Contacts of the helix formed by residues 70 - 81 (chain C) in PDB entry 1URP
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 ALA 70 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C PRO* 3.9 33.5 - - + +
46C GLU* 4.7 1.5 - - - +
66C THR* 5.0 1.3 - - - +
67C ASP* 2.8 27.2 + - + +
69C ASP* 1.3 73.1 - - - +
71C VAL* 1.3 59.8 + - - +
72C GLY 3.3 1.3 + - - -
73C ASN* 4.2 7.6 + - - +
74C ALA* 5.0 1.4 + - - +
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Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLU* 3.3 25.5 + - - +
63C ILE* 3.7 26.2 - - + -
65C PRO* 3.8 16.8 - - + -
67C ASP 3.2 12.4 + - - +
68C SER 3.3 19.3 - - - +
70C ALA* 1.3 75.3 - - - +
72C GLY* 1.3 64.4 + - - +
73C ASN 3.3 0.7 - - - -
74C ALA* 2.9 18.6 + - + -
75C VAL* 3.0 15.5 + - + +
92C ALA* 3.5 26.7 - - + -
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Residues in contact with GLY 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C SER 4.3 0.4 + - - -
69C ASP 3.6 9.7 + - - -
70C ALA 3.3 4.2 - - - -
71C VAL* 1.3 78.8 - - - +
73C ASN* 1.3 62.1 + - - +
75C VAL* 3.3 4.7 + - - +
76C LYS* 3.1 28.1 + - - +
94C LYS* 3.8 34.1 - - - +
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Residues in contact with ASN 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 4.0 15.6 - - + +
70C ALA 4.2 5.8 + - - +
71C VAL 3.1 1.2 + - - -
72C GLY* 1.3 70.7 - - - +
74C ALA* 1.3 65.4 + - - +
76C LYS* 3.2 25.6 + - - +
77C MET* 3.1 33.5 + - + +
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Residues in contact with ALA 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLU* 4.5 6.5 - - + +
47C LEU* 3.6 28.3 - - + +
50C VAL* 3.4 42.0 - - + +
61C LEU* 5.9 0.7 - - - -
63C ILE* 4.6 2.0 - - + -
70C ALA 5.0 0.8 + - - +
71C VAL* 2.9 24.1 + - + +
73C ASN* 1.3 76.5 - - - +
75C VAL* 1.3 62.1 + - - +
77C MET* 3.2 11.4 + - - +
78C ALA* 3.4 2.3 + - - +
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Residues in contact with VAL 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 5.6 1.3 - - - -
63C ILE* 4.9 6.5 - - + -
71C VAL* 3.0 21.6 + - + +
72C GLY 3.6 7.2 - - - +
74C ALA* 1.3 75.2 - - - +
76C LYS* 1.3 57.4 + - - +
78C ALA* 3.1 8.7 + - - +
79C ASN* 2.8 28.5 + - - +
85C VAL* 4.3 19.3 - - + -
92C ALA* 3.9 24.5 - - + -
94C LYS 4.1 3.4 - - - +
95C GLY* 3.6 24.0 - - - -
96C GLU 3.7 20.2 - - - +
97C VAL* 4.3 4.7 - - + -
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Residues in contact with LYS 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C GLY 3.1 17.4 + - - +
73C ASN* 3.2 27.2 + - - +
75C VAL* 1.3 72.6 - - - +
77C MET* 1.3 66.3 + - + +
79C ASN* 3.7 13.4 - - + +
80C GLN* 3.1 34.7 + - + +
94C LYS* 3.8 40.1 - - - +
95C GLY* 4.6 9.0 - - - +
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Residues in contact with MET 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C LEU* 4.3 15.3 - - + -
50C VAL* 4.5 8.5 - - + -
51C GLN* 3.5 37.0 - - + +
54C THR* 4.1 10.2 - - + +
73C ASN* 3.1 25.9 + - + +
74C ALA* 3.2 7.4 + - - +
76C LYS* 1.3 79.2 - - + +
78C ALA* 1.3 62.1 + - - +
80C GLN* 3.5 18.2 + - - +
81C ALA* 3.1 24.8 + - - +
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Residues in contact with ALA 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C VAL* 4.5 4.3 - - + -
54C THR* 4.3 10.5 - - + +
61C LEU* 4.1 16.6 - - + -
74C ALA 3.4 5.4 + - - +
75C VAL 3.1 8.0 + - - +
77C MET* 1.3 77.9 - - - +
79C ASN* 1.3 59.7 + - - +
81C ALA* 3.2 2.3 + - - -
82C ASN 2.9 9.0 + - - -
83C ILE* 2.9 39.8 + - + +
85C VAL* 3.5 23.6 - - + -
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Residues in contact with ASN 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C VAL* 2.8 24.6 + - - +
76C LYS* 3.7 11.5 - - + +
77C MET 3.4 0.2 - - - -
78C ALA* 1.3 74.2 - - - +
80C GLN* 1.3 60.3 + - + +
82C ASN* 3.3 17.1 + - - +
83C ILE 4.9 2.1 + - - -
85C VAL* 4.1 7.3 - - - +
95C GLY* 3.5 8.5 - - - -
96C GLU* 2.6 74.0 + - - +
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Residues in contact with GLN 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C LYS* 3.1 24.1 + - + +
77C MET* 3.6 18.5 - - - +
78C ALA 3.3 0.2 - - - -
79C ASN* 1.3 76.5 - - + +
81C ALA* 1.3 58.6 + - - +
82C ASN* 3.2 8.2 + - - -
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Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C THR* 4.1 14.4 - - + +
77C MET 3.1 16.8 + - - +
78C ALA 3.2 4.5 + - - +
80C GLN* 1.3 74.3 - - - +
82C ASN* 1.3 69.1 + - - +
83C ILE* 3.3 24.0 + - + +
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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