Contacts of the helix formed by residues 44 - 58 (chain B) in PDB entry 3GA5
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B SER 3.3 4.3 + - - +
42B GLN 3.3 8.5 - - - +
43B ASN* 1.3 79.7 - - - +
45B GLN* 1.3 64.9 + - - +
46B SER* 2.8 26.8 + - - -
47B LYS* 3.0 46.9 + - + +
48B GLN 3.1 8.8 + - - -
68B VAL* 3.7 6.6 - - - +
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Residues in contact with GLN 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ASP* 1.3 72.6 + - - +
46B SER* 1.3 57.2 + - - +
48B GLN* 3.0 25.0 + - - +
49B ASN* 2.8 56.8 + - - +
67B LEU* 4.0 4.9 - - - +
68B VAL* 2.9 29.2 + - + +
69B ASP* 2.9 38.1 + - + +
72B ALA* 3.6 29.5 - - + +
76B VAL* 4.2 2.8 - - - +
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Residues in contact with SER 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ASP* 2.8 17.7 + - - -
45B GLN* 1.3 78.3 - - - +
47B LYS* 1.3 59.2 + - - -
49B ASN* 3.4 12.0 + - - +
50B ASP* 3.3 26.1 + - - +
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Residues in contact with LYS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B SER 3.8 12.6 - - - +
42B GLN* 2.8 38.4 + - - +
44B ASP* 3.0 36.5 + - + +
46B SER* 1.3 76.9 - - - +
48B GLN* 1.3 58.7 + - - +
50B ASP* 3.2 8.7 + - - +
51B GLN* 2.9 38.0 + - + +
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Residues in contact with GLN 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR* 3.2 21.1 + - + +
10B TYR* 4.3 0.8 - - - +
41B SER* 3.1 33.5 + - - +
44B ASP 3.1 9.1 + - - +
45B GLN* 3.0 34.6 + - - +
47B LYS* 1.3 77.7 - - - +
49B ASN* 1.3 56.4 + - - +
51B GLN* 3.5 10.6 + - - +
52B ILE* 2.8 40.0 + - + +
65B ILE* 3.7 4.0 - - - +
66B ASN 2.9 24.4 + - - -
67B LEU* 3.5 18.0 - - - +
68B VAL* 3.9 7.6 - - + +
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Residues in contact with ASN 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLN* 2.8 51.9 + - - +
46B SER* 3.7 9.6 + - - +
47B LYS 3.3 0.4 - - - -
48B GLN* 1.3 76.3 - - - +
50B ASP* 1.3 65.2 + - - +
52B ILE* 3.4 3.9 + - - +
53B ASP* 3.3 24.8 + - - +
72B ALA* 4.9 1.9 - - - +
75B THR* 4.3 16.3 - - - +
76B VAL* 4.2 10.7 - - - +
79B LYS* 3.6 24.8 - - - +
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Residues in contact with ASP 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B SER 3.3 11.7 + - - +
47B LYS* 3.2 10.0 + - - +
48B GLN 3.2 0.4 - - - -
49B ASN* 1.3 77.0 - - - +
51B GLN* 1.3 66.0 + - + +
53B ASP* 3.3 13.7 + - - +
54B VAL* 3.0 27.0 + - + +
79B LYS* 5.7 0.3 + - - -
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Residues in contact with GLN 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR* 4.8 4.0 - - + -
39B ASN* 3.8 33.8 + - + +
40B ASP 2.9 27.6 + - - +
41B SER* 2.7 33.7 + - - +
42B GLN* 6.1 0.2 - - - -
47B LYS* 2.9 20.9 + - + +
48B GLN* 3.2 10.1 + - - +
50B ASP* 1.3 77.4 - - - +
52B ILE* 1.3 56.7 + - - +
54B VAL* 3.2 8.5 + - - +
55B LEU* 2.8 33.7 + - - +
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Residues in contact with ILE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B THR* 4.3 6.7 - - + -
48B GLN* 2.8 37.1 + - + +
49B ASN* 3.7 7.4 - - - +
50B ASP 3.2 0.4 - - - -
51B GLN* 1.3 76.6 - - - +
53B ASP* 1.3 62.7 + - - +
55B LEU* 3.3 7.3 + - + +
56B LEU* 3.1 30.0 + - + +
63B LEU* 4.0 22.0 - - + -
65B ILE* 3.9 22.9 - - + -
76B VAL* 3.6 39.7 - - + +
79B LYS* 4.0 20.6 - - + -
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Residues in contact with ASP 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ASN 3.3 7.9 + - - +
50B ASP* 3.3 17.7 + - - +
52B ILE* 1.3 76.0 - - - +
54B VAL* 1.3 60.2 + - + +
56B LEU* 3.4 8.7 + - - +
57B ALA* 3.0 29.0 + - - +
79B LYS* 3.0 43.1 + - - +
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ASN* 6.0 1.6 - - - +
50B ASP* 3.0 18.3 + - + +
51B GLN* 3.2 11.2 + - - +
53B ASP* 1.3 77.9 - - + +
55B LEU* 1.3 60.3 + - + +
57B ALA* 3.1 7.0 + - - +
58B LYS* 2.9 59.4 + - + +
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLY* 3.9 12.3 - - - -
8B THR* 4.0 19.1 - - + -
37B LEU* 3.8 30.1 - - + +
39B ASN* 3.2 36.1 - - - +
51B GLN 2.8 23.4 + - - +
52B ILE* 3.3 7.8 + - - +
54B VAL* 1.3 74.8 - - + +
56B LEU* 1.3 64.0 + - - +
58B LYS* 3.0 17.7 + - + +
59B GLY 3.4 6.9 + - - -
60B VAL* 3.4 18.5 - - + +
63B LEU* 3.8 26.7 - - + -
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ILE* 3.1 30.5 + - + +
53B ASP* 3.7 8.7 - - - +
55B LEU* 1.3 76.7 - - - +
57B ALA* 1.3 64.3 + - - +
59B GLY* 2.9 15.6 + - - -
60B VAL* 4.0 9.1 + - + +
63B LEU* 4.1 13.9 - - + -
79B LYS* 3.6 32.3 - - + +
80B ALA* 4.5 2.2 - - - +
83B GLN* 4.1 20.4 + - + -
85B VAL* 3.6 41.5 - - + -
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ASP 3.0 18.1 + - - +
54B VAL* 3.6 8.5 - - + +
56B LEU* 1.3 77.9 - - - +
58B LYS* 1.3 57.3 + - + +
59B GLY* 3.1 4.7 + - - -
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Residues in contact with LYS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ARG* 2.8 36.2 + - - +
37B LEU* 3.9 26.5 - - + -
54B VAL* 2.9 39.5 + - + +
55B LEU* 3.0 13.2 + - + +
57B ALA* 1.3 77.2 - - + +
59B GLY* 1.3 59.3 + - - +
60B VAL 3.6 1.1 - - - -
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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
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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