Contacts of the strand formed by residues 103 - 108 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A GLY 2.9 20.2 + - - -
47A ASN* 3.9 7.4 - - + +
34B PHE* 4.7 9.6 - - + -
46B LEU* 3.8 10.4 - - + +
49B TYR* 2.9 48.8 - - + +
50B GLY 4.0 2.7 - - - +
55B TYR* 5.1 3.1 - - - -
99C GLY* 3.5 1.0 - - - -
100C ALA* 2.7 36.5 + - - +
101C ARG 4.3 3.1 + - - -
102C ASP* 1.3 78.2 - - - +
104C TRP* 1.3 75.9 + - - +
106C ALA* 4.6 3.3 - - - +
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Residues in contact with TRP 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLU* 3.3 39.5 - - + -
46A GLY* 3.3 18.8 - - - -
47A ASN* 3.1 25.5 - - - +
50A PRO 3.6 3.3 + - - -
51A GLY* 3.5 24.5 - - - -
52A THR* 3.5 18.8 - - - -
34B PHE* 4.7 8.1 - + + -
46B LEU* 3.9 8.0 - - - +
91B SER* 3.4 30.1 + - - -
96B TYR* 3.6 20.9 - + + -
33C TRP* 3.9 16.6 - + + -
35C ASN* 4.2 14.1 - - - +
50C ASN* 6.2 0.2 - - - -
99C GLY* 3.7 3.4 - - - -
103C THR* 1.3 87.6 - - - +
105C PHE* 1.3 94.9 + + + +
106C ALA 3.2 4.0 + - - -
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Residues in contact with PHE 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B PHE* 3.6 26.5 - + - -
36B PHE* 3.3 32.5 - + + -
46B LEU* 3.4 14.6 - - - +
96B TYR* 4.5 11.9 - + + -
98B PHE* 4.0 22.4 - + - -
35C ASN* 3.6 19.7 - - + +
37C VAL* 4.8 8.3 - - + -
47C TRP* 4.1 18.4 - + - -
97C THR* 3.1 36.3 + - + -
98C ARG 3.9 5.3 + - - -
99C GLY* 3.6 7.7 - - - +
104C TRP* 1.3 83.3 - + + +
106C ALA* 1.3 59.9 + - - +
107C TYR 3.3 0.9 - - - -
108C TRP* 3.0 26.3 + + - +
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Residues in contact with ALA 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU* 3.7 17.1 + - + +
55B TYR* 3.4 36.5 + - + +
98C ARG 3.1 2.4 + - - -
99C GLY 3.8 4.3 - - - -
100C ALA* 3.8 20.0 - - + +
103C THR* 4.6 2.2 - - - +
104C TRP 3.2 1.6 + - - -
105C PHE* 1.3 80.2 - - - +
107C TYR* 1.3 76.2 + - + +
108C TRP* 4.3 4.1 - - - -
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Residues in contact with TYR 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B TYR* 4.0 10.8 + - - -
2C VAL* 3.2 56.8 - - + +
4C LEU* 4.3 8.1 - - + -
97C THR* 3.3 9.4 - - - -
98C ARG* 2.8 56.4 + - + +
99C GLY 3.8 9.0 - - - -
100C ALA* 4.1 5.8 - - + -
106C ALA* 1.3 99.0 - - + +
108C TRP* 1.3 64.5 + - - +
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Residues in contact with TRP 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PHE* 3.7 23.2 - + - -
43B SER* 4.1 11.8 + - - +
44B PRO* 3.6 59.4 + - + +
45B LYS* 5.1 2.5 - - - -
46B LEU 4.7 1.8 - - - +
98B PHE* 5.7 1.6 - + - -
4C LEU* 4.3 8.4 + - - +
37C VAL* 3.5 31.0 - - + -
45C LEU* 4.6 9.6 - - + -
95C TYR* 3.6 28.9 - + + -
96C CYS 3.9 2.2 - - - -
97C THR* 3.7 8.1 - - + -
105C PHE* 3.0 35.3 + + + -
106C ALA 4.3 2.9 - - - -
107C TYR* 1.3 83.8 - - - +
109C GLY* 1.3 69.8 + - - +
110C 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