Contacts of the helix formed by residues 54 - 62 (chain e) 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 ASP 54 (chain e).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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834A G 4.3 6.9 + - - +
2358A A 5.4 2.6 - - - -
2359A C 2.8 47.1 + - - +
2360A G 5.1 0.3 - - - +
51M GLU* 6.0 0.7 - - - -
57M LEU* 3.6 27.9 - - + +
60M ARG* 5.3 0.7 + - - -
50e VAL* 4.3 9.3 - - + +
51e SER* 3.4 9.1 + - - -
52e LYS 3.2 0.8 - - - -
53e GLY* 1.3 78.9 - - - +
55e LEU* 1.3 65.2 + - - +
56e GLY 3.0 5.0 + - - -
57e LEU* 3.1 22.9 + - + +
58e VAL* 3.0 21.8 + - - +
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Residues in contact with LEU 55 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938A G 5.0 12.6 - - - +
20e GLY 5.6 0.9 - - - +
21e GLY* 5.0 11.2 - - - -
22e PHE* 4.1 26.9 - - + +
50e VAL* 3.6 34.3 - - + +
51e SER 3.3 14.6 + - - +
52e LYS* 3.5 16.4 + - + +
53e GLY 3.7 0.2 - - - -
54e ASP* 1.3 78.1 - - - +
56e GLY* 1.3 56.2 + - - +
58e VAL* 3.8 3.1 - - + +
59e ILE* 2.9 47.8 + - + +
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Residues in contact with GLY 56 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834A G 6.2 0.2 - - - -
52e LYS 5.0 1.0 + - - -
53e GLY 5.0 2.2 + - - -
54e ASP 3.0 1.0 + - - -
55e LEU* 1.3 76.4 - - - +
57e LEU* 1.3 65.6 + - - +
59e ILE* 3.4 4.8 + - - +
60e ALA* 2.9 24.3 + - - +
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Residues in contact with LEU 57 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833A A 4.3 22.9 - - - +
834A G 4.7 15.5 + - - +
49M GLY* 4.1 25.6 - - - +
50M PHE 4.5 6.5 - - - +
51M GLU* 4.2 33.7 - - + +
57M LEU* 5.1 5.2 - - + -
54e ASP* 3.1 31.5 + - + +
56e GLY* 1.3 71.8 - - - +
58e VAL* 1.3 66.8 + - + +
60e ALA* 3.0 19.3 + - - +
61e CYS* 3.0 19.7 + - - -
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Residues in contact with VAL 58 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57M LEU* 3.6 26.5 - - + -
14e PHE* 4.1 22.8 - - + -
22e PHE* 3.5 43.9 - - + -
50e VAL* 4.0 13.5 - - + -
54e ASP 3.0 16.0 + - - +
55e LEU* 3.8 7.2 - - + +
57e LEU* 1.3 76.6 - - - +
59e ILE* 1.3 60.3 + - - +
61e CYS* 3.5 7.6 + - - +
62e LEU* 3.3 22.0 + - + +
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Residues in contact with ILE 59 (chain e).
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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594A U 6.3 3.4 - - - -
16e LYS* 5.0 7.9 - - - +
20e GLY 5.4 2.0 - - - +
22e PHE* 3.7 28.3 - - + -
55e LEU* 2.9 40.0 + - + +
56e GLY* 4.1 3.6 - - - +
58e VAL* 1.3 74.4 - - - +
60e ALA* 1.3 67.3 + - - +
62e LEU 3.3 24.7 + - - +
63e PRO* 3.7 6.0 - - + +
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Residues in contact with ALA 60 (chain e).
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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665A U 5.3 6.0 + - - +
48M ARG* 3.0 41.1 + - + -
49M GLY 5.2 1.6 - - - +
56e GLY 2.9 15.0 + - - +
57e LEU* 3.0 15.5 + - - +
59e ILE* 1.3 80.1 - - - +
61e CYS* 1.3 58.7 + - - +
63e PRO* 4.3 6.4 - - - +
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Residues in contact with CYS 61 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48M ARG* 4.0 4.1 + - - +
49M GLY* 4.0 28.9 - - - -
58M TYR* 4.4 19.3 - - - -
7e VAL* 3.2 50.1 + - + +
10e ALA* 4.1 13.0 - - + -
57e LEU* 3.0 18.3 + - - -
58e VAL* 3.5 8.9 + - - +
59e ILE 3.2 0.2 - - - -
60e ALA* 1.3 78.4 - - - +
62e LEU* 1.3 58.3 + - - +
63e PRO* 3.1 10.4 - - - +
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Residues in contact with LEU 62 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6e THR* 4.3 10.8 - - + +
7e VAL 3.6 20.9 - - - +
10e ALA* 3.7 15.0 - - + -
11e ALA* 3.9 19.1 - - + +
14e PHE* 4.3 21.1 - - + +
16e LYS* 5.5 1.0 + - - -
22e PHE* 4.3 15.7 - - + -
58e VAL 3.3 12.4 + - - +
59e ILE* 3.3 14.7 + - - +
61e CYS* 1.3 87.4 - - - +
63e PRO* 1.3 65.7 - - - +
64e TYR 3.2 2.0 - - - -
65e ALA* 3.4 33.9 + - + +
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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