Contacts of the strand formed by residues 40 - 46 (chain C) in PDB entry 4FQX
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 ASP 40 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C ALA* 3.2 3.2 - - - -
37C TYR 2.8 30.9 + - - +
38C ASP* 3.5 6.8 - - - +
39C GLU* 1.3 80.6 - - - +
41C GLN* 1.3 63.3 + - - +
42C LEU 3.4 0.2 + - - -
123D TYR* 4.1 6.6 + - - -
150D PRO* 5.2 3.0 - - - +
152D GLY* 4.9 9.7 + - - -
154D TRP* 3.3 58.7 + - + +
155D THR 5.4 0.3 - - - +
156D TYR* 2.6 35.7 + - - -
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Residues in contact with GLN 41 (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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34C SER* 2.6 27.5 + - - +
35C GLU 3.7 11.7 - - - +
36C ALA* 4.3 3.6 - - + +
40C ASP* 1.3 71.5 - - - +
42C LEU* 1.3 62.6 + - - +
43C PHE 3.9 8.5 - - - +
44C PHE* 3.5 36.9 - - - +
55C ARG* 3.0 35.2 - - + +
149C PHE* 4.3 9.2 - - - +
150C VAL 3.1 22.6 + - - +
151C SER* 3.4 18.6 + - - +
154D TRP* 2.9 24.5 + - - +
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Residues in contact with LEU 42 (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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18C PHE* 3.9 27.8 - - + -
35C GLU* 2.8 12.6 + - + +
37C TYR* 4.0 12.6 - - + +
40C ASP 3.4 1.4 + - - -
41C GLN* 1.3 72.8 - - - +
43C PHE* 1.3 95.9 + - + +
54C PRO* 3.5 0.7 - - - +
55C ARG* 3.0 24.9 + - - +
59C PHE* 4.1 27.6 - - + -
62C TRP* 6.4 0.2 - - + -
86D PHE* 4.6 9.2 - - + -
90D LEU* 3.9 31.9 - - + -
154D TRP* 4.0 20.0 - - + -
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Residues in contact with PHE 43 (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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18C PHE* 6.2 0.2 - + - -
33C LEU 4.2 0.3 - - - +
34C SER* 3.8 1.2 - - - -
35C GLU* 3.0 51.7 + - + +
41C GLN* 3.9 6.1 - - - +
42C LEU* 1.3 114.2 - - + +
44C PHE* 1.3 60.6 + - - +
45C PHE 4.1 0.4 - - - -
52C ARG* 3.6 31.9 - - + -
53C VAL 3.1 20.6 - - - +
54C PRO* 3.5 10.3 - - + -
55C ARG 4.8 0.9 - - - +
59C PHE* 3.4 31.4 - - + -
62C TRP* 4.0 23.6 - + + -
63C ALA* 4.4 9.6 - - - -
82D HIS* 6.1 0.4 - + - -
86D PHE* 4.5 19.3 - + - -
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Residues in contact with PHE 44 (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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33C LEU 3.6 7.4 - - - +
34C SER* 5.2 0.7 - - - -
41C GLN* 3.5 31.6 - - - +
43C PHE* 1.3 73.4 - - - +
45C PHE* 1.3 69.6 + - - +
46C ASP* 6.0 1.8 - - + -
53C VAL* 3.2 55.9 + - + +
54C PRO 4.1 11.4 - - - -
55C ARG* 5.0 2.5 - - - -
149C PHE* 4.3 26.2 - + + -
150C VAL 5.0 3.4 - - - +
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Residues in contact with PHE 45 (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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32C GLY* 5.4 1.2 - - - -
33C LEU* 3.1 36.1 + - + +
43C PHE* 4.1 1.6 + - - +
44C PHE* 1.3 79.2 - - - +
46C ASP* 1.3 69.7 + - - +
47C PHE* 3.5 50.1 + + + -
50C ASN* 3.3 53.6 - - - -
51C THR 3.6 2.5 - - - -
52C ARG* 4.2 31.6 - - + +
72C ILE* 3.6 36.6 - - + -
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Residues in contact with ASP 46 (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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44C PHE* 3.7 2.4 + - + +
45C PHE* 1.3 69.4 - - - +
47C PHE* 1.3 57.9 + - - +
48C SER* 3.0 32.8 + - - -
49C GLN* 3.1 18.9 + - - +
50C ASN 3.0 2.9 + - - -
51C THR* 2.4 56.6 + - - +
53C VAL* 3.9 18.1 - - + +
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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