Contacts of the helix formed by residues 72 - 81 (chain A) in PDB entry 5UHE
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 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A THR 3.6 13.2 - - - +
65A THR* 4.1 9.2 - - + +
66A VAL 5.8 0.4 - - - -
71A GLU* 1.3 73.7 - - - +
73A VAL* 1.3 63.1 + - - +
74A THR* 3.2 7.3 + - - -
75A GLU* 2.7 39.5 + - - +
76A ILE* 3.1 26.9 + - - +
655C ALA* 4.1 4.8 - - - +
674C LYS* 3.1 28.0 + - - +
675C PHE* 4.1 13.9 - - + -
685C ASN* 3.3 14.0 + - - -
687C CYS* 3.8 9.1 - - - -
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ILE* 4.1 20.2 - - + -
59A VAL* 4.1 14.1 - - + -
61A HIS 4.3 0.2 - - - +
62A GLU* 3.2 25.1 - - - +
64A THR* 3.0 38.0 + - + +
65A THR* 4.4 1.1 - - - +
66A VAL* 4.5 11.0 - - + -
72A ASP* 1.3 72.5 - - - +
74A THR* 1.3 56.3 + - - +
76A ILE* 3.2 7.9 + - + +
77A ILE* 2.9 47.7 + - + +
162A ILE* 4.3 7.9 - - + -
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Residues in contact with THR 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLU* 3.4 33.3 + - - +
63A PHE* 4.2 3.5 - - - -
72A ASP* 3.2 9.2 + - - +
73A VAL* 1.3 79.9 - - - +
75A GLU* 1.3 57.4 + - - +
77A ILE* 3.4 3.7 + - - +
78A LEU* 2.9 29.5 + - + +
619C VAL* 3.9 30.1 - - + +
675C PHE* 3.4 26.1 - - + -
685C ASN* 5.9 0.2 - - - -
750C ILE* 5.1 7.6 - - + -
876C LYS* 5.5 2.9 - - - +
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Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LYS 5.2 0.3 - - - +
71A GLU* 3.6 33.8 - - + +
72A ASP* 2.7 24.7 + - - +
74A THR* 1.3 74.8 - - - +
76A ILE* 1.3 58.2 + - - +
78A LEU* 3.6 13.3 - - + +
79A ASN* 2.8 43.3 + - - +
620C ARG* 5.8 2.6 + - - +
687C CYS* 4.5 18.9 - - - +
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Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ILE* 4.6 18.2 - - + -
66A VAL* 5.5 4.5 - - + -
69A VAL* 4.5 11.4 - - + -
71A GLU* 3.9 13.5 - - + +
72A ASP 3.1 19.4 + - - +
73A VAL* 3.2 13.0 + - + +
75A GLU* 1.3 74.9 - - - +
77A ILE* 1.3 60.1 + - + +
79A ASN* 3.2 9.4 + - - +
80A LEU* 3.0 39.2 + - + +
125A ILE* 4.3 16.4 - - + +
126A ALA* 4.3 22.0 - - + -
134A LEU* 4.4 20.9 - - + -
136A VAL* 6.1 3.4 - - + -
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Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ILE* 4.1 18.2 - - + -
62A GLU* 3.6 35.2 - - + +
73A VAL* 2.9 31.2 + - + +
74A THR* 3.7 4.3 - - - +
76A ILE* 1.3 76.7 - - + +
78A LEU* 1.3 60.8 + - - +
80A LEU* 3.2 19.2 + - + +
81A LYS* 3.2 23.1 + - - +
162A ILE* 3.6 23.3 - - + -
163A PRO 5.8 0.7 - - - +
164A VAL* 3.7 32.8 - - + +
876C LYS* 5.4 2.5 - - - +
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A THR* 2.9 18.7 + - + +
75A GLU* 3.6 13.9 - - + +
76A ILE 3.2 0.2 - - - -
77A ILE* 1.3 76.6 - - - +
79A ASN* 1.3 65.3 + - - +
81A LYS* 3.5 27.0 + - + +
82A SER* 4.5 2.8 + - - -
619C VAL* 3.7 30.3 - - + -
620C ARG* 3.2 55.6 - - + +
745C ASP* 5.6 10.1 - - + +
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Residues in contact with ASN 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLU* 4.4 4.6 + - - +
75A GLU* 2.8 42.8 + - - +
76A ILE* 3.5 6.2 - - - +
78A LEU* 1.3 83.6 - - - +
80A LEU* 1.3 59.7 + - - +
81A LYS 3.1 2.0 - - - -
82A SER* 2.4 28.5 + - - +
123A MET* 3.8 10.5 - - - +
124A HIS* 4.2 20.4 - - - +
125A ILE* 3.1 28.2 + - + +
620C ARG* 5.1 4.3 + - - -
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A VAL* 4.7 10.2 - - + +
54A ILE* 4.0 29.6 - - + -
76A ILE* 3.0 24.6 + - + +
77A ILE* 3.2 14.3 + - + +
79A ASN* 1.3 73.9 - - - +
81A LYS* 1.3 63.3 + - - +
82A SER 3.1 2.2 - - - -
83A LEU* 3.2 38.4 - - + +
110A ILE* 5.3 0.4 - - + -
123A MET* 4.8 1.1 - - + -
125A ILE* 4.2 26.2 - - + -
136A VAL* 5.4 3.4 - - + -
138A LEU* 3.7 35.2 - - + -
164A VAL* 5.9 4.9 - - + -
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Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ILE* 3.2 23.6 + - - +
78A LEU* 3.5 23.1 - - + +
79A ASN 3.1 0.6 - - - -
80A LEU* 1.3 79.3 - - - +
82A SER* 1.3 59.7 + - - +
83A LEU 3.2 6.2 + - - +
164A VAL* 3.7 22.9 - - + +
165A ASP* 3.1 45.0 + - + +
167A ILE* 4.9 22.4 - - + +
743C GLU 5.8 3.5 + - - +
745C ASP* 3.8 15.8 + - - -
876C LYS* 4.0 9.4 - - - +
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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