Contacts of the helix formed by residues 69 - 78 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B GLY* 6.1 0.2 - - - -
57B GLU* 3.4 55.3 + - + +
59B PHE* 3.9 28.0 - - + -
67B VAL 3.8 1.8 + - - -
68B ASP* 1.3 71.4 + - - +
70B ASP* 1.3 60.3 + - - +
71B LEU 3.0 2.9 - - - -
72B GLY* 2.7 22.1 + - - -
73B ASN* 2.8 26.2 + - - +
76B ARG* 5.3 2.0 - - - +
315B ALA* 4.3 10.1 - - + -
316B SER* 3.9 28.5 - - - +
529B PHE* 4.7 1.3 - - + -
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Residues in contact with ASP 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLY* 4.6 4.7 - - - -
38B LYS* 3.6 13.2 - - - -
68B ASP* 2.9 16.5 + - - +
69B LEU* 1.3 77.8 - - - +
71B LEU* 1.3 57.2 + - - +
73B ASN* 3.1 23.9 + - - +
74B TYR* 2.9 37.3 + - + -
146B GLU* 3.3 20.7 - - - +
601B ATP 2.8 48.0 + - - -
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B SER* 4.6 3.8 - - - +
38B LYS* 3.8 28.3 - - + +
59B PHE* 4.6 1.3 - - - -
61B LEU* 4.8 9.0 - - + -
67B VAL* 3.6 35.4 - - + -
68B ASP 3.1 8.5 + - - +
69B LEU 3.0 0.8 - - - -
70B ASP* 1.3 77.1 - - - +
72B GLY* 1.3 58.8 + - - +
74B TYR* 3.2 28.1 + - + +
75B GLU* 3.0 30.1 + - - +
82B LEU* 3.7 19.3 - - + +
86B ASN* 4.5 11.4 - - + +
87B ASN* 3.8 24.7 - - + +
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Residues in contact with GLY 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B PHE* 3.6 41.7 - - - -
69B LEU* 2.7 11.8 + - - -
71B LEU* 1.3 77.2 - - - +
73B ASN* 1.3 58.7 + - - +
75B GLU* 3.0 4.3 + - - +
76B ARG* 2.8 31.9 + - - +
532B ARG* 4.6 3.3 + - - -
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Residues in contact with ASN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLY 5.7 2.5 - - - +
18B ILE* 5.2 12.2 - - + +
21B SER* 5.0 4.7 - - - +
69B LEU* 2.8 25.7 + - - +
70B ASP* 3.3 32.9 + - - +
72B GLY* 1.3 75.5 - - - +
74B TYR* 1.3 67.4 + - + +
76B ARG* 2.7 47.2 + - - +
77B PHE* 3.0 28.1 + - + -
601B ATP 5.5 0.2 + - - -
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Residues in contact with TYR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLY* 3.5 24.9 - - - -
20B ALA* 3.3 21.0 - - + +
21B SER* 3.6 24.2 - - - -
36B SER* 3.6 24.7 - - - +
37B ILE 5.9 0.2 - - - -
38B LYS* 5.2 1.6 - - + -
70B ASP* 2.9 23.0 + - + -
71B LEU* 3.4 33.9 - - + +
73B ASN* 1.3 78.6 - - + +
75B GLU* 1.3 52.1 + - - +
77B PHE* 4.5 1.1 - - - +
78B LEU* 2.7 47.7 + - + +
80B ILE* 4.7 7.6 - - + -
82B LEU* 4.2 8.3 - - + -
146B GLU* 2.4 38.6 + - + +
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Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B PHE* 3.3 26.0 - - - -
61B LEU* 4.0 4.9 - - - +
62B ASP* 5.3 0.7 - - - +
71B LEU 3.0 15.1 + - - +
72B GLY* 3.0 7.6 + - - +
74B TYR* 1.3 74.1 - - - +
76B ARG* 1.3 60.8 + - - +
78B LEU 2.7 19.3 - - - +
79B ASP* 4.6 3.1 - - - +
80B ILE* 3.4 15.0 - - + +
81B ARG* 3.2 34.5 + - - +
82B LEU* 2.8 42.9 + - + +
477B ARG* 4.4 0.9 + - - -
532B ARG* 3.0 25.9 + - - +
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Residues in contact with ARG 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B PHE* 6.4 0.2 - - - -
69B LEU* 5.3 2.0 - - - +
72B GLY 2.8 12.8 + - - +
73B ASN* 2.7 45.0 + - - +
75B GLU* 1.3 81.3 - - - +
77B PHE* 1.3 74.6 + - + +
78B LEU 4.5 0.9 - - - +
79B ASP* 5.4 2.3 - - - +
284B LYS* 5.9 0.3 + - - -
316B SER* 4.2 22.2 + - - +
319B LYS* 3.6 34.5 - - - +
323B HIS* 3.7 23.6 + - - -
528B GLU 5.3 3.8 + - - -
531B SER 4.8 3.0 + - - -
532B ARG* 3.5 18.9 - - - +
533B PRO* 3.8 25.9 - - + +
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Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 6.5 0.4 - - + -
21B SER* 3.2 44.2 - - - +
22B SER* 4.1 11.0 - - - -
25B THR* 2.7 28.3 + - + -
28B LYS* 5.8 0.5 - - - +
73B ASN* 3.0 23.3 + - + +
76B ARG* 1.3 97.1 - - + +
78B LEU* 1.4 70.9 + - + +
79B ASP* 5.7 0.2 - - - -
250B ILE* 4.0 23.1 - - + -
251B TYR 5.7 0.4 - - - -
254B PRO* 4.4 3.4 - - + -
284B LYS* 4.3 9.1 + - - +
285B TRP* 3.5 40.8 - + - -
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B SER* 4.3 3.6 - - - +
24B GLY* 3.6 17.3 - - - +
25B THR* 3.8 17.5 - - - +
28B LYS* 3.9 16.2 - - + -
34B VAL* 3.5 36.1 - - + -
74B TYR* 2.7 25.4 + - + +
75B GLU* 2.7 32.1 - - - +
76B ARG 4.7 0.4 - - - -
77B PHE* 1.4 89.5 - - + +
79B ASP* 1.3 62.8 + - - +
80B ILE* 3.1 30.4 + - + +
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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