Contacts of the helix formed by residues 44 - 53 (chain C) in PDB entry 5V6Y
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 44 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ASN* 5.4 3.2 + - - -
42C PRO 3.7 0.8 + - - -
43C ASP* 1.3 80.2 - - + +
45C LEU* 1.3 59.6 + - - +
46C GLU* 3.2 17.7 - - - +
47C GLU* 3.0 31.8 + - + +
48C LYS* 2.8 25.0 + - + +
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Residues in contact with LEU 45 (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 TRP* 3.9 26.7 - - + -
13C ILE 3.5 35.0 - - - +
14C ASN* 3.5 18.3 + - + +
42C PRO* 3.7 26.1 + - + +
43C ASP 3.2 1.7 - - - -
44C LYS* 1.3 77.3 - - - +
46C GLU* 1.3 61.4 + - - +
47C GLU 3.1 0.2 - - - -
48C LYS* 3.5 10.3 - - - -
49C PHE* 2.9 32.2 + - - +
62C ILE* 3.9 29.6 - - + -
63C PHE 4.0 10.1 - - - +
64C TRP* 4.2 8.5 - - + -
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Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ASN* 5.4 0.2 - - - +
44C LYS* 3.6 18.9 - - - +
45C LEU* 1.3 83.0 + - - +
47C GLU* 1.3 79.8 + - + +
50C PRO* 3.3 10.7 - - - +
64C TRP* 3.3 52.3 - - + +
68C ARG* 4.0 33.0 + - - +
72C TYR* 2.9 27.6 + - - +
155C GLU* 5.4 3.6 - - - +
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Residues in contact with GLU 47 (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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44C LYS* 3.0 31.4 + - + +
46C GLU* 1.3 99.5 - - + +
48C LYS* 1.3 60.6 + - - +
49C PHE 3.5 0.7 - - - -
50C PRO* 3.4 15.5 - - - +
51C GLN* 3.4 25.4 + - - +
68C ARG* 5.1 8.6 + - - +
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Residues in contact with LYS 48 (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 TRP* 3.6 26.6 - - + -
42C PRO* 4.1 24.3 - - + +
43C ASP 4.5 6.5 - - - +
44C LYS 2.8 19.6 + - - +
45C LEU* 3.3 6.9 + - - -
47C GLU* 1.3 73.0 - - - +
49C PHE* 1.3 66.4 + - - +
51C GLN* 3.0 11.1 + - - +
52C VAL* 2.9 45.0 + - + +
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Residues in contact with PHE 49 (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 TRP* 3.8 12.9 - + + -
45C LEU 2.9 19.0 + - - +
48C LYS* 1.3 77.0 - - - +
50C PRO* 1.3 66.5 - - + +
52C VAL* 4.6 1.3 - - - +
53C ALA* 3.0 39.8 + - + +
58C GLY* 5.2 0.2 - - - -
59C PRO* 3.5 44.6 - - + -
62C ILE* 3.4 46.0 - - + -
72C TYR* 3.9 26.7 - + - -
77C LEU* 4.2 30.7 - - + -
78C LEU* 4.3 5.6 - - + -
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Residues in contact with PRO 50 (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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46C GLU 3.3 24.7 - - - +
47C GLU* 3.4 16.6 - - - +
49C PHE* 1.3 92.3 - - + +
51C GLN* 1.3 59.4 + - + +
53C ALA 4.4 0.9 - - - -
54C ALA* 4.2 12.6 + - - +
72C TYR* 3.8 18.4 - - + -
77C LEU* 3.6 31.6 - - + +
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Residues in contact with GLN 51 (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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47C GLU* 3.4 24.9 + - - +
48C LYS* 3.0 11.6 + - - +
50C PRO* 1.3 81.9 - - + +
52C VAL* 1.3 66.7 - - + +
53C ALA 3.3 1.9 + - - -
54C ALA* 3.5 15.3 + - - +
55C THR* 4.5 4.9 + - - +
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Residues in contact with VAL 52 (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 TRP* 4.3 13.2 - - + -
48C LYS* 2.9 43.9 + - + +
49C PHE* 4.4 1.6 - - - +
51C GLN* 1.3 78.3 - - + +
53C ALA* 1.3 59.6 + - - +
54C ALA 3.3 0.2 - - - -
55C THR* 3.4 5.7 + - - +
57C ASP* 3.1 46.1 - - - +
58C GLY* 4.2 6.7 - - - -
59C PRO* 5.7 0.4 - - + -
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Residues in contact with ALA 53 (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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49C PHE* 3.0 34.9 + - + +
51C GLN 3.3 0.2 - - - -
52C VAL* 1.3 76.3 - - - +
54C ALA* 1.3 61.0 + - - +
55C THR 3.3 1.3 - - - -
56C GLY* 3.3 13.6 + - - -
57C ASP 4.6 0.2 - - - +
58C GLY* 4.4 13.2 - - - +
77C LEU* 4.0 34.1 - - + +
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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