Contacts of the helix formed by residues 59 - 71 (chain D) in PDB entry 3UDB
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 ASP 59 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D GLU 4.2 10.3 - - - +
57D LYS* 2.9 17.2 + - - +
58D ILE* 1.3 77.8 - - - +
60D GLU* 1.3 77.8 + - + +
61D ASN* 2.6 29.9 + - - +
62D VAL* 2.8 17.9 + - - +
63D LYS* 3.3 21.0 + - - +
312D ILE* 5.2 1.6 - - - +
316D THR* 5.7 0.3 - - - +
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Residues in contact with GLU 60 (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 ASP* 1.3 84.9 + - + +
61D ASN* 1.3 75.5 + - - +
62D VAL 3.4 0.2 - - - -
63D LYS* 3.6 20.6 - - - +
64D ARG* 2.7 39.3 + - - +
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Residues in contact with ASN 61 (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 ASP* 2.6 15.7 + - - +
60D GLU* 1.3 96.2 + - - +
62D VAL* 1.3 59.4 + - + +
64D ARG* 2.5 40.8 + - - +
65D GLU* 2.9 38.1 + - - +
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Residues in contact with VAL 62 (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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52D ILE* 3.7 34.5 - - + -
57D LYS 3.9 19.1 - - - +
58D ILE* 4.7 9.6 - - + -
59D ASP* 2.8 26.6 + - - +
61D ASN* 1.3 74.6 - - + +
63D LYS* 1.3 62.4 + - - +
65D GLU* 3.4 12.3 + - - +
66D ILE* 3.0 39.1 + - + +
90D LEU* 4.8 6.7 - - + -
163D TYR* 4.9 4.9 - - + -
312D ILE* 5.8 1.6 - - + -
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Residues in contact with LYS 63 (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 ASP 3.3 17.2 + - - +
60D GLU* 3.6 17.2 - - - +
61D ASN 3.3 0.4 - - - -
62D VAL* 1.3 81.2 - - - +
64D ARG* 1.3 68.3 + - - +
66D ILE* 3.3 1.4 + - - +
67D ILE* 3.0 30.5 + - + +
309D MET* 2.6 40.8 - - + +
312D ILE* 4.0 22.7 - - + -
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Residues in contact with ARG 64 (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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60D GLU* 2.7 27.5 + - - +
61D ASN* 2.5 44.0 + - - +
63D LYS* 1.3 77.7 - - - +
65D GLU* 1.3 75.8 + - - +
67D ILE* 3.1 6.9 + - - +
68D ASN* 2.9 56.7 + - - +
139D ARG* 6.0 1.4 - - - +
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Residues in contact with GLU 65 (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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61D ASN* 2.9 21.4 + - - +
62D VAL* 3.7 9.6 - - - +
64D ARG* 1.3 92.9 + - - +
66D ILE* 1.3 62.3 + - - +
68D ASN* 3.4 8.1 + - - +
69D HIS* 3.0 27.5 + - - +
139D ARG* 5.0 7.5 + - - +
161D PHE 3.8 16.8 - - - +
162D GLY* 3.6 5.5 - - - -
163D TYR* 2.9 46.5 + - + +
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Residues in contact with ILE 66 (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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62D VAL* 3.0 27.3 + - + +
63D LYS 3.3 4.7 + - - +
65D GLU* 1.3 74.6 - - - +
67D ILE* 1.3 68.6 + - + +
69D HIS* 4.0 1.4 - - - +
70D ARG* 3.0 26.4 + - + +
80D PHE* 4.2 21.5 - - + -
83D VAL* 3.9 15.7 - - + -
90D LEU* 3.8 29.8 - - + -
92D ILE* 4.0 10.5 - - + -
163D TYR* 4.0 22.2 - - + -
308D ILE* 4.4 7.4 - - + -
312D ILE* 4.0 16.8 - - + -
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Residues in contact with ILE 67 (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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63D LYS* 3.0 24.1 + - + +
64D ARG* 3.7 4.9 - - - +
66D ILE* 1.3 84.9 - - + +
68D ASN* 1.3 72.4 + - - +
70D ARG* 3.1 9.8 + - + +
71D SER* 3.1 22.2 + - - -
305D ILE* 3.7 26.5 - - + -
308D ILE* 4.5 4.0 - - + -
309D MET* 3.8 29.4 - - + -
312D ILE* 4.3 4.7 - - + -
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Residues in contact with ASN 68 (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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64D ARG* 2.9 46.1 + - - +
65D GLU* 3.7 7.2 - - - +
67D ILE* 1.3 81.7 - - - +
69D HIS* 1.3 59.7 + - - +
71D SER* 2.8 25.4 + - - -
72D LEU* 3.7 11.3 - - - +
135D GLN* 5.2 17.2 + - + +
139D ARG* 5.0 14.6 - - - +
161D PHE 5.7 0.7 - - - +
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Residues in contact with HIS 69 (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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65D GLU 3.0 18.3 + - - +
66D ILE 4.0 2.9 - - - +
68D ASN* 1.3 75.0 - - - +
70D ARG* 1.3 65.4 + - - +
72D LEU* 3.1 30.1 + - + +
78D VAL* 2.4 34.2 + - + +
79D ARG 4.0 0.9 - - - -
80D PHE* 3.6 31.2 + - + +
94D MET* 3.9 19.3 - - + -
160D ASP 4.1 12.1 - - - -
161D PHE* 3.5 27.3 + - + +
163D TYR* 3.2 22.4 + - - +
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Residues in contact with ARG 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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66D ILE* 3.0 20.9 + - + +
67D ILE* 3.1 10.5 + - + +
69D HIS* 1.3 77.6 - - - +
71D SER* 1.3 61.5 + - - +
72D LEU 3.3 1.3 + - - +
73D ARG* 4.3 16.2 + - - +
80D PHE* 3.5 35.3 - - + +
297D GLU* 3.1 40.2 + - - +
300D GLN* 3.9 24.9 - - - +
302D GLY 4.8 0.2 - - - +
303D GLN 3.3 26.9 + - - +
304D SER 3.8 0.6 - - - +
305D ILE* 3.7 20.4 - - - +
308D ILE* 3.4 20.3 - - + +
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Residues in contact with SER 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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67D ILE* 3.1 10.6 + - - -
68D ASN* 2.8 22.6 + - - -
69D HIS 3.1 0.4 - - - -
70D ARG* 1.3 78.2 - - - +
72D LEU* 1.3 67.1 + - - +
73D ARG* 3.4 4.2 + - - +
130D TYR* 3.2 14.9 + - - -
134D MET* 4.2 18.7 + - - +
135D GLN* 6.0 1.0 - - - +
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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