Contacts of the strand formed by residues 48 - 55 (chain H) in PDB entry 6CMO
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 LEU 48 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H VAL* 3.7 28.0 - - + -
41H ARG 3.5 15.0 - - - +
42H GLN* 3.7 29.4 - - + -
46H LYS 5.3 0.2 - - - +
47H GLY* 1.3 77.6 - - - -
49H GLU* 1.3 62.9 + - - +
98H TYR* 4.6 12.8 - - + -
121H TRP* 6.2 1.8 - - + -
39L GLN* 5.6 6.1 - - + -
45L PRO* 5.9 5.2 - - + -
88L TYR* 3.6 33.6 - - + +
99L PHE* 3.5 41.5 - - + +
100L GLY 4.6 7.4 + - - +
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Residues in contact with GLU 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H VAL* 3.3 6.3 - - - +
41H ARG* 2.6 72.7 + - + +
47H GLY 5.5 2.0 - - - +
48H LEU* 1.3 76.2 - - - +
50H TRP* 1.3 62.9 + - - +
51H VAL* 5.3 3.4 - - + +
99L PHE* 4.7 2.0 - - - -
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Residues in contact with TRP 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H HIS* 3.7 16.7 + + + +
39H TRP 3.4 17.3 - - - -
40H VAL* 3.9 17.7 - - + -
49H GLU* 1.3 74.8 - - - +
51H VAL* 1.3 68.8 + - - +
52H ALA 2.9 25.4 + - - -
53H SER* 3.7 22.7 - - - -
55H TYR* 5.2 0.4 - - - -
62H SER* 3.2 31.2 - - - -
63H TYR 5.1 7.2 - - - -
64H ALA* 3.8 13.8 - - - +
118H MET* 6.1 2.0 - - + -
95L SER 3.6 9.9 - - - -
96L LEU* 4.1 7.9 - - + -
97L ILE* 3.5 63.2 + - + +
99L PHE* 4.6 14.4 - + + +
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Residues in contact with VAL 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H TRP* 3.4 18.8 - - + +
40H VAL* 4.4 1.8 - - - -
41H ARG* 3.7 44.9 - - + +
49H GLU* 4.9 4.0 - - + +
50H TRP* 1.3 89.5 - - - +
52H ALA* 1.3 69.1 + - + +
62H SER 4.1 0.9 - - - +
63H TYR* 3.5 5.2 - - - +
64H ALA* 2.8 34.0 + - + +
67H VAL* 4.1 28.8 - - + +
71H PHE* 5.8 6.1 - - + -
84H LEU* 6.1 0.9 - - + -
97H TYR* 4.9 5.4 - - + -
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Residues in contact with ALA 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H TRP* 3.2 19.3 + - + -
50H TRP* 2.9 18.8 + - - -
51H VAL* 1.3 86.4 - - + +
53H SER* 1.3 61.9 + - - +
62H SER 4.1 4.9 - - - -
63H TYR* 4.5 15.5 - - + -
67H VAL* 6.5 0.2 - - + -
71H PHE* 5.4 9.2 - - + -
73H ILE* 4.9 5.6 - - + -
84H LEU* 4.0 27.4 - - + -
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Residues in contact with SER 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H ILE 3.4 9.1 + - - -
38H HIS* 3.1 32.9 + - - -
39H TRP* 5.4 1.6 - - - -
50H TRP* 3.7 13.9 - - - -
52H ALA* 1.3 78.8 - - - +
54H ILE* 1.3 69.3 + - - +
55H TYR* 3.2 20.7 - - - -
61H THR* 3.3 22.5 - - - +
62H SER* 3.8 9.4 + - - +
63H TYR* 4.9 1.2 - - - -
73H ILE* 4.1 5.9 - - - +
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Residues in contact with ILE 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H PHE* 5.0 4.3 - - + -
36H SER* 3.4 9.2 - - - -
37H ILE* 3.0 33.2 + - + +
39H TRP* 4.9 12.8 - - + +
53H SER* 1.3 79.8 + - - +
55H TYR* 1.3 72.7 + - - +
56H SER* 4.1 8.2 + - - +
61H THR* 3.8 2.9 - - + -
73H ILE* 3.8 24.0 - - + -
74H SER 4.1 7.0 - - - +
75H ALA* 3.8 19.3 - - + -
82H ALA* 3.8 23.1 - - + -
83H TYR 3.4 26.2 - - - +
84H LEU* 6.4 0.2 - - + -
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Residues in contact with TYR 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H SER* 3.7 11.2 - - - -
38H HIS* 4.1 3.7 - + - -
50H TRP* 5.2 0.2 - - - -
53H SER* 3.2 21.8 + - - -
54H ILE* 1.3 84.8 - - - +
56H SER* 1.3 62.5 + - - +
57H TYR 5.0 0.9 - - - +
58H SER* 4.2 15.7 - - - +
59H GLY* 3.6 19.3 + - - +
60H SER 3.1 24.0 - - - +
61H THR* 3.5 13.4 - - + +
62H SER* 3.9 17.9 + - - -
104H TRP* 3.2 49.2 - + - -
95L SER* 3.9 20.1 + - - -
97L ILE* 5.1 0.9 - - - +
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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