Contacts of the helix formed by residues 44 - 52 (chain A) in PDB entry 3GA1
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 HIS 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LEU* 3.7 24.0 - - + -
23A GLN* 3.5 13.6 + - - -
24A ARG* 4.1 5.4 - - + -
28A LEU 3.3 23.5 + - - -
29A TYR 3.0 23.8 + - - -
30A CYS* 4.0 11.6 - - - -
31A ASP* 3.3 7.2 - - - +
32A VAL* 4.3 2.0 - - - -
43A ALA* 1.3 72.5 - - - +
45A ARG* 1.3 65.7 + - - +
46A ALA* 4.4 4.9 - - + +
47A VAL* 3.1 27.6 + - + +
48A LEU* 3.2 13.2 + - - +
86A TYR* 2.8 33.7 + + - +
46B ALA* 3.6 17.7 - - + +
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Residues in contact with ARG 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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31A ASP* 2.8 54.7 + - - +
32A VAL* 3.8 19.7 - - + +
44A HIS* 1.3 71.0 - - - +
46A ALA* 1.3 57.8 + - - +
48A LEU* 3.3 3.4 + - - +
49A ALA* 2.8 32.8 + - - +
59A PHE* 3.4 53.9 + - + +
62A SER* 3.6 17.0 + - - -
63A ARG* 4.1 26.2 + - - +
64A SER 2.6 33.5 + - - -
65A ALA* 3.7 5.5 - - - +
67A VAL* 5.7 0.6 - - - +
29B TYR* 4.4 16.4 - - + +
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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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31A ASP* 5.0 0.6 + - - -
44A HIS* 3.2 5.3 - - + +
45A ARG* 1.3 79.9 - - - +
47A VAL* 1.3 58.8 + - + +
49A ALA* 3.5 0.4 + - - -
50A ALA* 3.0 25.1 + - - +
20B LEU* 3.7 12.0 - - + +
23B GLN* 3.1 32.8 + - - +
29B TYR* 3.9 10.5 + - + +
44B HIS* 3.4 29.8 - - + +
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Residues in contact with VAL 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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17A LEU* 4.5 7.6 - - + -
20A LEU* 3.8 28.9 - - + -
44A HIS* 3.1 19.1 + - + +
46A ALA* 1.3 74.8 - - + +
48A LEU* 1.3 65.8 + - - +
50A ALA* 3.4 18.1 + - - +
51A SER* 3.6 9.7 + - - -
85A CYS* 3.5 24.5 - - + +
86A TYR* 3.6 42.2 - - + -
16B ILE* 5.2 3.1 - - + +
20B LEU* 4.6 8.7 - - + -
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Residues in contact with LEU 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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32A VAL* 4.4 2.5 - - + -
34A VAL* 4.1 24.7 - - + -
43A ALA* 4.1 14.6 - - + -
44A HIS 3.2 9.7 + - - +
45A ARG 3.7 6.1 - - - +
47A VAL* 1.3 76.6 - - - +
49A ALA* 1.3 59.0 + - - +
51A SER* 3.2 4.0 + - - -
52A SER* 2.9 32.4 + - - -
55A PHE* 3.8 35.0 - - + -
59A PHE* 4.0 18.4 - - + -
78A PHE* 5.1 2.7 - - + -
81A ILE* 6.5 0.2 - - + -
82A LEU* 3.7 27.6 - - + -
85A CYS* 4.3 20.8 - - + -
86A TYR* 4.9 2.7 - - + -
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ARG 2.8 17.3 + - - +
46A ALA 3.6 4.5 - - - +
48A LEU* 1.3 76.4 - - - +
50A ALA* 1.3 52.9 + - - +
51A SER 3.2 0.7 + - - -
52A SER 3.5 10.4 - - - +
55A PHE* 4.2 3.3 - - - +
56A ARG* 2.7 49.6 + - + +
59A PHE* 4.9 0.4 - - + -
23B GLN* 3.9 2.0 - - - +
29B TYR* 3.6 39.9 - - + -
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ALA 3.0 14.7 + - - +
47A VAL 3.5 10.3 - - - +
48A LEU 3.2 0.2 - - - -
49A ALA* 1.3 77.4 - - - +
51A SER* 1.3 58.5 + - - +
56A ARG* 3.6 3.0 + - - +
110A GLN* 3.5 12.0 - - - +
16B ILE* 4.1 33.4 - - + +
19B CYS* 3.7 34.3 - - + -
20B LEU* 4.6 1.3 - - + -
23B GLN* 3.7 1.5 - - - +
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Residues in contact with SER 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 VAL 3.6 3.3 + - - -
48A LEU 3.2 3.0 + - - -
50A ALA* 1.3 78.3 - - - +
52A SER* 1.3 60.0 + - - +
84A PHE* 4.7 9.4 - - - -
85A CYS* 3.9 30.3 + - - -
109A ILE* 3.4 15.5 - - - +
110A GLN* 3.4 27.3 + - - +
111A GLU* 6.0 3.3 - - - +
12B PHE* 3.6 26.0 - - - -
16B ILE* 3.7 8.1 - - - +
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Residues in contact with SER 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 LEU 2.9 15.5 + - - +
49A ALA 3.5 6.0 + - - +
51A SER* 1.3 80.8 - - - +
53A SER* 1.3 57.5 + - - +
54A TYR* 3.6 0.2 - - - +
55A PHE* 3.0 34.1 + - - -
56A ARG* 2.9 26.2 + - - +
85A CYS* 5.5 2.5 - - - -
107A LEU 2.6 24.2 + - - -
108A GLN 3.7 4.0 - - - -
109A ILE* 4.4 9.2 - - - -
110A GLN* 4.0 0.9 - - - -
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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