Contacts of the strand formed by residues 37 - 42 (chain C) in PDB entry 6MOL
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 VAL 37 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C PHE* 3.9 27.1 - - + -
28C CYS* 3.3 1.9 - - - +
29C PHE* 2.9 56.0 + - + +
31C GLU* 6.0 1.1 - - - +
35C ASP* 4.0 15.0 - - + +
36C LEU* 1.3 80.3 - - - +
38C CYS* 1.3 69.4 + - - +
39C PHE* 5.2 0.7 - - + -
82C TRP* 4.3 16.2 - - + -
83C CYS 3.6 11.2 - - - +
84C SER* 4.0 14.4 - - - +
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Residues in contact with CYS 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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26C LEU* 4.4 5.2 - - + -
27C LEU 3.3 3.8 - - - +
28C CYS* 2.0 45.3 - - - -
36C LEU* 3.8 19.9 - - - +
37C VAL* 1.3 73.7 - - - +
39C PHE* 1.3 61.0 + - - +
40C TRP* 5.3 1.3 - - - -
55C PHE* 3.9 27.2 - - + -
82C TRP* 3.3 2.4 - - - +
83C CYS* 2.9 34.3 + - - +
85C LEU* 4.8 1.6 - - + -
98C LEU* 3.9 13.2 - - - -
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Residues in contact with PHE 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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11C PHE* 4.9 3.4 - + + -
15C ALA* 3.4 39.3 - - + -
18C LEU* 4.1 4.7 - - + -
19C ALA* 4.5 7.4 - - + -
26C LEU* 3.8 1.4 - - - +
27C LEU* 2.9 74.1 + - + +
29C PHE* 3.8 35.7 - + - -
37C VAL* 5.2 1.1 - - + -
38C CYS* 1.3 76.7 - - - +
40C TRP* 1.3 71.8 + - - +
41C GLU* 4.8 2.5 - - + -
80C ARG* 3.6 29.4 - - + -
81C PHE 3.4 7.0 - - - +
82C TRP* 3.5 20.2 - - + -
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Residues in contact with TRP 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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24C GLU 6.0 0.2 - - - -
25C GLU 4.2 14.1 - - - +
26C LEU* 3.7 18.6 - - + -
27C LEU* 6.0 0.7 - - - -
38C CYS 5.4 1.6 - - - -
39C PHE* 1.3 83.8 - - - +
41C GLU* 1.3 63.4 + - - +
42C GLU* 3.7 26.3 + - + -
53C TYR* 4.1 14.8 - + + -
55C PHE* 4.2 7.4 - + - -
69C LEU* 3.7 24.9 - - + -
80C ARG* 3.5 2.0 - - - -
81C PHE* 3.1 72.6 + + + -
82C TRP 5.9 0.2 - - - -
100C VAL* 3.7 38.1 - - + -
108C ARG* 3.7 11.8 - - + +
109C TYR* 3.6 32.8 - + + +
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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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19C ALA* 3.9 21.4 - - + +
23C PRO* 6.6 0.2 - - + -
24C GLU* 4.3 25.8 + - - +
25C GLU 5.4 0.6 + - - -
39C PHE* 4.8 2.9 - - + -
40C TRP* 1.3 75.8 - - - +
42C GLU* 1.3 61.2 + - - +
74C THR* 3.5 15.5 - - + +
75C ALA* 4.2 16.1 - - - +
78C ALA* 5.0 7.3 - - + +
79C VAL 3.7 5.8 - - - +
80C ARG* 2.6 54.1 + - + +
109C TYR* 5.1 1.2 + - - -
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Residues in contact with GLU 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 GLU* 5.1 1.8 - - - -
40C TRP* 3.7 15.8 + - + +
41C GLU* 1.3 74.8 - - - +
43C ALA* 1.3 64.9 + - - +
44C ALA* 3.8 28.9 - - + +
53C TYR* 2.8 41.8 + - - -
78C ALA* 3.9 4.9 - - - +
79C VAL* 3.1 34.5 + - - +
81C PHE* 4.3 7.0 - - + -
108C ARG* 3.5 24.3 + - - +
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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