Contacts of the strand formed by residues 37 - 43 (chain F) in PDB entry 3F5O
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 LYS 37 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32F SER* 4.2 1.7 + - - +
33F ALA* 3.7 0.7 - - - -
34F ALA* 2.9 41.1 + - + +
35F PRO 3.1 6.0 + - - +
36F GLY* 1.3 81.7 - - - +
38F VAL* 1.3 68.6 + - - +
39F ILE* 4.2 16.9 - - + +
71F ALA* 4.3 1.8 + - - +
103F THR* 3.8 25.0 - - - +
104F ALA 3.3 12.1 - - - +
105F HIS* 4.3 12.1 - - + -
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Residues in contact with VAL 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LEU* 3.6 25.8 - - + -
30F LEU* 3.9 21.8 - - + -
32F SER 3.4 4.3 - - - +
33F ALA* 4.5 0.9 - - + -
37F LYS* 1.3 78.2 - - - +
39F ILE* 1.3 66.0 + - - +
40F CYS* 4.0 7.6 - - - -
67F ILE* 4.0 20.3 - - + +
70F MET* 4.3 5.4 - - + -
71F ALA* 3.7 28.6 - - - +
74F CYS* 3.8 10.5 - - - -
102F ILE 3.7 1.4 - - - +
103F THR* 3.5 1.7 - - - -
104F ALA* 2.8 35.3 + - - +
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Residues in contact with ILE 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F LEU* 3.6 3.8 - - - +
31F VAL* 2.8 41.0 + - + -
32F SER* 2.9 40.2 + - - +
37F LYS* 4.2 22.2 - - + +
38F VAL* 1.3 79.0 - - - +
40F CYS* 1.3 64.9 + - - +
101F VAL* 3.5 29.6 - - + -
102F ILE 3.3 3.6 - - - +
103F THR* 4.0 17.9 - - + +
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Residues in contact with CYS 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ILE* 4.3 5.4 - - - -
28F ILE* 4.1 26.2 - - + -
29F THR 3.1 12.3 - - - +
30F LEU* 3.8 21.1 - - - -
31F VAL* 4.1 4.0 - - - +
38F VAL* 4.0 11.6 - - - -
39F ILE* 1.3 79.7 - - - +
41F GLU* 1.3 65.5 + - - +
67F ILE* 4.1 16.6 - - + -
70F MET* 4.3 1.3 - - - -
101F VAL* 3.5 6.6 - - - +
102F ILE* 2.8 39.5 + - + +
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Residues in contact with GLU 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F LYS 4.3 0.3 - - - +
28F ILE* 3.4 2.3 - - - -
29F THR* 2.8 54.4 + - - +
31F VAL* 3.6 20.5 - - + +
40F CYS* 1.3 76.0 - - - +
42F MET* 1.3 65.0 + - - +
99F ASP* 5.1 4.9 - - - +
100F ILE 3.3 15.9 - - - +
101F VAL* 4.4 8.2 - - + +
102F ILE* 4.2 3.8 - - - -
123F LYS* 2.9 42.5 + - - +
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Residues in contact with MET 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F VAL 5.6 0.9 - - - +
25F LEU* 5.3 2.9 - - - -
27F LYS* 4.3 14.1 - - + +
28F ILE* 3.9 26.0 - - + -
41F GLU* 1.3 78.2 - - - +
43F LYS* 1.3 70.6 + - - +
44F VAL* 3.9 7.1 + - + -
48F HIS* 3.8 42.4 - - + +
55F LEU* 4.0 17.7 - - + -
59F LEU* 4.5 2.5 - - + -
63F LEU* 4.2 12.1 - - + -
99F ASP* 3.5 3.5 - - - -
100F ILE* 2.8 64.7 + - + +
102F ILE* 4.4 2.2 - - + -
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Residues in contact with LYS 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F LYS* 5.3 2.3 + - - +
42F MET* 1.3 76.5 - - - +
44F VAL* 1.3 70.1 + - - +
45F GLU* 3.2 32.3 + - + +
48F HIS* 3.5 11.3 + - - -
97F GLY* 3.7 31.0 - - - +
98F GLU 3.5 3.4 - - - -
99F ASP* 3.3 22.6 + - - +
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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