Contacts of the helix formed by residues 54 - 64 (chain A) in PDB entry 5JQE
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 LYS 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ASN* 5.5 3.0 + - - -
52A PRO 3.3 1.8 + - - -
53A ASP* 1.3 90.4 + - - +
55A LEU* 1.3 65.6 + - - +
56A GLU* 3.3 19.1 + - - +
57A GLU* 3.2 42.1 + - + +
58A LYS* 3.5 14.9 + - - +
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Residues in contact with LEU 55 (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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22A TRP* 3.9 16.4 - - + -
23A ILE 3.4 40.4 - - - +
24A ASN* 3.9 8.7 + - - +
52A PRO* 3.5 28.9 - - + +
53A ASP 3.4 0.8 - - - -
54A LYS* 1.3 74.9 - - - +
56A GLU* 1.3 67.5 + - - +
58A LYS* 3.9 10.0 - - - +
59A PHE* 3.0 28.1 + - - +
72A ILE* 3.6 26.5 - - + -
73A PHE 4.4 1.1 - - - +
74A TRP* 3.4 33.6 - - + -
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Residues in contact with GLU 56 (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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54A LYS* 3.3 12.5 - - - +
55A LEU* 1.3 89.7 + - - +
57A GLU* 1.3 80.7 + - + +
60A PRO* 3.2 12.3 - - - +
74A TRP* 3.4 48.8 - - + +
78A ARG* 3.7 23.2 + - + +
82A TYR* 2.8 30.2 + - - +
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Residues in contact with GLU 57 (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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54A LYS* 3.2 45.2 + - + +
55A LEU 3.3 0.6 - - - -
56A GLU* 1.3 97.7 - - + +
58A LYS* 1.3 56.9 + - + +
60A PRO* 3.4 14.1 - - - +
61A GLN* 3.6 20.0 + - - +
78A ARG* 4.7 11.4 + - - +
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Residues in contact with LYS 58 (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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22A TRP* 4.3 17.0 - - + -
52A PRO* 4.7 7.4 - - + +
53A ASP* 3.0 35.1 + - - +
54A LYS* 3.5 12.0 + - - +
55A LEU* 4.0 9.9 - - - +
56A GLU 3.4 0.2 - - - -
57A GLU* 1.3 77.4 - - + +
59A PHE* 1.3 64.8 + - - +
60A PRO 3.5 0.7 - - - -
61A GLN* 3.5 20.7 + - - +
62A VAL* 3.3 31.1 + - + +
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Residues in contact with PHE 59 (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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22A TRP* 4.1 9.4 - + + -
55A LEU 3.0 18.9 + - - +
56A GLU 4.4 0.9 - - - +
58A LYS* 1.3 75.7 - - - +
60A PRO* 1.3 74.3 - - + +
61A GLN 3.2 0.2 + - - -
62A VAL* 3.3 4.6 + - - -
63A ALA* 3.0 38.2 + - + +
68A GLY* 4.5 2.0 - - - -
69A PRO* 3.9 32.5 - - + -
72A ILE* 4.5 25.8 - - + -
82A TYR* 3.6 45.1 - + + +
87A LEU* 4.1 19.7 - - + -
88A LEU* 4.8 2.7 - - + -
279A ASN* 4.0 22.4 - - + -
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Residues in contact with PRO 60 (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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56A GLU 3.2 17.9 - - - +
57A GLU 3.4 10.1 - - - +
59A PHE* 1.3 93.2 - - + +
61A GLN* 1.3 59.6 + - + +
63A ALA* 4.4 0.5 - - - +
64A ALA* 3.6 22.2 + - - +
78A ARG* 4.8 7.0 - - - +
82A TYR* 3.5 27.8 - - + -
87A LEU* 4.0 21.3 - - + +
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Residues in contact with GLN 61 (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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57A GLU* 3.6 24.6 + - - +
58A LYS* 3.8 18.2 - - - +
59A PHE 3.1 0.6 - - - -
60A PRO* 1.3 79.3 - - + +
62A VAL* 1.3 63.5 + - + +
64A ALA* 4.1 6.3 + - - +
65A THR* 3.4 15.8 + - - -
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Residues in contact with VAL 62 (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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22A TRP* 4.0 20.9 - - + -
58A LYS* 3.4 25.8 - - + +
59A PHE* 3.5 7.9 - - - +
61A GLN* 1.3 80.8 - - + +
63A ALA* 1.3 64.2 + - - +
64A ALA 3.4 0.2 - - - -
65A THR* 3.5 12.3 + - - -
66A GLY 3.6 0.2 + - - -
67A ASP* 3.0 31.8 + - + +
68A GLY* 3.4 21.6 + - - +
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Residues in contact with ALA 63 (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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59A PHE* 3.0 41.8 + - + +
60A PRO 4.4 0.9 - - - +
62A VAL* 1.3 75.2 - - - +
64A ALA* 1.3 58.0 + - - +
65A THR 3.0 4.9 - - - -
66A GLY* 2.9 20.7 + - - -
68A GLY 4.1 8.3 - - - +
87A LEU* 3.9 23.8 - - + +
279A ASN* 4.1 11.0 - - - +
281A ALA* 4.6 7.8 - - - +
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Residues in contact with ALA 64 (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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60A PRO 3.6 15.1 + - - +
61A GLN* 4.4 5.2 - - - +
62A VAL 3.4 0.6 - - - -
63A ALA* 1.3 76.9 - - - +
65A THR* 1.3 57.6 + - - +
87A LEU* 4.4 10.4 - - + +
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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