Contacts of the helix formed by residues 61 - 71 (chain A) in PDB entry 5ABT
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 GLN 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LEU* 3.0 34.5 + - - +
10A ASP* 3.5 10.4 - - - +
11A GLY 2.8 28.8 + - - -
50A ASP* 2.8 34.7 + - - +
52A THR* 3.7 9.6 + - + -
59A LYS 4.2 6.7 - - - +
60A ARG* 1.3 70.8 - - - +
62A ILE* 1.3 64.0 + - - +
63A PRO* 3.4 6.7 - - - -
64A LEU* 3.3 22.5 + - + +
65A ILE* 3.0 29.0 + - + +
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Residues in contact with ILE 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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60A ARG* 3.2 47.8 + - + +
61A GLN* 1.3 76.0 - - - +
63A PRO* 1.4 71.6 - - + +
65A ILE* 3.4 8.0 + - + +
66A LYS* 3.1 50.5 + - + +
90A ALA* 6.5 0.4 - - + -
91A LEU* 6.2 4.0 - - + -
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Residues in contact with PRO 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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60A ARG 4.8 2.5 - - - +
61A GLN* 3.6 4.9 - - - -
62A ILE* 1.4 96.3 - - + +
64A LEU* 1.3 61.7 + - - +
66A LYS* 3.3 11.9 + - + +
67A THR* 3.2 25.7 + - - -
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Residues in contact with LEU 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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8A LEU* 3.9 22.0 - - + -
11A GLY* 3.8 21.5 - - - +
31A PRO* 4.4 8.5 - - + -
61A GLN* 3.3 35.7 + - + +
63A PRO* 1.3 80.2 - - - +
65A ILE* 1.3 65.0 + - + +
67A THR* 3.1 11.8 + - + -
68A LEU* 3.1 48.9 + - + +
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Residues in contact with ILE 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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8A LEU* 5.3 8.5 - - + -
48A LEU* 5.0 7.9 - - + -
50A ASP* 3.8 28.5 - - + +
60A ARG* 5.2 7.2 - - - +
61A GLN* 3.0 23.9 + - + +
62A ILE* 3.7 7.4 - - - +
64A LEU* 1.3 76.4 - - + +
66A LYS* 1.3 63.4 + - + +
68A LEU* 3.3 8.3 + - - +
69A VAL* 3.0 28.9 + - + +
78A VAL* 4.0 44.4 - - + -
91A LEU* 4.2 19.1 - - + -
96A VAL* 4.7 1.6 - - + -
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Residues in contact with LYS 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 ILE* 3.1 40.1 + - + +
63A PRO* 3.6 11.2 - - + +
65A ILE* 1.3 78.2 - - + +
67A THR* 1.3 63.1 + - - +
69A VAL* 3.6 5.0 + - - +
70A ALA* 3.1 27.0 + - - +
90A ALA* 5.4 5.6 - - - -
91A LEU* 6.4 1.6 - - + -
94A ALA* 4.0 31.2 - - + +
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Residues in contact with THR 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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32A LEU* 4.4 18.8 - - + +
63A PRO 3.2 11.0 + - - -
64A LEU* 3.1 17.2 + - + -
66A LYS* 1.3 77.4 - - - +
68A LEU* 1.3 60.9 + - + +
70A ALA* 3.9 4.5 - - - +
71A GLY* 3.1 25.1 + - - -
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Residues in contact with LEU 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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8A LEU* 3.7 30.1 - - + -
31A PRO* 4.0 17.3 - - + -
32A LEU* 3.7 43.8 - - + +
35A LEU* 4.0 11.0 - - + +
48A LEU* 4.0 24.9 - - + -
64A LEU* 3.1 30.6 + - + +
65A ILE* 3.3 4.7 + - - +
67A THR* 1.3 77.7 - - + +
69A VAL* 1.3 64.3 + - - +
71A GLY* 3.2 10.2 + - - -
72A VAL* 3.6 18.4 + - - +
76A VAL* 5.5 0.4 - - - -
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Residues in contact with VAL 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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48A LEU* 4.7 2.2 - - + -
65A ILE* 3.0 27.1 + - + +
66A LYS* 4.0 4.7 - - - +
68A LEU* 1.3 76.2 - - - +
70A ALA* 1.3 61.3 + - - +
71A GLY 3.3 0.7 + - - -
72A VAL* 3.4 18.4 + - - +
74A VAL 5.3 0.7 - - - +
76A VAL* 4.1 34.8 - - + +
78A VAL* 4.2 1.1 - - + -
94A ALA 3.6 23.1 - - - +
95A GLY* 3.6 24.2 - - - +
96A VAL* 3.8 22.0 - - + +
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Residues in contact with ALA 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 LYS 3.1 19.3 + - - +
67A THR* 4.1 4.3 - - - +
69A VAL* 1.3 78.7 - - - +
71A GLY* 1.3 59.4 + - - +
72A VAL 3.3 5.1 + - - +
73A ASN* 5.1 3.6 + - - -
94A ALA 5.5 3.8 - - - +
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Residues in contact with GLY 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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32A LEU* 3.9 12.6 - - - -
36A GLN* 2.9 28.6 + - - +
67A THR 3.1 17.1 + - - -
68A LEU 3.2 3.1 + - - -
69A VAL 3.2 1.2 - - - -
70A ALA* 1.3 77.8 - - - +
72A VAL* 1.3 63.7 + - - +
73A ASN* 5.4 2.2 - - - +
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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