Contacts of the helix formed by residues 69 - 78 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57D GLU* 3.4 54.7 + - + +
59D PHE* 3.9 27.6 - - + -
67D VAL 3.8 1.6 + - - -
68D ASP* 1.3 71.6 + - - +
70D ASP* 1.3 59.5 + - - +
71D LEU 3.0 2.9 - - - -
72D GLY* 2.7 21.5 + - - -
73D ASN* 2.8 26.1 + - - +
76D ARG* 5.3 2.2 - - - +
315D ALA* 4.3 10.3 - - + -
316D SER* 3.9 27.4 - - - +
529D PHE* 4.7 1.3 - - + -
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Residues in contact with ASP 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D GLY* 4.6 4.7 - - - -
38D LYS* 3.6 13.4 - - + -
68D ASP* 2.9 16.1 + - - +
69D LEU* 1.3 78.4 - - - +
71D LEU* 1.3 56.3 + - - +
73D ASN* 3.1 22.7 + - - +
74D TYR* 2.9 36.7 + - + -
146D GLU* 3.3 21.2 - - - +
601D ATP 2.8 46.6 + - - -
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Residues in contact with LEU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D SER* 4.6 3.6 - - - +
38D LYS* 3.8 27.6 - - + +
59D PHE* 4.6 1.3 - - - -
61D LEU* 4.8 9.4 - - + -
67D VAL* 3.6 35.7 - - + -
68D ASP 3.1 8.7 + - - +
69D LEU 3.0 0.2 - - - -
70D ASP* 1.3 76.6 - - - +
72D GLY* 1.3 59.6 + - - +
74D TYR* 3.2 26.9 + - + +
75D GLU* 3.0 29.6 + - - +
82D LEU* 3.7 19.0 - - + +
86D ASN* 4.5 11.4 - - + +
87D ASN* 3.8 24.7 - - + +
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Residues in contact with GLY 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D PHE* 3.6 41.2 - - - -
69D LEU* 2.7 11.6 + - - -
71D LEU* 1.3 77.8 - - - +
73D ASN* 1.3 59.3 + - - +
75D GLU* 3.0 3.9 + - - +
76D ARG* 2.8 31.6 + - - +
532D ARG* 4.6 2.9 + - - -
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Residues in contact with ASN 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D GLY 5.7 2.8 - - - +
18D ILE* 5.2 12.8 - - + +
21D SER* 5.0 4.3 - - - +
69D LEU* 2.8 25.4 + - - +
70D ASP* 3.1 33.8 + - + +
72D GLY* 1.3 75.7 - - - +
74D TYR* 1.3 69.4 + - + +
76D ARG* 2.7 44.7 + - - +
77D PHE* 3.0 28.8 + - + -
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Residues in contact with TYR 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D GLY* 3.5 24.1 - - - -
20D ALA* 3.3 20.9 - - + +
21D SER* 3.6 24.0 - - - -
36D SER* 3.6 24.7 - - - +
38D LYS* 5.2 1.8 - - + -
70D ASP* 2.9 22.6 + - + -
71D LEU* 3.4 34.1 - - + +
72D GLY 3.1 0.2 - - - -
73D ASN* 1.3 78.6 - - + +
75D GLU* 1.3 51.0 + - - +
77D PHE* 3.3 1.2 + - - -
78D LEU* 2.7 47.4 + - + +
80D ILE* 4.7 7.6 - - + -
82D LEU* 4.2 8.3 - - + -
144D VAL* 6.3 0.2 - - + -
146D GLU* 2.4 37.7 + - + +
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Residues in contact with GLU 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D PHE* 3.3 26.9 - - - -
61D LEU* 4.0 4.7 - - - +
62D ASP* 5.3 0.9 - - - +
71D LEU 3.0 15.0 + - - +
72D GLY* 3.0 8.0 + - - +
74D TYR* 1.3 73.2 - - - +
76D ARG* 1.3 57.1 + - - +
78D LEU 2.7 22.2 - - - +
79D ASP* 4.6 2.8 - - - +
80D ILE* 3.4 16.2 - - + +
81D ARG* 3.2 33.8 + - - +
82D LEU* 2.8 43.7 + - + +
477D ARG* 4.4 0.9 + - - -
532D ARG* 3.0 24.8 + - - +
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Residues in contact with ARG 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D PHE* 6.4 0.2 - - - -
69D LEU* 5.3 1.6 - - - +
72D GLY 2.8 12.7 + - - +
73D ASN* 2.7 44.8 + - - +
75D GLU* 1.3 80.5 - - - +
77D PHE* 1.3 74.5 + - + +
78D LEU 3.6 1.2 + - - +
79D ASP* 5.4 2.3 - - - +
284D LYS* 5.9 0.5 + - - -
316D SER* 4.2 22.4 + - - +
319D LYS* 3.6 33.2 - - - +
323D HIS* 3.7 21.7 + - - -
528D GLU 5.3 4.2 + - - -
531D SER 4.8 2.8 + - - -
532D ARG* 3.5 19.4 - - - +
533D PRO* 3.8 25.9 - - + +
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Residues in contact with PHE 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ILE* 6.5 0.4 - - + -
21D SER* 3.2 45.3 - - - +
22D SER* 4.1 10.8 - - - -
25D THR* 2.7 28.9 + - + -
28D LYS* 5.8 0.5 - - - +
73D ASN* 3.0 23.4 + - + +
76D ARG* 1.3 97.1 - - + +
78D LEU* 1.4 71.3 + - + +
79D ASP* 5.7 0.2 - - - -
250D ILE* 4.0 22.9 - - + -
251D TYR* 5.7 0.2 - - - -
254D PRO* 4.4 3.6 - - + -
284D LYS* 4.3 8.8 + - - +
285D TRP* 3.5 39.5 - + - -
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Residues in contact with LEU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D SER* 4.3 4.0 - - - +
24D GLY* 3.6 16.6 - - - +
25D THR* 3.8 17.0 - - - +
28D LYS* 3.9 17.0 - - + -
34D VAL* 3.5 36.1 - - + -
74D TYR* 2.7 25.2 + - + +
75D GLU* 2.7 33.0 - - - +
76D ARG 4.7 0.7 - - - -
77D PHE* 1.4 88.4 - - + +
79D ASP* 1.3 61.4 + - - +
80D ILE* 3.1 30.0 + - + -
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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