Contacts of the helix formed by residues 57 - 65 (chain p) in PDB entry 5JPQ
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 ASN 57 (chain p).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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850 PRO* 5.9 2.2 - - - +
4462 A 2.8 36.4 + - - +
4472 U 3.5 4.3 - - - -
5252 A 5.8 5.0 + - - +
49p LYS* 3.6 4.7 - - - -
56p LEU* 1.3 85.7 - - + +
58p GLY* 1.3 73.9 + - - +
59p ARG* 3.1 38.4 + - - +
60p ASP* 2.7 34.5 + - - +
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Residues in contact with GLY 58 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4462 A 5.4 0.2 - - - -
4472 U 2.4 23.7 + - - -
49p LYS* 3.0 17.7 + - - -
57p ASN* 1.3 76.8 + - - +
59p ARG* 1.3 61.9 + - - -
61p VAL* 3.2 21.1 + - - +
62p THR* 3.5 7.7 + - - -
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Residues in contact with ARG 59 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820 LYS 4.5 8.1 + - - -
830 TYR 3.5 16.1 + - - -
840 GLU 4.0 5.3 + - - -
850 PRO* 3.0 44.8 - - - +
860 ASN* 4.2 8.0 + - - +
1390 LYS* 4.9 5.9 - - - +
4552 C 5.3 13.2 + - + +
57p ASN* 3.1 20.2 + - - +
58p GLY* 1.3 73.2 - - - +
60p ASP* 1.3 64.3 + - - +
62p THR* 3.1 16.1 + - + -
63p LEU* 3.1 40.5 + - + +
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Residues in contact with ASP 60 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160 LEU* 3.5 9.2 - - + +
180 ARG* 3.0 29.5 + - - -
55p ALA* 3.8 4.7 - - + -
56p LEU* 3.2 24.2 - - - +
57p ASN* 2.7 48.4 + - - +
58p GLY 3.0 0.2 - - - -
59p ARG* 1.3 79.7 - - - +
61p VAL* 1.3 62.6 + - - +
63p LEU* 3.4 13.3 + - - +
64p ILE* 3.2 23.7 + - - +
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Residues in contact with VAL 61 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45p SER* 4.0 20.9 - - - -
48p LEU* 4.2 8.7 - - + -
49p LYS* 3.3 38.4 - - + +
55p ALA* 4.0 7.6 - - + -
58p GLY 3.2 8.8 + - - +
59p ARG 3.1 0.4 - - - -
60p ASP* 1.3 74.4 - - - +
62p THR* 1.3 58.6 + - - +
63p LEU 2.5 18.3 + - - -
64p ILE* 2.6 22.1 + - - -
65p LEU* 3.1 36.2 + - + -
82p LYS* 4.3 17.0 - - + -
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Residues in contact with THR 62 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4552 C 2.2 80.2 + - + +
58p GLY 3.5 9.6 + - - -
59p ARG* 3.3 19.0 - - + -
61p VAL* 1.3 80.9 - - - +
63p LEU* 1.3 52.1 - - + +
65p LEU* 5.7 1.1 - - - -
66p ASN* 2.9 22.1 + - - +
82p LYS* 3.7 27.2 + - - +
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Residues in contact with LEU 63 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160 LEU* 3.9 23.8 - - + -
820 LYS 5.5 1.6 - - - +
830 TYR* 4.0 37.2 - - + +
4552 C 3.4 25.4 - - + +
59p ARG* 3.3 38.4 - - + +
60p ASP* 3.4 11.7 - - - +
61p VAL 2.5 5.6 + - - -
62p THR* 1.3 70.1 - - - +
64p ILE* 1.3 61.0 + - - +
66p ASN 2.8 2.8 + - - -
67p ASP* 2.6 40.5 + - + +
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Residues in contact with ILE 64 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130 ASN* 4.7 0.2 - - - +
150 LEU* 3.9 27.6 - - + -
160 LEU* 3.7 23.3 - - + -
48p LEU* 4.2 12.8 - - + -
54p TYR* 5.0 0.2 - - + -
55p ALA* 4.0 29.6 - - + +
60p ASP 3.2 16.4 - - - +
61p VAL* 2.6 10.4 + - - +
63p LEU* 1.3 77.7 - - - +
65p LEU* 1.3 75.3 + - + +
66p ASN 3.6 0.2 + - - -
67p ASP* 3.9 6.1 + - - +
70p GLN* 5.1 0.7 + - - -
71p ASN* 3.2 50.4 + - + +
72p VAL* 4.4 3.1 - - + -
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Residues in contact with LEU 65 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44p LEU* 3.8 15.7 - - + -
48p LEU* 4.1 7.6 - - + -
61p VAL* 3.1 23.3 + - + +
62p THR* 5.3 1.3 - - - +
64p ILE* 1.3 84.4 - - + +
66p ASN* 1.3 60.7 + - - +
67p ASP 3.6 0.4 - - - -
70p GLN* 6.6 0.2 - - - -
72p VAL* 3.6 38.8 - - + -
79p ARG 4.9 0.4 - - - -
80p ARG* 3.0 50.2 - - - +
81p ASP 3.6 37.2 - - - +
82p LYS* 3.7 11.9 - - + +
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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