Contacts of the strand formed by residues 42 - 47 (chain c) in PDB entry 5FLX
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 42 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31c ARG* 4.7 0.4 - - - +
32c VAL* 3.0 39.4 + - + +
34c PHE* 5.1 0.7 - - + -
40c ARG* 2.9 70.2 - - + +
41c SER* 1.3 77.4 - - - +
43c ILE* 1.3 65.5 + - - +
44c ARG* 5.4 10.5 - - + +
58c LEU* 4.6 16.4 - - + -
61c SER 3.1 15.7 - - - +
63c ARG 4.8 12.8 - - - +
307z G 6.1 0.7 - - + -
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Residues in contact with ILE 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 LEU* 5.8 2.9 - - + -
29c GLN* 3.6 26.2 - - + +
30c VAL 3.9 10.1 - - - +
31c ARG* 4.0 28.9 - - + +
41c SER 5.2 2.5 - - - +
42c ILE* 1.3 78.5 - - - +
44c ARG* 1.3 60.2 + - - +
45c ASN* 5.7 0.4 - - - -
63c ARG 4.2 2.0 - - - +
64c GLU* 4.0 25.0 - - - +
65c ALA 4.8 3.6 + - - +
66c ARG* 3.4 29.2 - - - +
330z A 4.7 22.9 - - + +
331z G 4.6 7.9 - - - +
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Residues in contact with ARG 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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123F GLU* 5.3 2.4 + - - -
138F ALA 3.9 18.4 + - - -
139F VAL* 5.4 1.3 - - - +
140F ASP* 3.4 36.0 + - - +
204F ARG* 5.9 4.0 - - - +
29c GLN* 5.4 1.3 - - - -
30c VAL 3.1 23.8 + - - +
32c VAL* 4.6 8.6 - - + +
42c ILE* 4.1 11.7 + - + -
43c ILE* 1.3 73.6 - - - +
45c ASN* 1.3 74.7 + - + +
46c VAL* 3.6 9.4 + - - +
58c LEU* 4.7 9.4 - - + -
59c LEU 4.5 16.0 + - - -
60c GLU* 4.3 10.3 + - - +
61c SER 5.6 0.6 + - - -
63c ARG* 2.5 68.2 + - - +
64c GLU* 4.3 3.1 - - - +
65c ALA 5.2 2.0 - - - +
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Residues in contact with ASN 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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139F VAL* 3.8 24.8 - - + +
140F ASP* 3.2 27.1 + - - +
21c THR* 4.1 17.0 + - - +
27c CYS* 5.1 6.8 - - + +
28c THR 4.0 6.5 - - - +
29c GLN* 4.5 11.5 - - - +
44c ARG* 1.3 82.3 - - + +
46c VAL* 1.3 60.3 + - - +
65c ALA* 2.3 47.7 + - - +
66c ARG* 3.9 11.1 - - - +
67c ARG* 5.3 6.5 - - - +
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Residues in contact with VAL 46 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F VAL* 4.6 3.1 - - - -
140F ASP* 3.4 18.8 - - + +
141F VAL 4.2 4.7 - - - +
142F SER* 4.1 8.3 - - - +
14c VAL* 6.3 0.2 - - + -
27c CYS* 3.4 4.6 - - - +
28c THR* 2.8 42.4 + - - +
30c VAL* 4.1 20.0 - - + +
32c VAL* 5.2 0.7 - - + -
44c ARG 3.6 10.5 - - - +
45c ASN* 1.3 81.2 - - - +
47c LYS* 1.3 75.1 + - - +
48c GLY 4.8 0.4 - - - +
50c VAL* 4.1 21.3 - - + -
56c LEU* 4.0 21.3 - - + -
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Residues in contact with LYS 47 (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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12201 A 5.4 11.1 - - - -
124F ASP* 3.7 5.8 - - - +
125F SER* 0.9 110.0 + - - +
139F VAL* 3.8 10.1 - - + -
140F ASP 2.5 20.7 + - - +
141F VAL* 4.4 1.6 - - - -
142F SER* 2.4 37.8 + - - -
145F ARG* 3.0 28.6 - - - +
26c GLN* 5.4 13.2 + - + +
27c CYS* 4.6 11.7 - - - +
46c VAL* 1.3 73.7 - - - +
48c GLY* 1.3 62.4 + - - +
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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