Contacts of the strand formed by residues 78 - 83 (chain I) in PDB entry 1FSK
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 THR 78 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I SER* 4.7 1.9 - - - -
22I CYS 3.2 19.2 + - - -
23I LYS* 3.6 19.9 - - + +
29I PHE* 3.6 9.4 - - - -
72I VAL* 3.5 1.0 - - - -
73I ASP* 2.9 27.6 + - - -
76I SER* 2.6 47.3 - - - +
77I SER* 1.3 73.3 - - - +
79I ALA* 1.3 62.0 + - - +
80I TYR* 3.4 27.3 - - - +
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Residues in contact with ALA 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I SER* 3.6 1.4 - - - -
22I CYS* 2.8 39.5 + - + +
29I PHE* 4.0 8.6 - - + -
34I ILE* 4.4 21.5 - - + -
36I TRP* 3.7 15.6 - - + +
51I ILE* 5.1 1.6 - - + -
71I THR 3.5 11.0 - - - +
72I VAL* 4.1 11.4 - - + +
78I THR* 1.3 72.5 + - - +
80I TYR* 1.3 65.1 + - - +
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Residues in contact with TYR 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I ILE* 3.7 28.5 - - + -
20I LEU 3.0 5.4 - - - +
21I SER* 3.7 23.6 - - - -
36I TRP* 4.0 4.2 + - - -
69I THR 3.6 2.0 - - - +
70I LEU* 3.3 4.2 - - - +
71I THR* 2.8 52.4 + - - +
72I VAL* 4.5 3.4 - - - -
73I ASP* 4.1 17.4 + - + +
76I SER* 4.3 4.3 + - - -
78I THR* 3.4 36.6 + - - +
79I ALA* 1.3 76.3 - - - +
81I MET* 1.3 60.6 + - - +
82I GLN* 5.9 1.8 - - + -
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Residues in contact with MET 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I ILE* 3.8 0.6 - - - -
20I LEU* 2.8 44.2 + - + +
36I TRP* 3.5 45.4 - - + -
48I VAL* 3.4 34.5 - - + -
64I PHE* 5.0 4.9 - - + -
68I ALA* 3.7 17.7 - - + -
69I THR 3.9 2.9 - - - -
70I LEU* 3.9 11.4 - - + -
80I TYR* 1.3 73.8 - - - +
82I GLN* 1.3 64.2 + - - +
83I VAL* 4.2 10.1 - - + -
94I TYR* 4.0 33.0 - - + -
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Residues in contact with GLN 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I SER* 3.1 17.1 + - - -
18I VAL 3.4 2.2 - - - +
19I ILE* 3.3 31.9 - - + +
67I LYS 3.7 1.0 - - - +
68I ALA* 3.2 6.8 - - - +
69I THR* 2.9 50.3 + - + +
71I THR* 6.1 0.2 - - - +
80I TYR* 5.5 2.0 - - + -
81I MET* 1.3 74.6 - - - +
83I VAL* 1.3 65.2 + - - +
84I ASN* 2.4 37.9 + - - +
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Residues in contact with VAL 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I ALA 4.3 0.9 - - - +
17I SER* 3.7 2.6 + - - -
18I VAL* 2.9 49.5 + - + +
20I LEU* 4.8 8.3 - - + -
67I LYS* 3.8 23.3 - - + +
68I ALA* 4.6 1.3 - - + +
81I MET* 4.2 24.0 - - + -
82I GLN* 1.3 82.4 - - - +
84I ASN* 1.3 74.4 + - - +
85I SER 4.2 0.2 + - - -
86I PRO* 4.5 6.1 - - + -
90I ASP* 4.1 15.7 - - + +
94I TYR* 5.0 11.2 - - + +
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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