Contacts of the helix formed by residues 39 - 51 (chain U) in PDB entry 5GAG
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 THR 39 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1598A A 4.3 9.5 + - - +
1599A U 3.4 25.8 - - - -
37U ASP 3.7 10.3 - - - +
38U ALA* 1.3 76.4 - - - +
40U LYS* 1.3 67.2 + - - +
41U ALA* 3.5 13.9 + - - +
42U GLU* 2.9 38.6 + - - +
43U ILE* 2.9 14.7 + - - +
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Residues in contact with LYS 40 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1342A A 2.8 42.5 + - - -
1343A G 4.5 8.1 + - - -
1597A A 6.0 1.8 - - - +
1598A A 4.4 18.7 + - - +
1599A U 2.9 36.5 + - - +
39U THR* 1.3 71.7 - - - +
41U ALA* 1.3 57.5 + - - +
43U ILE* 3.6 8.1 + - - +
44U LYS* 2.9 30.5 + - - +
57U VAL* 5.9 0.6 - - - +
58U VAL* 3.2 34.6 + - + +
59U ASN* 4.1 2.2 + - - -
60U THR* 3.8 25.5 - - + +
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Residues in contact with ALA 41 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1597A A 5.4 8.8 + - - +
1598A A 5.5 0.8 + - - -
2U ILE* 4.6 8.3 - - + -
39U THR* 3.0 9.3 + - - +
40U LYS* 1.3 75.4 - - - +
42U GLU* 1.3 65.9 + - + +
44U LYS* 3.2 8.5 + - - +
45U ALA* 3.0 25.1 + - - +
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Residues in contact with GLU 42 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2U ILE* 3.9 24.2 - - + +
6U ARG* 3.4 39.4 + - + +
7U LEU* 3.8 5.3 - - + +
10U VAL* 4.0 13.9 - - + +
37U ASP 4.3 0.2 - - - +
38U ALA* 3.2 13.2 - - - +
39U THR* 2.9 41.8 + - - +
41U ALA* 1.3 76.4 - - + +
43U ILE* 1.3 58.4 + - - +
45U ALA* 3.4 2.3 + - - +
46U ALA* 2.9 32.3 + - - +
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Residues in contact with ILE 43 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10U VAL* 4.2 7.6 - - + -
11U LEU* 4.5 13.7 - - + -
32U LEU* 5.5 0.2 - - + -
34U VAL* 3.8 32.3 - - + -
38U ALA* 3.9 21.5 - - + +
39U THR 2.9 17.4 + - - +
40U LYS* 3.8 4.5 - - - +
42U GLU* 1.3 73.7 - - - +
44U LYS* 1.3 65.8 + - - +
46U ALA* 3.2 6.4 + - - +
47U VAL* 3.0 25.8 + - + +
58U VAL* 4.2 7.0 - - + -
60U THR* 4.2 23.1 - - + -
81U LYS* 5.2 0.4 - - + -
83U ALA* 4.2 2.5 - - + -
85U VAL* 4.2 24.2 - - + -
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Residues in contact with LYS 44 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1596A A 4.1 17.8 + - - -
40U LYS 2.9 19.6 + - - +
41U ALA* 3.5 6.5 - - - +
43U ILE* 1.3 77.7 - - - +
45U ALA* 1.3 65.2 + - - +
47U VAL* 3.4 1.6 + - - +
48U GLN* 3.0 38.7 + - - +
55U VAL* 3.8 40.2 + - + +
56U GLU 4.1 15.3 + - - +
57U VAL* 5.6 2.5 - - - -
58U VAL* 4.4 13.6 - - + +
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Residues in contact with ALA 45 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2U ILE* 4.5 14.4 - - + -
7U LEU* 4.0 15.1 - - + +
41U ALA 3.0 15.7 + - - +
42U GLU 3.8 3.8 - - - +
44U LYS* 1.3 75.9 - - - +
46U ALA* 1.3 57.2 + - - +
48U GLN* 3.3 12.8 + - - +
49U LYS* 2.9 30.0 + - - +
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Residues in contact with ALA 46 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7U LEU* 3.6 37.9 - - + +
10U VAL* 5.0 3.6 - - + -
11U LEU* 4.3 15.5 - - + -
42U GLU 2.9 19.4 + - - +
43U ILE* 3.5 7.2 - - - +
44U LYS 3.2 0.2 - - - -
45U ALA* 1.3 74.3 - - - +
47U VAL* 1.3 60.0 + - - +
49U LYS* 3.2 1.5 + - - -
50U LEU* 2.9 36.8 + - + +
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Residues in contact with VAL 47 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11U LEU* 4.1 9.9 - - + -
30U ILE* 4.8 6.1 - - + -
32U LEU* 3.7 29.6 - - + -
43U ILE* 3.0 17.1 + - + +
44U LYS 4.1 2.0 - - - +
46U ALA* 1.3 76.7 - - - +
48U GLN* 1.3 64.8 + - - +
51U PHE* 3.2 42.4 + - + +
52U GLU 3.8 0.9 + - - -
53U VAL* 3.7 21.9 - - + +
55U VAL* 3.8 16.4 - - + -
85U VAL* 4.5 17.3 - - + -
87U LEU* 4.6 3.4 - - + -
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Residues in contact with GLN 48 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44U LYS* 3.0 33.3 + - - +
45U ALA* 3.6 11.1 - - - +
47U VAL* 1.3 78.9 - - - +
49U LYS* 1.3 59.5 + - - +
52U GLU* 3.4 19.2 - - - +
53U VAL 3.2 22.7 + - - +
54U GLU* 4.1 7.4 - - - +
55U VAL* 3.3 37.1 + - + +
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Residues in contact with LYS 49 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4U GLU* 3.6 43.9 + - + +
7U LEU* 3.7 23.7 - - + +
45U ALA 2.9 16.3 + - - +
46U ALA 3.8 2.7 - - - +
48U GLN* 1.3 76.2 - - - +
50U LEU* 1.3 80.1 + - + +
52U GLU* 3.3 19.4 + - - +
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Residues in contact with LEU 50 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4U GLU* 5.5 1.8 - - + +
7U LEU* 3.7 29.2 - - + +
8U LEU* 4.1 23.1 - - + -
11U LEU* 4.0 7.6 - - + -
46U ALA* 2.9 20.8 + - - +
49U LYS* 1.3 94.4 - - + +
51U PHE* 1.3 67.2 + - + +
52U GLU* 3.8 2.1 + - - +
96U VAL* 6.0 2.4 - - - +
26Z PHE* 3.8 40.3 - - + -
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Residues in contact with PHE 51 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11U LEU* 4.0 22.4 - - + -
30U ILE* 5.0 9.0 - - + -
32U LEU* 4.7 12.8 - - + -
47U VAL* 3.2 37.5 + - + +
50U LEU* 1.3 82.8 - - + +
52U GLU* 1.3 71.5 + - - +
53U VAL* 3.4 18.7 + - + +
94U ASP* 4.2 31.5 - - + +
95U PHE* 5.4 1.3 - + - -
96U VAL* 5.0 16.4 - - + -
26Z PHE* 4.9 7.4 - + - -
30Z MET* 3.8 34.8 - - + -
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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