Contacts of the helix formed by residues 68 - 77 (chain A) in PDB entry 5UAK
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 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A TRP* 3.8 6.5 - - - -
60A GLU* 3.8 9.6 + - - +
66A ASN 3.5 9.4 + - - +
67A PRO* 1.3 73.1 - - - +
69A LEU* 1.3 63.7 + - - +
70A ILE* 4.4 11.0 - - + +
71A ASN* 3.6 26.5 - - + +
72A ALA 3.4 15.1 + - - -
372A GLN* 4.2 5.8 - - - +
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Residues in contact with LEU 69 (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 TRP* 3.6 25.0 - - + -
67A PRO 3.8 0.6 + - - -
68A LYS* 1.3 69.9 - - - +
70A ILE* 1.3 55.3 + - - +
72A ALA* 3.4 1.4 + - + +
73A LEU* 2.8 51.9 + - + +
156A MET* 5.8 3.6 - - + -
368A ILE* 3.7 23.8 - - + +
371A ILE* 3.9 17.0 - - + -
372A GLN* 3.4 46.4 + - + +
375A LEU* 3.9 27.8 - - + -
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Residues in contact with ILE 70 (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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68A LYS* 3.4 10.7 - - + -
69A LEU* 1.3 78.7 - - - +
71A ASN* 1.3 52.8 + - - +
73A LEU* 3.8 6.7 - - + +
74A ARG* 2.8 58.1 + - + +
365A LEU* 3.7 31.0 - - + +
368A ILE* 3.7 26.9 - - + -
369A ASN* 5.5 7.6 - - + +
372A GLN* 4.0 15.5 - - - +
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Residues in contact with ASN 71 (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 GLU* 3.5 24.0 + - - -
64A LYS* 4.9 9.5 - - - +
68A LYS* 3.5 31.0 + - + +
69A LEU 3.2 0.6 - - - -
70A ILE* 1.3 79.1 - - - +
72A ALA* 1.3 52.8 + - - +
74A ARG* 3.8 3.3 - - - +
75A ARG* 2.8 61.7 + - - +
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Residues in contact with ALA 72 (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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53A LEU* 4.9 3.4 - - - +
56A GLU* 4.5 20.9 - - + +
57A TRP* 4.2 15.3 - - + +
60A GLU* 4.1 22.4 + - + -
68A LYS 3.4 9.8 + - - +
69A LEU* 3.4 5.6 + - + +
71A ASN* 1.3 77.3 - - - +
73A LEU* 1.3 65.6 + - - +
75A ARG* 4.1 12.0 - - - +
76A CYS* 3.5 21.7 + - - +
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Residues in contact with LEU 73 (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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53A LEU* 4.3 30.7 - - + -
69A LEU* 2.8 30.5 + - + +
70A ILE* 3.8 5.6 - - + +
72A ALA* 1.3 73.1 - - - +
74A ARG* 1.3 63.2 + - + +
77A PHE* 3.6 22.7 + - + +
152A MET* 3.4 47.3 - - + +
156A MET* 4.7 9.9 - - + -
191A PHE* 4.6 7.9 - - + -
368A ILE* 4.4 34.1 - - + -
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Residues in contact with ARG 74 (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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70A ILE* 2.8 42.5 + - + +
71A ASN* 3.8 4.0 - - - +
73A LEU* 1.3 72.4 - - + +
75A ARG* 1.3 56.6 + - + +
76A CYS 3.1 2.5 - - - -
77A PHE* 2.8 12.4 + - - -
78A PHE* 2.8 56.7 + - + +
81A PHE* 3.6 40.0 - - - +
152A MET* 5.8 4.3 - - - -
195A LEU* 5.2 11.1 - - - +
198A ALA* 5.8 3.2 - - - +
361A TRP* 3.9 33.2 - - - -
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Residues in contact with ARG 75 (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* 2.9 35.2 + - - +
59A ARG* 5.0 11.7 - - - +
60A GLU* 5.2 7.0 + - - +
71A ASN* 2.8 52.9 + - - +
72A ALA* 4.1 10.0 - - - +
73A LEU 3.6 0.2 - - - -
74A ARG* 1.3 72.7 - - + +
76A CYS* 1.3 59.9 + - - +
78A PHE* 4.5 8.9 + - - +
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Residues in contact with CYS 76 (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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52A LYS* 4.0 32.1 - - - -
53A LEU* 4.5 7.6 - - + -
56A GLU* 3.9 22.8 + - - +
72A ALA 3.5 12.0 + - - +
73A LEU 4.2 0.7 - - - +
74A ARG 3.1 0.8 - - - -
75A ARG* 1.3 80.8 - - - +
77A PHE* 1.3 90.8 + - + +
78A PHE 3.6 1.4 + - - -
79A TRP 5.4 0.5 + - - -
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Residues in contact with PHE 77 (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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49A LEU* 5.5 5.4 - - + -
52A LYS* 5.3 11.9 - - + -
53A LEU* 4.0 18.8 - - + -
73A LEU* 3.6 8.9 + - + +
74A ARG* 2.8 15.4 + - - -
76A CYS* 1.3 97.4 - - + +
78A PHE* 1.3 56.6 + - - +
79A TRP 3.6 1.3 - - - +
80A ARG* 5.0 2.9 - - - +
81A PHE* 3.4 23.4 + - - +
148A ILE* 4.5 16.3 - - + +
151A GLN* 3.6 48.2 - - + -
152A MET* 3.3 34.3 - - + -
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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