Contacts of the strand formed by residues 37 - 43 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C SER* 4.2 2.0 + - - +
33C ALA* 3.6 1.0 - - - -
34C ALA* 2.8 43.4 + - + +
35C PRO 3.2 5.6 + - - +
36C GLY* 1.3 80.3 - - - +
38C VAL* 1.3 69.4 + - - +
39C ILE* 4.0 19.3 - - + +
71C ALA* 4.3 2.2 + - - +
103C THR* 3.9 12.3 - - - +
104C ALA 3.2 10.5 - - - +
105C HIS* 3.4 37.1 + - + +
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Residues in contact with VAL 38 (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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8C LEU* 3.8 24.0 - - + -
30C LEU* 3.9 22.2 - - + -
32C SER 3.6 3.4 - - - -
33C ALA* 4.5 2.0 - - - -
37C LYS* 1.3 81.5 - - - +
39C ILE* 1.3 65.7 + - - +
40C CYS* 4.0 6.7 - - - -
67C ILE* 4.0 21.0 - - + +
70C MET* 4.3 6.1 - - + -
71C ALA* 3.7 31.3 - - + +
74C CYS* 3.8 9.6 - - - -
102C ILE 3.7 1.2 - - - +
103C THR* 3.6 1.7 - - - -
104C ALA* 2.9 33.7 + - - +
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Residues in contact with ILE 39 (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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30C LEU* 3.7 3.8 - - - +
31C VAL* 2.8 44.1 + - + -
32C SER* 3.0 33.8 + - - +
37C LYS* 4.0 24.5 - - + +
38C VAL* 1.3 77.5 - - - +
40C CYS* 1.3 65.2 + - - +
41C GLU* 5.4 0.2 - - - +
101C VAL* 3.5 29.8 - - + -
102C ILE 3.4 3.8 - - - +
103C THR* 4.0 17.7 - - + +
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Residues in contact with CYS 40 (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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12C ILE* 4.5 1.6 - - - -
28C ILE* 4.1 23.6 - - + -
29C THR 3.1 14.6 - - - +
30C LEU* 4.0 18.6 - - - -
31C VAL* 4.1 2.2 - - - +
38C VAL* 4.0 11.6 - - - +
39C ILE* 1.3 78.0 - - - +
41C GLU* 1.3 71.0 + - - +
67C ILE* 3.9 21.5 - - + -
70C MET* 4.3 9.9 - - - -
101C VAL* 3.5 2.8 - - - +
102C ILE* 2.8 33.4 + - + -
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Residues in contact with GLU 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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28C ILE* 3.4 3.1 - - - +
29C THR* 2.8 46.2 + - - +
31C VAL* 3.5 25.7 - - + +
39C ILE* 5.4 0.2 - - - +
40C CYS* 1.3 78.8 - - - +
42C MET* 1.3 62.7 + - - +
99C ASP* 6.3 1.1 - - + -
100C ILE 3.2 13.7 - - - +
101C VAL* 3.6 16.8 - - + +
102C ILE* 4.2 3.1 - - - -
123C LYS* 2.6 46.9 + - + +
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Residues in contact with MET 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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24C VAL 5.6 0.2 - - - +
25C LEU* 5.0 4.3 - - - -
27C LYS* 4.2 7.0 - - - +
28C ILE* 3.9 33.4 - - + +
41C GLU* 1.3 76.8 - - - +
43C LYS* 1.3 69.5 + - - +
44C VAL* 4.5 5.6 - - + -
48C HIS* 3.8 44.0 - - + +
55C LEU* 4.0 16.4 - - + -
59C LEU* 4.5 2.7 - - + -
63C LEU* 4.2 14.4 - - + -
99C ASP* 3.6 3.5 - - - -
100C ILE* 2.7 62.6 + - + +
102C ILE* 4.2 4.3 - - + -
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Residues in contact with LYS 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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27C LYS* 2.7 36.4 + - - +
42C MET* 1.3 75.0 - - - +
44C VAL* 1.3 70.3 + - - +
45C GLU* 3.2 21.0 + - + +
48C HIS* 3.5 5.5 + - - -
97C GLY* 2.6 42.6 + - - +
98C GLU 3.5 3.4 - - - +
99C ASP* 3.5 23.6 + - - +
95F LYS* 5.7 8.7 - - - +
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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