Contacts of the strand formed by residues 34 - 39 (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 ILE 34 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4L LEU* 4.7 10.8 - - + -
22L CYS* 5.1 5.4 - - - -
24L ALA* 5.7 0.7 - - + -
27L TYR* 3.5 22.7 - - - +
29L PHE* 4.6 10.3 - - + -
32L TYR 4.5 3.6 - - - +
33L TRP* 1.3 82.5 - - - +
35L ASN* 1.3 64.9 + - - +
36L TRP* 3.3 34.8 - - + +
50L ASN* 3.3 3.6 - - - -
51L ILE* 3.1 39.6 + - + +
53L PRO* 5.0 2.9 - - + -
72L VAL* 6.3 0.4 - - + -
79L ALA* 4.4 18.4 - - + -
96L CYS* 4.2 12.3 - - + -
97L THR 3.3 11.9 - - - +
98L ARG* 4.6 6.1 - - + -
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Residues in contact with ASN 35 (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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45J GLU* 5.1 1.2 + - - -
96K TYR* 3.3 18.0 - - - -
33L TRP* 3.9 19.6 - - - +
34L ILE* 1.3 76.8 - - - +
36L TRP* 1.3 62.6 + - - +
47L TRP* 2.7 25.3 + - - +
49L GLY 3.8 2.5 - - - -
50L ASN* 3.3 13.1 + - - +
97L THR* 2.8 56.1 + - - +
98L ARG* 5.8 1.4 - - - +
104L TRP* 4.2 18.1 - - - +
105L PHE* 3.6 16.7 - - + +
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Residues in contact with TRP 36 (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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6L GLN* 4.2 11.0 - - - -
20L LEU* 3.6 34.5 - - + -
21L SER 4.4 0.7 - - - -
22L CYS* 3.7 24.5 - - + -
34L ILE* 3.3 27.2 - - + +
35L ASN* 1.3 73.0 - - - +
37L VAL* 1.3 53.4 + - - +
47L TRP* 4.0 4.1 - - - -
48L VAL* 2.6 51.4 + - + +
49L GLY 3.0 13.7 + - - +
51L ILE* 4.5 4.8 - - + +
70L LEU* 4.1 20.2 - - + +
79L ALA* 3.7 25.0 - - + +
80L TYR 5.0 0.8 + - - -
81L MET* 3.5 42.8 - - + -
94L TYR* 4.7 6.5 - - + -
95L TYR 3.4 11.7 - - - -
96L CYS* 3.9 17.3 - - + -
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Residues in contact with VAL 37 (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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98K PHE* 4.3 9.4 - - + -
35L ASN 4.6 0.2 - - - +
36L TRP* 1.3 75.6 - - - +
38L LYS* 1.3 66.6 + - - +
45L LEU* 3.8 20.6 - - + -
46L GLU 3.2 30.1 - - - +
47L TRP* 4.5 3.8 - - - -
48L VAL* 4.0 1.3 - - - -
94L TYR* 3.7 2.9 - - - +
95L TYR* 2.9 39.7 + - + +
97L THR* 4.0 9.9 - - + -
105L PHE* 4.8 7.6 - - + -
108L TRP* 3.5 32.5 - - + -
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Residues in contact with LYS 38 (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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37L VAL* 1.3 73.6 - - - +
39L GLN* 1.3 67.3 + - - +
40L ARG* 4.1 17.0 - - - +
45L LEU 3.8 0.3 - - - -
46L GLU* 3.0 52.2 + - + +
48L VAL* 3.6 11.8 - - + +
64L PHE* 4.0 22.0 - - + -
89L GLU* 3.2 36.4 + - - -
90L ASP* 3.8 11.5 + - - -
92L ALA* 4.4 6.1 - - + -
93L VAL 3.5 4.9 - - - -
94L TYR* 3.3 47.2 + - + +
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Residues in contact with GLN 39 (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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38K GLN* 3.0 41.2 + - - -
85K ASP* 5.7 0.4 + - - -
87K HIS* 4.5 2.2 + - - -
38L LYS* 1.3 78.4 - - - +
40L ARG* 1.3 67.6 + - - +
41L PRO 4.1 0.2 - - - -
42L GLY 5.7 1.3 - - - +
43L GLN 3.0 29.1 + - - +
44L GLY 4.1 4.5 - - - +
45L LEU* 3.4 25.1 - - + +
92L ALA* 3.8 4.0 - - - -
93L VAL* 2.9 51.8 + - + +
95L TYR* 3.4 20.7 + - + -
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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