Contacts of the strand formed by residues 68 - 73 (chain L) 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 ALA 68 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48L VAL* 4.5 4.7 - - + -
60L TYR* 3.2 20.3 - - + -
64L PHE* 3.1 22.5 + - + +
65L LYS 3.6 9.2 - - - +
66L ASP 4.5 1.2 - - - -
67L LYS* 1.3 81.2 - - + +
69L THR* 1.3 69.8 + - - +
70L LEU* 5.0 1.1 - - + -
81L MET* 3.7 31.9 - - + -
82L GLN 3.2 7.9 - - - +
83L VAL* 4.6 2.5 - - + +
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Residues in contact with THR 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60L TYR* 3.4 9.7 + - - +
66L ASP 5.9 0.2 - - - -
68L ALA* 1.3 83.0 + - - +
70L LEU* 1.3 63.8 + - - +
71L THR* 3.9 20.9 + - + +
80L TYR 3.6 2.6 - - - +
82L GLN* 2.9 46.7 + - + +
84L ASN* 4.0 11.4 + - - -
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Residues in contact with LEU 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L TRP* 4.1 16.4 - - + +
48L VAL* 4.7 8.7 - - + -
49L GLY* 3.7 26.0 - - - +
50L ASN* 3.4 29.2 - - - +
51L ILE* 3.8 22.7 - - + +
58L THR* 4.9 3.3 - - + +
59L ASN 4.7 1.1 - - - +
60L TYR* 2.8 30.0 + - + +
68L ALA* 5.0 0.4 - - + -
69L THR* 1.3 75.5 - - - +
71L THR* 1.3 74.9 + - - +
80L TYR 3.3 5.6 - - - +
81L MET* 3.9 30.3 - - + -
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Residues in contact with THR 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51L ILE* 3.7 9.0 - - - +
56L SER* 6.0 0.4 - - - -
69L THR* 3.9 20.0 + - + +
70L LEU* 1.3 88.0 - - - +
72L VAL* 1.3 71.3 + - - +
79L ALA* 3.5 2.6 - - - +
80L TYR* 2.8 44.2 + - - +
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Residues in contact with VAL 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L PHE* 4.0 13.0 - - + -
34L ILE* 6.3 0.4 - - + -
51L ILE* 3.6 27.6 - - + +
53L PRO* 4.1 17.5 - - + -
56L SER* 4.1 16.3 + - - +
71L THR* 1.3 85.7 - - - +
73L ASP* 1.3 64.2 + - - +
74L LYS* 3.8 25.9 + - + +
78L THR 3.5 12.6 - - - +
79L ALA* 4.1 10.1 - - + +
80L TYR* 4.5 4.3 - - - -
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Residues in contact with ASP 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L PHE* 4.6 0.2 - - - -
72L VAL* 1.3 75.1 - - - +
74L LYS* 1.3 64.6 + - - +
75L SER* 2.4 30.0 + - - -
76L SER* 2.7 25.2 + - - +
77L SER* 2.9 16.6 + - - -
78L THR 2.9 14.4 + - - +
80L TYR* 4.1 16.0 + - + -
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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