Contacts of the strand formed by residues 79 - 84 (chain A) in PDB entry 4F8Q
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 LYS 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A CYS 3.8 4.7 - - - +
24A HIS* 4.1 14.4 - - + -
71A LEU 4.4 1.4 - - - +
73A ASP 5.0 0.2 + - - -
74A GLY* 3.1 27.5 + - - +
75A ILE* 3.2 25.4 + - - +
77A ALA* 4.4 14.1 - - + +
78A GLY* 1.3 80.5 - - - +
80A ALA* 1.3 62.8 + - - +
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Residues in contact with ALA 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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22A PRO* 3.4 2.3 - - - +
23A CYS 2.8 32.0 + - - +
36A LEU* 4.0 9.2 - - + -
38A TRP* 3.9 16.1 - - + -
70A ILE* 5.1 0.4 - - + -
71A LEU 3.3 13.5 - - - +
75A ILE* 3.9 11.4 - - + -
78A GLY 4.0 0.2 + - - -
79A LYS* 1.3 75.8 - - - +
81A ALA* 1.3 64.0 + - - +
99A PHE* 3.9 19.3 - - + -
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Residues in contact with ALA 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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20A ASP* 4.7 6.1 - - + -
21A LEU 3.0 20.9 - - - +
22A PRO* 3.7 11.4 - - + -
38A TRP* 3.7 9.9 - - - -
70A ILE* 3.5 3.3 - - - -
71A LEU* 2.8 52.9 + - + +
80A ALA* 1.3 77.4 - - - +
82A LEU* 1.3 60.2 + - - +
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Residues in contact with LEU 82 (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 ALA 3.4 2.3 - - - +
20A ASP* 3.3 2.4 - - - -
21A LEU* 2.8 43.4 + - + +
38A TRP* 3.6 40.9 - - + +
47A VAL* 3.8 25.6 - - + -
48A ASN* 4.3 10.3 - - + -
68A THR* 3.5 27.1 - - - +
69A SER 3.6 12.6 - - - +
70A ILE* 4.4 5.2 - - + +
81A ALA* 1.3 74.1 - - - +
83A ARG* 1.3 59.3 + - - +
84A ILE* 3.9 24.9 - - + -
95A TYR* 4.8 4.0 - - + -
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Residues in contact with ARG 83 (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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18A ASP* 4.3 15.3 + - + +
19A ALA 3.3 4.0 - - - +
20A ASP* 2.8 38.2 + - - +
67A ARG 4.1 0.2 - - - +
68A THR* 3.1 8.3 - - - -
69A SER* 2.8 47.0 + - - +
71A LEU* 3.6 29.5 - - + +
81A ALA 3.9 1.2 + - - -
82A LEU* 1.3 73.2 - - - +
84A ILE* 1.3 69.4 + - - +
85A HIS* 3.4 31.2 - - + +
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Residues in contact with ILE 84 (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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18A ASP* 3.4 6.1 - - - +
19A ALA* 2.9 37.3 + - + +
21A LEU* 4.6 6.7 - - + -
64A TYR* 4.5 7.4 - - + -
67A ARG* 3.9 24.7 - - - +
68A THR* 4.4 9.0 - - + -
82A LEU* 3.9 26.0 - - + +
83A ARG* 1.3 76.6 - - - +
85A HIS* 1.3 72.7 + - - +
87A VAL* 4.1 12.8 - - + +
91A ASP* 3.9 11.2 - - + +
95A TYR* 3.9 27.4 - - + +
112A LEU* 4.3 15.5 - - + -
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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