Contacts of the strand formed by residues 73 - 77 (chain L) in PDB entry 3FKS
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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L ALA 3.1 7.3 - - - +
42L ARG* 3.5 3.0 - - - -
43L VAL* 2.9 40.0 + - + +
45L GLY 3.7 11.9 - - - +
46L LEU* 4.7 6.5 - - + +
49L ILE* 4.7 7.0 - - + -
65L ALA* 4.1 6.3 - - + -
67L ASN 3.5 12.3 - - - +
68L LEU* 3.8 14.1 - - + -
71L GLY 5.4 0.4 - - - +
72L GLN* 1.3 76.1 - - - +
74L GLY* 1.3 61.7 + - - +
75L ILE* 3.5 23.1 + - + +
72M ARG* 3.2 38.6 - - - +
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Residues in contact with GLY 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L ILE* 5.6 0.9 - - - -
41L ALA 4.0 2.7 - - - -
42L ARG* 5.2 5.2 - - - -
65L ALA* 3.4 4.2 - - - +
66L LEU* 3.0 25.5 + - - +
67L ASN* 2.8 33.1 + - - +
69L GLU* 5.3 3.6 + - - +
72L GLN* 4.3 1.6 - - - +
73L VAL* 1.3 69.0 - - - +
75L ILE* 1.3 59.2 + - - -
287L LEU* 4.5 13.7 - - - -
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Residues in contact with ILE 75 (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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40L ILE* 3.6 3.2 - - - +
41L ALA* 2.9 46.3 + - + +
43L VAL* 4.2 15.5 - - + -
46L LEU* 4.1 23.8 - - + -
55L VAL* 3.6 30.1 - - + -
57L PHE* 4.3 10.3 - - + -
63L GLY* 3.9 3.6 - - - -
64L MET 3.2 29.4 - - - +
65L ALA* 3.7 12.8 - - + -
73L VAL* 3.9 12.3 - - + +
74L GLY* 1.3 79.3 - - - +
76L VAL* 1.3 67.6 + - - +
90L VAL* 4.7 2.5 - - + -
287L LEU* 4.7 1.4 - - - +
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Residues in contact with VAL 76 (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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39L GLY 3.4 4.9 - - - +
40L ILE* 3.5 24.5 - - + -
63L GLY* 3.4 2.1 - - - -
64L MET* 2.9 52.1 + - + +
66L LEU* 3.9 19.3 - - + +
75L ILE* 1.3 75.0 - - - +
77L LEU* 1.3 62.7 + - - +
78L PHE* 4.4 0.7 - - - -
243L PRO* 3.8 26.2 - - + -
283L LEU* 4.3 13.0 - - + -
287L LEU* 4.0 23.3 - - + -
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Residues in contact with LEU 77 (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 VAL* 4.4 9.9 - - + -
39L GLY* 2.8 29.2 + - - +
40L ILE 4.5 3.6 - - - +
41L ALA* 4.9 2.2 - - + -
57L PHE* 3.5 44.6 - - + -
61L VAL* 4.3 8.5 - - + -
62L LYS 4.2 1.1 - - - +
76L VAL* 1.3 75.0 - - - +
78L PHE* 1.3 61.8 + - - +
79L GLY 3.4 11.2 - - - +
80L SER 3.5 22.0 - - - +
81L ASP* 3.9 22.2 - - - +
84L VAL* 4.1 13.0 - - + -
241L ALA* 3.8 3.3 - - - +
243L PRO* 3.2 25.6 - - - +
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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