Contacts of the strand formed by residues 103 - 108 (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 THR 103 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46J GLY* 2.6 36.6 + - - -
47J ASN* 3.6 9.0 - - + +
34K PHE* 4.7 9.9 - - + -
46K LEU* 3.9 10.6 - - + +
49K TYR* 3.0 46.7 - - + +
50K GLY 4.1 3.1 - - - +
55K TYR* 5.2 3.1 - - - -
99L GLY* 3.5 0.5 - - - -
100L ALA* 2.7 31.1 + - - +
101L ARG 4.3 3.3 + - - -
102L ASP* 1.3 79.0 - - - +
104L TRP* 1.3 70.2 + - - +
106L ALA* 4.6 2.9 - - - +
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Residues in contact with TRP 104 (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* 3.5 32.8 - - + -
46J GLY* 3.5 17.0 - - - -
47J ASN* 3.0 24.7 - - - +
50J PRO 3.3 20.8 + - - -
51J GLY* 3.3 26.9 - - - -
52J THR* 3.4 13.2 - - - -
34K PHE* 4.8 8.3 - + + -
46K LEU* 4.0 7.8 - - - +
91K SER* 3.4 31.8 + - - -
96K TYR* 3.4 15.9 + + + -
33L TRP* 3.9 16.2 - + + -
35L ASN* 4.2 14.4 - - - +
50L ASN* 6.2 0.2 - - - -
99L GLY* 3.7 3.4 - - - -
103L THR* 1.3 86.5 - - - +
105L PHE* 1.3 94.7 + + + +
106L ALA 3.2 4.0 + - - -
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Residues in contact with PHE 105 (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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34K PHE* 3.6 27.1 - + - -
36K PHE* 3.4 33.1 - + + -
46K LEU* 3.5 14.1 - - - +
96K TYR* 4.4 12.3 - + + -
98K PHE* 3.9 25.4 - + - -
35L ASN* 3.6 19.2 - - + +
37L VAL* 4.8 6.1 - - + -
47L TRP* 4.1 18.2 - + - -
97L THR* 3.1 36.3 + - + -
98L ARG 3.9 5.1 + - - -
99L GLY* 3.6 8.3 - - - +
104L TRP* 1.3 84.7 - + + +
106L ALA* 1.3 61.5 + - - +
107L TYR 3.3 1.6 - - - +
108L TRP* 3.0 25.4 + + - +
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Residues in contact with ALA 106 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46K LEU* 3.8 17.8 + - + +
55K TYR* 3.6 36.0 + - + +
98L ARG 3.1 2.6 + - - -
99L GLY* 3.8 4.7 - - - -
100L ALA* 3.8 20.2 - - + +
103L THR* 4.6 2.7 - - - +
104L TRP 3.2 1.2 + - - -
105L PHE* 1.3 80.2 - - - +
107L TYR* 1.3 77.0 + - + +
108L TRP* 4.3 3.8 - - - -
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Residues in contact with TYR 107 (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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55K TYR* 4.2 10.4 + - - -
2L VAL* 3.2 56.7 - - + +
3L GLN* 6.3 0.2 - - - -
4L LEU* 4.3 9.0 - - + -
97L THR* 3.3 9.7 - - - -
98L ARG* 2.8 56.0 + - + +
99L GLY 3.8 9.6 - - - -
100L ALA* 4.1 5.8 - - + -
106L ALA* 1.3 98.6 - - + +
108L TRP* 1.3 65.9 + - - +
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Residues in contact with TRP 108 (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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36K PHE* 3.7 29.9 - + - -
43K SER* 4.1 12.4 + - - +
44K PRO* 3.6 55.8 + - + +
45K LYS* 5.1 2.0 - - - -
46K LEU 4.7 2.0 - - - +
98K PHE* 5.6 1.6 - + - -
4L LEU* 4.3 8.8 + - - +
37L VAL* 3.5 30.5 - - + -
45L LEU* 4.6 10.5 - - + -
95L TYR* 3.6 29.6 - + + -
96L CYS 3.9 2.0 - - - -
97L THR* 3.7 7.0 - - + -
105L PHE* 3.0 32.8 + + + -
106L ALA 4.3 3.1 - - - -
107L TYR* 1.3 83.8 - - - +
109L GLY* 1.3 69.5 + - - +
110L GLN 3.9 0.2 + - - -
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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