Contacts of the helix formed by residues 60 - 71 (chain A) in PDB entry 3UJG
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 GLU 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ASP* 1.3 78.1 - - - +
61A ASN* 1.3 68.2 + - - +
62A VAL 3.3 0.9 - - - -
63A LYS* 3.1 42.7 + - - +
64A ARG* 3.1 41.1 + - + +
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Residues in contact with ASN 61 (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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59A ASP* 3.4 15.1 - - + +
60A GLU* 1.3 82.6 - - - +
62A VAL* 1.3 61.2 + - - +
64A ARG* 4.3 3.7 - - - +
65A GLU* 3.2 29.2 + - - +
166A SER* 5.1 11.9 - - - +
168A VAL* 5.1 9.9 - - + -
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Residues in contact with VAL 62 (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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52A ILE* 3.9 17.0 - - + -
57A LYS 4.4 6.7 - - - +
58A ILE* 3.5 20.2 - - + -
59A ASP* 3.3 30.4 - - - +
61A ASN* 1.3 77.3 - - - +
63A LYS* 1.3 68.7 + - - +
65A GLU* 4.1 2.2 - - - +
66A ILE* 3.3 37.8 + - + +
90A LEU* 5.0 7.9 - - + -
92A ILE* 5.9 0.4 - - + -
161A PHE* 5.4 2.7 - - + -
168A VAL* 3.7 30.9 - - + +
312A ILE* 4.0 4.5 - - + -
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Residues in contact with LYS 63 (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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59A ASP 4.2 5.2 - - - +
60A GLU* 3.1 44.0 + - - +
61A ASN 3.3 0.4 - - - -
62A VAL* 1.3 80.1 - - - +
64A ARG* 1.3 95.3 + - - +
66A ILE* 3.3 5.4 + - - +
67A ILE* 3.1 33.4 + - + +
308A ILE* 6.3 0.9 - - + -
309A MET* 3.6 40.2 - - + +
312A ILE* 3.3 31.2 - - + -
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Residues in contact with ARG 64 (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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60A GLU* 3.1 28.4 + - + +
61A ASN* 4.3 4.0 - - - +
63A LYS* 1.3 109.6 - - - +
65A GLU* 1.3 54.0 + - - +
67A ILE* 3.4 12.2 + - - +
68A ASN* 2.8 50.6 + - - +
309A MET* 5.6 1.8 - - - -
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Residues in contact with GLU 65 (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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61A ASN 3.2 18.2 + - - +
62A VAL 4.1 3.8 - - - +
64A ARG* 1.3 80.4 - - - +
66A ILE* 1.3 59.9 + - - +
68A ASN* 3.7 7.0 - - + +
69A HIS* 3.2 22.9 + - - +
161A PHE* 3.6 32.6 - - + +
164A SER* 3.2 23.7 + - - +
166A SER* 4.0 4.1 - - - +
167A SER* 2.8 25.4 + - - -
168A VAL* 3.1 30.1 + - - +
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Residues in contact with ILE 66 (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 VAL* 3.3 24.6 + - + +
63A LYS* 3.8 4.9 - - - +
64A ARG 3.3 0.4 - - - -
65A GLU* 1.3 75.6 - - - +
67A ILE* 1.3 63.2 + - + +
69A HIS* 3.1 4.3 + - - +
70A ARG* 2.8 27.0 + - - +
80A PHE* 4.0 31.2 - - + -
83A VAL* 4.4 9.9 - - + -
90A LEU* 4.4 10.5 - - + -
92A ILE* 3.3 29.2 - - + -
161A PHE* 3.8 24.0 - - + -
308A ILE* 4.2 22.0 - - + -
312A ILE* 5.8 3.8 - - + -
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Residues in contact with ILE 67 (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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63A LYS* 3.1 27.1 + - + +
64A ARG* 4.0 13.9 - - - +
66A ILE* 1.3 75.7 - - + +
68A ASN* 1.3 66.1 + - - +
70A ARG* 3.4 12.3 - - + +
71A SER* 3.3 18.5 + - - -
305A ILE* 3.2 37.0 - - + -
308A ILE* 3.7 35.2 - - + -
309A MET* 5.1 3.8 - - - -
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Residues in contact with ASN 68 (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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64A ARG* 2.8 34.6 + - - +
65A GLU* 3.7 8.1 - - - +
67A ILE* 1.3 74.6 - - - +
69A HIS* 1.3 58.5 + - - +
71A SER* 2.7 34.5 + - - -
72A LEU* 3.7 7.5 + - - +
135A GLN* 5.7 3.5 + - - -
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Residues in contact with HIS 69 (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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65A GLU 3.2 13.3 + - - +
66A ILE 3.1 4.9 + - - +
68A ASN* 1.3 78.5 - - - +
70A ARG* 1.3 61.4 + - - +
72A LEU* 3.1 32.0 + - + +
77A ILE* 4.5 2.8 - - - +
78A VAL 2.8 24.0 + - - -
79A ARG* 4.6 0.9 - - - -
80A PHE* 4.0 14.1 + - + +
94A MET* 3.5 17.8 - - + +
159A CYS* 3.2 32.3 + - - -
160A ASP 3.4 4.6 + - - -
161A PHE* 3.4 40.4 + + + -
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Residues in contact with ARG 70 (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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66A ILE 2.8 17.1 + - - +
67A ILE* 3.4 16.9 - - - +
69A HIS* 1.3 78.0 - - - +
71A SER* 1.3 57.9 + - - +
72A LEU 3.2 2.6 + - - +
73A ARG* 4.0 21.4 + - - +
80A PHE* 3.5 40.1 - - + +
303A GLN 2.5 33.8 + - - -
304A SER* 3.5 9.4 - - - +
305A ILE* 3.8 25.1 - - - +
308A ILE* 3.9 13.3 - - + +
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Residues in contact with SER 71 (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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67A ILE 3.3 9.1 + - - -
68A ASN* 2.7 21.3 + - - -
70A ARG* 1.3 77.4 - - - +
72A LEU* 1.3 62.8 + - - +
73A ARG* 3.5 6.4 + - - +
130A TYR* 3.4 5.5 + - - -
134A MET* 3.3 28.7 - - - +
294A GLN* 3.6 8.7 + - - +
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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