL 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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13A ILE* 4.2 17.7 - - + -
15A LYS* 4.6 5.8 - - + -
23A LEU* 4.2 12.3 - - + -
48A THR* 2.8 25.3 + - + +
49A LEU* 3.3 9.4 - - + +
51A ASN* 1.3 76.8 - - - +
53A ILE* 1.3 66.6 + - + +
55A GLY* 3.0 12.5 + - - -
57A LEU* 3.6 27.6 - - + +
58A LYS 4.3 9.4 - - - +
59A ALA* 3.9 29.8 - - + +
64A VAL* 4.7 8.4 - - + +
73A ASN* 5.4 3.9 + - - +
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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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8A LEU* 4.1 23.1 - - + -
10A THR* 3.8 26.9 - - + -
28A ILE* 4.2 9.9 - - + -
49A LEU* 2.9 32.3 + - + +
50A ILE* 3.6 7.4 - - - +
52A VAL* 1.3 80.6 - - + +
54A THR* 1.3 64.6 + - + +
55A GLY 3.2 1.2 + - - -
64A VAL* 4.2 21.2 - - + +
71A ILE* 4.9 7.6 - - + +
79A LEU* 3.4 13.0 - - - +
84A ILE* 4.9 7.0 - - + +
174A MET* 6.1 0.4 - - - -
176A VAL* 5.3 4.3 - - + -
207A LEU* 4.1 24.0 - - + -
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Residues in contact with THR 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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50A ILE 3.0 20.5 + - - +
51A ASN* 3.4 4.9 + - - -
53A ILE* 1.3 75.7 - - + +
55A GLY* 1.3 60.2 + - - +
56A PHE* 3.1 24.5 + - - -
76A PRO* 3.7 15.9 - - - +
79A LEU* 3.1 15.4 - - - +
84A ILE* 4.8 8.0 - - + +
85A VAL* 6.2 0.2 - - - -
86A ARG* 3.5 36.2 + - + +
176A VAL* 3.7 31.2 - - + -
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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
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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