Contacts of the helix formed by residues 53 - 61 (chain H) in PDB entry 3B4V
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 ASN 53 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61E THR* 3.7 27.3 + - + +
65E HIS* 4.6 17.6 - - - +
68E MET* 4.9 13.5 - - + +
23F ILE* 4.3 15.8 - - - +
25F TRP* 3.0 31.4 + - - -
51H PRO 3.8 0.7 + - - +
52H GLY* 1.3 69.2 - - - -
54H LYS* 1.3 61.6 + - - +
55H ILE 3.3 0.9 - - - -
56H ASN* 3.3 18.1 - - - +
57H LEU 3.1 19.6 + - - -
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Residues in contact with LYS 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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24F GLY 3.2 25.6 + - - +
25F TRP* 4.4 13.2 - - + +
27F ASP* 3.4 28.4 + - - -
28F TRP* 3.4 45.1 - - + -
239G EDO 5.2 3.4 + - - -
50H HIS* 3.6 19.5 - - + -
51H PRO* 3.4 25.2 - - + +
52H GLY 3.0 1.4 - - - -
53H ASN* 1.3 77.0 + - - +
55H ILE* 1.3 66.1 + - - +
57H LEU* 3.2 4.5 + - - -
58H LEU 3.0 17.8 + - - -
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Residues in contact with ILE 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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11H VAL* 3.7 19.7 - - + -
13H TRP* 3.6 21.3 - - + -
25H VAL* 4.2 10.1 - - + -
28H THR* 4.2 21.5 - - + -
48H LEU 3.6 23.8 - - - +
49H THR* 4.1 1.8 - - + -
50H HIS* 3.7 37.8 - - - +
52H GLY 3.4 11.2 + - - +
54H LYS* 1.3 79.5 - - - +
56H ASN* 1.3 80.3 + - - +
58H LEU* 3.1 27.3 + - + +
59H GLY 3.2 8.7 + - - -
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Residues in contact with ASN 56 (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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55E SER* 5.6 0.8 - - - +
56E LEU* 4.4 21.2 + - - +
61E THR* 3.7 18.8 + - + +
13H TRP* 5.4 0.2 - - - -
23H SER 5.1 0.7 - - - +
25H VAL* 4.4 20.1 - - - +
52H GLY 4.0 0.9 - - - +
53H ASN* 3.3 26.7 + - + +
54H LYS 3.2 0.2 - - - -
55H ILE* 1.3 89.0 - - - +
57H LEU* 1.3 58.6 + - - +
59H GLY* 2.9 18.7 + - - -
60H PHE* 3.1 32.7 + - + -
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Residues in contact with LEU 57 (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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58E PHE* 4.1 17.9 - - + -
25F TRP* 3.5 55.2 - - + +
28F TRP* 3.4 32.5 - - + -
29F ILE* 4.5 6.3 - - + -
53H ASN 3.1 9.6 + - - +
54H LYS* 3.4 9.6 - - + +
56H ASN* 1.3 77.6 - - - +
58H LEU* 1.3 58.3 + - - +
60H PHE* 3.2 9.0 + - + -
61H LEU* 2.9 51.8 + - + +
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Residues in contact with LEU 58 (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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28F TRP* 3.5 29.5 - - + -
96F ASP* 6.3 1.6 - - + -
46H SER* 5.9 0.9 - - - +
48H LEU* 5.6 6.3 - - + +
50H HIS* 4.2 14.8 - - + +
54H LYS 3.0 11.5 + - - +
55H ILE* 3.3 27.1 - - + +
57H LEU* 1.3 75.5 - - - +
59H GLY* 1.3 57.7 + - - +
61H LEU* 4.1 1.3 - - - +
62H GLY 3.4 1.0 + - - -
63H LEU* 2.8 59.5 + - + +
64H VAL* 3.3 35.8 - - + +
65H HIS 5.2 0.4 - - - +
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Residues in contact with GLY 59 (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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13H TRP* 3.9 11.0 - - - -
21H THR* 6.0 0.2 - - - +
22H CYS 3.9 7.8 - - - +
23H SER* 4.1 20.1 - - - -
55H ILE 3.2 5.5 + - - -
56H ASN 2.9 9.2 + - - -
58H LEU* 1.3 75.4 - - - +
60H PHE* 1.3 59.5 + - - +
62H GLY* 2.9 21.7 + - - -
64H VAL* 3.7 14.7 - - - +
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Residues in contact with PHE 60 (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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56E LEU 3.3 24.9 - - - -
57E SER* 3.4 5.8 - - - -
58E PHE* 3.4 61.2 - + + -
61E THR* 3.5 15.9 - - - -
25F TRP* 4.3 4.9 - + - -
103F LYS* 4.9 1.7 + - - -
105F ILE* 3.8 21.2 - - + +
23H SER* 4.6 14.6 - - - -
24H LEU* 5.4 2.7 - - + -
56H ASN* 3.1 31.5 + - + -
57H LEU* 3.2 15.7 + - + +
59H GLY* 1.3 75.5 - - - +
61H LEU* 1.3 62.8 + - + +
62H GLY* 3.4 1.2 + - - -
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Residues in contact with LEU 61 (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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28F TRP* 4.1 16.8 - - + -
29F ILE* 5.1 2.5 - - + -
91F MET* 4.9 8.3 - - + -
93F TYR* 3.6 52.5 + - + -
103F LYS* 3.9 7.5 + - - -
105F ILE* 3.9 27.6 - - + -
57H LEU* 2.9 49.4 + - + +
58H LEU 4.4 0.2 - - - +
60H PHE* 1.3 76.5 - - - +
62H GLY* 1.3 61.3 + - - +
63H LEU* 3.5 31.7 - - + +
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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