Contacts of the helix formed by residues 70 - 81 (chain A) in PDB entry 1ABF
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 LEU 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A GLY* 3.5 34.8 - - - +
46A THR* 4.5 6.1 - - - +
47A LEU* 4.5 22.7 - - + -
65A THR* 3.8 9.0 - - - +
66A PRO* 4.1 7.6 - - + -
67A ASP* 3.2 39.2 + - + +
69A LYS* 1.4 75.0 - - - +
71A GLY* 1.3 64.0 + - - +
72A SER 3.3 1.1 - - - -
73A ALA* 3.0 12.0 + - + +
74A ILE* 3.0 32.8 + - + +
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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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67A ASP 4.5 0.2 + - - -
68A PRO 3.1 9.2 + - - -
69A LYS 3.1 4.9 - - - -
70A LEU* 1.3 75.7 - - - +
72A SER* 1.4 63.3 + - - +
74A ILE* 3.2 5.4 + - - +
75A VAL* 3.0 26.2 + - - +
92A PHE* 3.7 34.0 - - - -
93A VAL 4.5 0.2 - - - -
100A MET* 4.0 8.7 - - - -
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Residues in contact with SER 72 (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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69A LYS 4.2 8.3 + - - -
70A LEU 3.3 0.8 - - - -
71A GLY* 1.4 74.1 - - - +
73A ALA* 1.4 65.0 + - - +
75A VAL* 3.4 4.0 + - - +
76A ALA* 3.0 24.1 + - - +
93A VAL 4.7 2.8 + - - -
94A ASN* 4.9 6.9 - - - +
95A ALA 5.2 2.3 + - - -
100A MET* 3.8 19.3 - - - -
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Residues in contact with ALA 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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47A LEU* 4.2 24.5 - - + -
69A LYS 5.3 0.2 + - - -
70A LEU* 3.0 17.4 + - + +
72A SER* 1.4 79.9 - - - +
74A ILE* 1.4 55.0 + - - +
76A ALA* 3.4 7.2 + - - +
77A LYS* 2.8 37.6 + - - +
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Residues in contact with ILE 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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46A THR* 3.9 24.9 - - + -
47A LEU* 4.4 5.2 - - + -
50A ILE* 4.0 13.7 - - + +
61A PHE* 3.8 31.4 - - + -
63A ILE* 4.1 7.0 - - + -
65A THR* 3.7 23.3 - - - +
70A LEU* 3.0 29.8 + - + +
71A GLY 3.7 3.1 - - - +
73A ALA* 1.4 75.4 - - - +
75A VAL* 1.3 59.7 - - - +
77A LYS* 3.5 1.7 + - - +
78A ALA* 2.9 27.5 + - - +
85A VAL* 4.5 4.0 - - + -
92A PHE* 4.0 30.3 - - + -
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Residues in contact with VAL 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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71A GLY 3.0 19.7 + - - +
72A SER* 3.8 5.8 - - - +
74A ILE* 1.3 74.6 - - - +
76A ALA* 1.3 52.8 + - - +
78A ALA* 3.2 6.0 + - - +
79A ARG* 2.7 76.1 + - - +
85A VAL* 5.6 4.9 - - + -
92A PHE* 4.2 8.7 - - + -
100A MET* 3.8 11.9 - - + -
103A VAL* 3.7 30.7 - - + -
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Residues in contact with ALA 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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72A SER 3.0 13.6 + - - +
73A ALA* 3.4 12.3 - - - +
75A VAL* 1.3 74.8 - - - +
77A LYS* 1.3 63.1 + - - +
79A ARG* 3.3 12.1 + - - +
80A GLY* 3.2 17.8 + - - -
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Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A LEU* 3.2 48.0 - - + +
50A ILE* 3.7 22.2 - - + -
51A ASP* 2.6 34.3 + - - +
73A ALA 2.8 21.1 + - - +
74A ILE 3.8 2.5 - - - +
76A ALA* 1.3 71.9 - - - +
78A ALA* 1.4 64.1 + - - +
80A GLY* 3.2 3.9 + - - -
81A TYR* 3.1 34.8 + - + -
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Residues in contact with ALA 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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50A ILE* 4.6 2.4 - - - +
61A PHE* 4.1 10.1 - - + -
74A ILE 2.9 16.3 + - - +
75A VAL* 3.7 4.7 - - - +
77A LYS* 1.4 76.4 - - - +
79A ARG* 1.3 63.5 + - - +
81A TYR 3.0 10.0 + - - -
83A MET* 3.1 40.3 + - + +
85A VAL* 3.5 32.8 - - + -
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Residues in contact with ARG 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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75A VAL* 2.7 59.0 + - + +
76A ALA* 3.8 10.0 - - - +
78A ALA* 1.3 72.5 - - - +
80A GLY* 1.3 56.1 + - - +
82A ASP* 3.1 25.9 + - - +
83A MET 4.9 3.1 - - - -
102A THR* 5.8 1.8 + - - -
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Residues in contact with GLY 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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76A ALA 3.2 7.3 + - - -
77A LYS* 3.2 8.7 + - - -
78A ALA 3.1 1.0 - - - -
79A ARG* 1.3 77.9 - - - +
81A TYR* 1.4 67.4 + - - +
82A ASP* 3.7 3.6 + - - +
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Residues in contact with TYR 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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50A ILE* 3.8 23.6 - - + -
51A ASP* 2.4 38.4 + - - +
54A ALA* 3.5 29.6 - - + -
59A LYS* 4.9 2.1 + - - -
77A LYS* 3.1 28.7 + - + -
78A ALA 3.0 7.4 + - - +
80A GLY* 1.4 85.5 - - - +
82A ASP* 1.3 70.1 + - - +
83A MET* 3.3 20.2 + - + +
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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