Contacts of the helix formed by residues 58 - 70 (chain D) in PDB entry 1UU1
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 58 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D TYR* 2.8 33.1 + - - -
55D ASP* 3.9 9.3 - - - +
56D SER 2.8 5.1 + - - -
57D PRO* 1.3 72.5 - - - +
59D GLU* 1.3 75.7 + - - +
60D GLU* 3.8 11.3 + - - +
61D LEU* 3.5 11.8 - - + +
62D ILE* 3.0 27.8 + - - +
238D GLN* 2.7 22.3 + - - +
242D LYS* 3.1 27.5 + - - +
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Residues in contact with GLU 59 (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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5B ASP* 4.8 9.0 - - - +
9B LYS* 5.3 0.5 - - - -
55D ASP* 5.7 0.8 - - - +
57D PRO 4.0 0.8 + - - -
58D ASP* 1.3 81.4 + - - +
60D GLU* 1.3 63.4 + - - +
62D ILE* 3.4 7.5 + - - +
63D GLU* 3.0 49.9 + - + +
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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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226A ARG* 5.9 0.7 + - - -
13B PRO* 5.9 3.6 - - - +
44D ARG* 3.0 20.1 + - - -
58D ASP* 3.4 7.1 + - - +
59D GLU* 1.3 79.0 + - + +
61D LEU* 1.3 67.3 + - - +
63D GLU* 3.1 17.4 + - + +
64D LYS* 2.9 50.8 + - + +
242D LYS* 3.2 27.3 + - + -
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Residues in contact with LEU 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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56D SER 4.5 3.6 - - - +
57D PRO* 5.4 0.7 - - + -
58D ASP* 3.5 21.1 + - + +
59D GLU 3.3 0.8 - - - -
60D GLU* 1.3 79.5 - - - +
62D ILE* 1.3 65.2 + - + +
64D LYS* 3.2 1.4 + - - +
65D ILE* 2.9 44.1 + - + +
81D VAL* 4.8 16.6 - - + -
200D PHE* 5.1 0.4 - - + -
211D VAL* 5.0 2.9 - - + -
238D GLN* 3.7 37.2 - - + +
241D ALA* 4.2 21.3 - - + -
242D LYS* 3.6 28.6 - - + +
245D LEU* 4.5 6.1 - - + -
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Residues in contact with ILE 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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57D PRO* 4.0 27.1 - - + +
58D ASP 3.0 19.9 + - - +
59D GLU* 3.8 6.7 - - - +
61D LEU* 1.3 76.8 - - + +
63D GLU* 1.3 66.6 + - + +
65D ILE* 3.0 10.0 + - + +
66D LEU* 2.8 48.7 + - + +
76D LYS* 3.7 34.8 - - + +
79D VAL* 4.3 22.4 - - + +
80D SER* 5.8 0.9 - - - -
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Residues in contact with GLU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LYS* 2.9 40.2 + - - +
59D GLU* 3.0 44.9 + - + +
60D GLU* 3.3 18.5 - - - +
62D ILE* 1.3 78.7 - - + +
64D LYS* 1.3 59.2 + - + +
66D LEU* 3.2 10.0 + - - +
67D SER* 2.8 28.3 + - - -
76D LYS* 6.4 1.6 - - + -
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Residues in contact with LYS 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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44D ARG* 3.7 5.1 - - - +
60D GLU* 2.9 47.7 + - + +
61D LEU* 3.6 3.4 - - - +
63D GLU* 1.3 76.3 - - + +
65D ILE* 1.3 60.5 + - - +
67D SER* 3.3 9.1 + - - -
68D TYR* 2.8 29.1 + - - +
242D LYS* 3.5 37.9 - - + +
245D LEU* 3.5 22.5 - - + +
246D ASP* 2.7 40.1 + - - +
248D ARG* 4.9 1.0 + - - -
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Residues in contact with ILE 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 LEU* 2.9 40.5 + - + +
62D ILE* 3.0 9.4 + - + +
64D LYS* 1.3 72.9 - - - +
66D LEU* 1.3 62.4 + - - +
68D TYR* 3.0 8.5 + - + +
69D LEU* 2.8 46.3 + - + +
79D VAL* 3.7 24.0 - - + -
80D SER 5.5 0.4 - - - +
81D VAL* 5.6 4.9 - - + -
200D PHE* 4.6 10.3 - - + -
211D VAL* 6.1 0.2 - - + -
213D TYR* 3.8 40.8 - - + -
245D LEU* 4.1 16.2 - - + -
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Residues in contact with LEU 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 ILE* 2.8 47.4 + - + +
63D GLU* 3.4 10.1 - - - +
65D ILE* 1.3 75.7 - - - +
67D SER* 1.3 64.6 - - - +
69D LEU* 2.9 8.8 + - - +
70D ASP* 2.8 19.9 + - - -
71D THR* 4.5 2.1 + - - -
74D LEU* 3.4 42.2 - - + +
75D SER* 3.8 13.5 - - - +
76D LYS* 3.8 16.4 - - + +
79D VAL* 3.8 16.8 - - + -
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Residues in contact with SER 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 GLU 2.8 14.1 + - - -
64D LYS* 3.3 14.8 - - - -
66D LEU* 1.3 77.7 - - - +
68D TYR* 1.3 63.0 + - - +
70D ASP* 3.1 19.3 + - - +
248D ARG* 4.8 8.2 + - - -
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Residues in contact with TYR 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 LYS 2.8 14.3 + - - +
65D ILE* 3.3 10.1 - - - +
67D SER* 1.3 78.8 + - - +
69D LEU* 1.3 66.7 + - + +
70D ASP* 3.2 5.4 + - - +
177D TYR* 4.2 9.9 - + - -
178D GLU* 2.8 36.5 + - - +
198D ARG* 4.4 5.2 - - - -
200D PHE* 5.8 0.4 - + - -
204D PHE* 3.8 19.2 - + - -
213D TYR* 3.4 29.2 - + - -
245D LEU* 4.0 15.7 - - + -
248D ARG* 3.3 53.7 + - - +
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Residues in contact with LEU 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 ILE* 2.8 42.1 + - + +
66D LEU* 3.3 10.8 - - - +
68D TYR* 1.3 77.9 - - + +
70D ASP* 1.3 68.0 + - - +
71D THR* 3.2 11.4 + - + +
74D LEU* 4.0 27.1 - - + -
79D VAL* 4.4 4.7 - - + -
185D VAL* 4.8 5.6 - - + -
198D ARG* 3.7 34.3 - - - +
213D TYR* 4.3 10.1 - - + +
215D VAL* 4.0 24.5 - - + -
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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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66D LEU 2.8 11.1 + - - -
67D SER* 3.1 15.5 + - - +
68D TYR 3.9 4.5 - - - +
69D LEU* 1.3 80.3 - - - +
71D THR* 1.3 63.5 + - - +
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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