Contacts of the strand formed by residues 73 - 79 (chain A) in PDB entry 3H8E
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 VAL 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LEU* 3.2 21.3 - - + +
20A ILE* 4.1 12.3 - - + -
43A ILE* 4.4 9.6 - - + -
60A LEU 3.7 1.4 - - - +
61A LEU* 3.6 2.8 - - - -
62A LEU* 2.8 48.1 + - + +
63A GLN 4.6 1.3 + - - +
65A LEU* 4.1 10.8 - - + -
68A LEU* 3.6 30.5 - - + -
70A ALA* 4.5 5.2 - - + +
72A ARG* 1.3 78.1 - - - +
74A LEU* 1.3 61.6 + - - +
75A LEU* 3.8 25.5 + - + -
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Residues in contact with LEU 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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17A THR* 4.0 11.9 - - + +
18A LEU 2.8 10.9 + - - +
19A VAL* 3.3 22.7 - - + +
20A ILE* 3.0 26.9 + - - +
59A THR* 3.7 29.8 - - + -
60A LEU 3.7 11.7 - - - +
61A LEU* 4.0 21.7 - - + +
73A VAL* 1.3 72.1 - - - +
75A LEU* 1.3 63.9 + - - +
76A VAL* 5.1 0.2 - - + -
96A VAL* 4.2 20.9 - - + +
99A VAL* 4.0 32.8 - - + -
100A LEU* 4.6 5.4 - - + -
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Residues in contact with LEU 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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20A ILE* 3.4 35.9 - - + -
22A VAL* 3.9 9.2 - - + -
43A ILE* 3.9 18.4 - - + +
46A VAL* 5.4 1.3 - - + -
47A LEU* 3.9 31.2 - - + -
52A LEU* 3.6 16.3 - - + +
59A THR* 3.1 8.8 - - - +
60A LEU* 2.8 52.3 + - + +
62A LEU* 4.2 17.7 - - + -
73A VAL* 3.8 12.3 - - + -
74A LEU* 1.3 72.7 - - - +
76A VAL* 1.3 59.8 + - - +
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Residues in contact with VAL 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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19A VAL* 3.9 19.7 - - + -
20A ILE 2.9 18.6 + - - +
21A PRO* 3.2 9.8 - - + +
22A VAL* 2.8 30.7 + - - +
52A LEU* 4.9 0.2 - - - -
57A GLY* 3.9 11.4 - - - +
58A GLN 3.3 9.9 - - - +
59A THR* 4.2 7.9 - - + -
74A LEU* 5.1 0.9 - - + -
75A LEU* 1.3 74.8 - - - +
77A GLY* 1.3 68.5 + - - +
92A LEU* 3.8 23.1 - - + +
95A SER* 5.2 0.4 - - - -
96A VAL* 3.8 23.3 - - + -
112A LEU* 4.1 10.8 - - + -
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Residues in contact with GLY 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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22A VAL* 3.2 10.1 - - - -
52A LEU* 4.7 3.1 - - - +
54A GLY* 3.5 12.1 - - - -
55A LYS 3.3 19.1 - - - -
56A PRO* 3.3 0.9 - - - +
57A GLY 2.9 19.2 + - - -
58A GLN* 2.7 15.4 + - - -
75A LEU 4.3 0.2 - - - -
76A VAL* 1.3 72.6 - - - +
78A SER* 1.3 60.1 + - - -
79A GLY 3.6 1.3 - - - -
92A LEU* 3.4 10.3 - - - +
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Residues in contact with SER 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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21A PRO* 4.2 19.6 - - - +
22A VAL 2.9 16.9 + - - -
23A GLY* 3.5 11.4 + - - -
56A PRO* 4.2 6.3 - - - -
77A GLY* 1.3 73.1 - - - -
79A GLY* 1.3 61.5 + - - +
80A LYS 3.9 4.3 + - - +
82A GLU 5.1 0.3 - - - +
84A LEU* 3.4 22.7 - - - +
92A LEU* 4.0 13.5 - - - -
115A VAL* 4.4 13.7 - - - -
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Residues in contact with GLY 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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22A VAL 4.4 0.2 + - - -
23A GLY* 3.5 6.2 - - - -
24A GLU* 3.0 36.3 + - - -
54A GLY 2.8 17.1 + - - -
56A PRO* 3.6 17.6 - - - -
77A GLY 3.6 1.0 - - - -
78A SER* 1.3 75.7 + - - +
80A LYS* 1.3 67.3 + - - +
84A LEU* 5.3 0.2 - - - -
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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