Contacts of the strand formed by residues 36 - 42 (chain C) in PDB entry 2JC6
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 GLU 36 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C THR* 3.0 40.6 + - + -
30C GLY 3.5 5.6 - - - +
31C THR* 4.1 12.7 + - + +
35C SER* 1.3 77.7 - - - +
37C VAL* 1.3 65.9 + - - +
38C VAL* 3.3 18.2 - - + +
51C VAL 3.6 1.2 - - - +
52C LYS* 3.4 2.4 - - - -
53C CYS* 2.9 40.0 + - + +
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Residues in contact with VAL 37 (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 THR* 3.6 3.5 - - - +
29C LEU* 2.7 35.5 + - + -
30C GLY 2.8 15.7 + - - +
35C SER* 5.5 1.1 - - - +
36C GLU* 1.3 73.5 - - - +
38C VAL* 1.3 60.0 + - - +
50C ALA* 4.1 25.1 - - + -
51C VAL 3.5 8.3 - - - +
52C LYS* 4.1 26.2 - - + -
98C MET* 4.4 11.2 - - + -
1314C QPP 4.0 37.7 - - + -
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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
----------------------------------------------------------
25C PHE* 3.7 25.1 - - + -
26C LYS 3.7 13.9 - - - +
27C GLU 3.1 18.8 - - - +
28C THR* 4.1 3.1 - - - +
29C LEU* 4.4 4.0 - - - -
36C GLU* 3.3 31.4 - - + +
37C VAL* 1.3 79.8 - - - +
39C LEU* 1.3 71.9 + - - +
40C ALA 3.5 0.5 + - - -
50C ALA* 3.8 0.5 - - - -
51C VAL* 2.9 33.8 + - - +
53C CYS* 4.1 17.3 - - - -
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Residues in contact with LEU 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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26C LYS* 2.7 45.9 + - + -
27C GLU* 2.7 41.8 + - + +
29C LEU* 3.8 22.9 - - + +
38C VAL* 1.3 73.4 - - - +
40C ALA* 1.3 54.4 + - - +
48C LEU* 4.2 25.1 - - + -
49C PHE 3.6 16.6 - - - +
100C LEU* 3.8 33.4 - - + -
1314C QPP 6.2 0.4 - - + -
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Residues in contact with ALA 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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23C PHE* 4.0 18.2 - - + -
24C GLU 3.3 10.5 - - - +
25C PHE* 4.5 10.1 - - + -
26C LYS* 4.8 0.2 - - - -
38C VAL 4.3 0.7 - - - +
39C LEU* 1.3 76.1 - - - +
41C GLU* 1.3 60.2 + - - +
42C GLU 4.0 0.7 + - - -
47C LYS 3.9 0.3 - - - +
48C LEU* 3.4 5.7 - - - -
49C PHE* 2.8 38.3 + - - +
51C VAL* 3.5 30.7 - - + -
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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
----------------------------------------------------------
23C PHE* 3.3 3.7 - - - -
24C GLU* 2.8 61.4 + - + +
26C LYS* 4.0 18.9 - - + +
40C ALA* 1.3 71.4 - - - +
42C GLU* 1.3 77.3 + - - +
43C LYS* 3.2 2.7 + - - +
46C GLY* 3.3 29.6 - - - +
47C LYS 3.5 3.1 - - - -
48C LEU* 3.5 21.7 - - + +
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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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22C ILE* 3.7 15.5 - - + +
23C PHE* 3.5 28.5 - - + -
41C GLU* 1.3 69.4 - - - +
43C LYS* 1.3 59.1 + - - +
44C ALA* 4.3 7.5 - - + +
45C THR* 2.7 41.2 + - + +
46C GLY* 2.8 34.1 + - - -
47C LYS* 2.8 18.4 + - - +
49C PHE* 3.6 20.2 - - + -
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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