Contacts of the strand formed by residues 83 - 90 (chain U) 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 ARG 83 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13911 C 2.8 35.2 + - - -
13921 U 2.8 27.9 + - - -
11D PHE* 5.7 0.2 - - - -
26U SER 4.4 2.3 - - - +
27U ARG* 3.7 19.7 + - - +
28U ASN* 5.3 0.3 - - - -
58U THR* 4.0 22.4 + - + +
59U LYS 3.9 1.6 - - - -
60U THR* 4.7 9.0 + - + +
81U GLN* 4.3 11.5 + - + -
82U MET* 1.3 73.6 - - - +
84U ILE* 1.3 62.0 - - - +
85U HIS* 3.8 27.1 - - + +
55d LEU* 4.0 24.5 - - + +
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Residues in contact with ILE 84 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D LYS* 4.5 6.7 - - + +
8D LYS* 3.8 44.9 - - + +
11D PHE* 3.6 26.7 - - + -
25U THR* 3.7 23.8 - - + -
26U SER 4.6 2.7 - - - -
57U PRO 4.0 2.3 - - - +
58U THR* 3.5 9.4 - - - +
59U LYS* 3.1 53.7 + - + +
61U LEU* 6.0 0.2 - - + -
82U MET* 4.5 16.8 - - + +
83U ARG* 1.3 74.8 - - - +
85U HIS* 1.3 63.3 + - - +
86U LYS* 4.3 2.0 + - + -
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Residues in contact with HIS 85 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14461 A 4.2 6.2 + - - -
14471 G 2.9 36.7 + - - +
24U LEU 3.8 1.7 - - - +
25U THR* 3.3 24.7 - - - +
26U SER* 3.5 11.4 + - - +
28U ASN 5.1 2.2 - - - -
29U VAL* 4.4 23.6 - - + +
32U LEU* 3.6 21.2 - - + +
56U MET 4.9 5.0 + - - +
58U THR* 3.0 37.5 + - + -
83U ARG* 3.8 31.2 + - + +
84U ILE* 1.3 76.3 + - - +
86U LYS* 1.3 60.4 + - - +
87U ARG* 4.9 3.1 - - - +
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Residues in contact with LYS 86 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14041 U 2.9 29.4 + - - +
15791 A 4.6 10.9 + - - -
15801 A 4.2 11.1 + - - +
15811 C 4.5 5.9 - - - +
7D LYS* 4.2 24.1 - - + +
23U THR* 3.6 22.0 - - + -
25U THR* 3.4 20.2 - - + +
56U MET* 3.1 49.2 + - + +
57U PRO 5.3 0.8 + - - +
59U LYS* 4.6 15.9 - - - +
84U ILE* 4.3 2.6 + - + -
85U HIS* 1.3 73.0 - - - +
87U ARG* 1.3 65.3 + - - +
88U LEU* 3.6 13.0 - - + -
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Residues in contact with ARG 87 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14471 G 3.7 21.0 + - - -
22U ILE 4.0 1.0 - - - +
23U THR* 3.3 7.6 - - - +
24U LEU* 3.0 40.7 + - + +
32U LEU* 3.5 38.4 - - + +
33U GLU* 2.4 34.2 + - - -
36U CYS* 4.0 28.4 - - + +
53U PRO* 4.6 9.6 - - + +
54U VAL 3.6 6.7 - - - -
55U ARG* 3.2 48.6 - - - +
56U MET 5.5 0.2 - - - +
85U HIS* 4.9 2.4 - - - +
86U LYS* 1.3 77.1 + - - +
88U LEU* 1.3 66.3 + - - +
89U ILE* 5.6 2.9 - - + -
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Residues in contact with LEU 88 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14041 U 3.5 27.4 - - + +
21U ARG* 3.4 33.2 - - - +
22U ILE 4.3 2.9 - - - -
23U THR* 4.0 11.9 - - + +
52U GLY 3.5 2.6 - - - +
54U VAL* 3.2 42.3 + - + +
56U MET* 3.7 22.0 - - + -
86U LYS* 3.6 32.8 - - + -
87U ARG* 1.3 81.9 - - - +
89U ILE* 1.3 63.6 + - - +
90U ASP* 5.1 3.1 - - - +
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Residues in contact with ILE 89 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21U ARG* 3.2 15.8 - - - +
22U ILE* 3.3 28.7 + - + +
36U CYS* 5.9 1.8 - - - -
39U LEU* 3.6 33.7 - - + -
40U ILE* 4.2 18.8 - - + -
50U VAL* 5.6 2.0 - - + -
51U LYS* 3.8 11.9 - - - +
52U GLY 3.7 16.4 - - - +
53U PRO* 3.8 16.6 - - + -
87U ARG* 5.6 3.1 - - + -
88U LEU* 1.3 78.6 - - - +
90U ASP* 1.3 70.3 + - - +
91U LEU* 4.9 17.9 - - + -
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Residues in contact with ASP 90 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14041 U 5.2 3.8 + - - -
20U ILE 3.7 5.2 - - - +
21U ARG* 3.2 37.7 + - - +
49U LYS 4.1 4.9 - - - +
50U VAL* 4.9 0.2 - - - +
51U LYS* 3.6 53.2 + - + +
88U LEU* 5.1 2.1 - - - +
89U ILE* 1.3 83.2 + - - +
91U LEU* 1.3 71.0 + - - +
92U HIS* 4.2 3.2 + - - +
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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