Contacts of the helix formed by residues 69 - 78 (chain A) in PDB entry 5U03
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 LEU 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A GLU* 3.4 54.3 + - + +
59A PHE* 3.9 28.0 - - + -
67A VAL 3.8 1.6 + - - -
68A ASP* 1.3 71.3 + - - +
70A ASP* 1.3 60.0 + - - +
71A LEU 3.0 2.7 - - - -
72A GLY* 2.7 22.2 + - - -
73A ASN* 2.8 27.1 + - - +
76A ARG* 5.3 2.0 - - - +
315A ALA* 4.3 9.9 - - + -
316A SER* 3.9 29.2 - - - +
529A PHE* 4.7 1.1 - - + -
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Residues in contact with ASP 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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17A GLY* 4.6 4.9 - - - -
38A LYS* 3.6 13.1 - - + -
68A ASP* 2.9 16.5 + - - +
69A LEU* 1.3 78.9 - - - +
71A LEU* 1.3 56.3 + - - +
73A ASN* 3.1 23.1 + - + +
74A TYR* 2.9 36.7 + - + -
146A GLU* 3.3 21.3 - - - +
601A ATP 2.8 45.5 + - - -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER* 4.6 3.4 - - - +
38A LYS* 3.8 28.0 - - + +
59A PHE* 4.6 1.6 - - - -
61A LEU* 4.8 9.2 - - + -
67A VAL* 3.6 35.4 - - + -
68A ASP 3.1 9.1 + - - +
69A LEU 3.0 0.6 - - - -
70A ASP* 1.3 76.2 - - - +
72A GLY* 1.3 59.8 + - - +
74A TYR* 3.2 27.1 + - + +
75A GLU* 3.0 29.6 + - - +
82A LEU* 3.7 19.4 - - + +
86A ASN* 4.5 11.9 - - + +
87A ASN* 3.8 24.0 - - + +
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Residues in contact with GLY 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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59A PHE* 3.6 40.4 - - - -
69A LEU* 2.7 11.6 + - - -
71A LEU* 1.3 77.2 - - - +
73A ASN* 1.3 58.2 + - - +
75A GLU* 3.0 4.5 + - - +
76A ARG* 2.8 31.9 + - - +
532A ARG* 4.6 3.1 + - - -
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Residues in contact with ASN 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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17A GLY 5.7 3.0 - - - +
18A ILE* 5.2 12.7 - - + +
21A SER* 5.0 4.7 - - - +
69A LEU* 2.8 24.7 + - - +
70A ASP* 3.1 33.1 + - - +
72A GLY* 1.3 75.6 - - - +
74A TYR* 1.3 68.1 + - + +
76A ARG* 2.7 46.9 + - - +
77A PHE* 2.9 28.0 + - + -
601A ATP 5.5 0.2 + - - -
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Residues in contact with TYR 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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17A GLY* 3.5 23.3 - - - -
20A ALA* 3.3 22.2 - - + +
21A SER* 3.6 24.5 - - - -
36A SER* 3.6 24.0 - - - +
37A ILE 5.9 0.2 - - - -
38A LYS* 5.2 1.8 - - + -
70A ASP* 2.9 22.4 + - + -
71A LEU* 3.4 33.7 - - + +
72A GLY 3.1 0.2 - - - -
73A ASN* 1.3 79.4 - - + +
75A GLU* 1.3 52.1 + - - +
77A PHE* 4.5 1.1 - - - +
78A LEU* 2.7 47.6 + - + +
80A ILE* 4.7 7.6 - - + -
82A LEU* 4.2 8.1 - - + -
146A GLU* 2.4 38.4 + - + +
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Residues in contact with GLU 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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59A PHE* 3.3 25.9 - - - -
61A LEU* 4.0 4.2 - - - +
62A ASP* 5.3 0.7 - - - +
71A LEU 3.0 15.2 + - - +
72A GLY* 3.0 8.9 + - - +
74A TYR* 1.3 73.3 - - - +
76A ARG* 1.3 58.2 + - - +
78A LEU 2.7 21.9 - - - +
79A ASP* 4.6 3.1 - - - +
80A ILE* 3.4 15.7 - - + +
81A ARG* 3.2 34.7 + - - +
82A LEU* 2.8 42.7 + - + +
477A ARG* 5.1 0.7 + - - -
532A ARG* 3.0 24.7 + - - +
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Residues in contact with ARG 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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59A PHE* 6.4 0.2 - - - -
69A LEU* 5.3 2.2 - - - +
72A GLY 2.8 12.2 + - - +
73A ASN* 2.7 45.1 + - - +
75A GLU* 1.3 79.9 - - - +
77A PHE* 1.3 72.7 + - + +
78A LEU 3.6 1.2 + - - +
79A ASP* 5.4 2.3 - - - +
284A LYS* 5.9 0.5 + - - -
316A SER* 4.2 22.0 + - - +
319A LYS* 3.6 34.6 - - - +
323A HIS* 3.7 22.6 + - - -
528A GLU 5.3 4.2 + - - -
531A SER 4.8 3.2 + - - -
532A ARG* 3.5 19.1 - - - +
533A PRO* 3.8 25.8 - - + +
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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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18A ILE* 6.5 0.4 - - + -
21A SER* 3.2 46.9 - - - +
22A SER* 4.1 10.8 - - - -
25A THR* 2.7 28.9 + - + -
28A LYS* 5.8 0.5 - - - +
73A ASN* 2.9 22.8 + - + +
76A ARG* 1.3 97.0 - - + +
78A LEU* 1.4 70.9 + - + +
79A ASP* 5.7 0.4 - - - -
250A ILE* 4.0 23.6 - - + -
251A TYR 5.7 0.2 - - - -
254A PRO* 4.4 3.6 - - + -
284A LYS* 4.3 8.4 + - - +
285A TRP* 3.5 40.4 - + - -
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Residues in contact with LEU 78 (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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21A SER* 4.3 3.8 - - - +
24A GLY* 3.6 16.8 - - - +
25A THR* 3.8 17.7 - - - +
28A LYS* 3.9 16.6 - - + -
34A VAL* 3.5 35.4 - - + -
74A TYR* 2.7 25.6 + - + +
75A GLU* 2.7 32.3 - - - +
76A ARG 4.7 0.2 - - - -
77A PHE* 1.4 88.8 - - + +
79A ASP* 1.3 62.7 + - - +
80A ILE* 3.1 28.6 + - + -
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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