Contacts of the helix formed by residues 50 - 55 (chain C) in PDB entry 4H7Y
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 PRO 50 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B LYS* 6.3 0.4 - - + -
44B GLN* 4.1 7.9 - - - +
11C ASN* 5.1 2.7 - - - +
48C ALA 3.3 11.4 - - - +
49C LEU* 1.3 80.2 - - - +
51C PRO* 1.3 72.2 - - + +
52C ASP* 3.2 16.8 - - - +
53C LYS* 3.2 33.4 + - + -
54C TYR* 3.3 27.2 - - + -
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Residues in contact with PRO 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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40B GLY* 3.6 17.0 - - - +
43B SER* 3.5 21.3 - - - +
44B GLN* 3.7 21.8 - - + +
49C LEU 3.3 8.5 - - - +
50C PRO* 1.3 83.1 - - + +
52C ASP* 1.3 62.1 + - - +
54C TYR 4.5 0.2 - - - +
55C GLY* 3.1 25.5 + - - -
60C PHE* 3.8 18.1 - - + -
64C GLN* 4.9 2.2 - - - +
89C ASN* 3.6 31.6 - - + +
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Residues in contact with ASP 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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143A LYS* 3.0 28.2 + - - +
144A GLN* 6.0 0.2 + - - -
33B ALA 4.7 2.8 - - - +
36B ASN* 3.6 37.4 + - + +
37B LYS* 3.7 31.2 + - - +
40B GLY* 4.8 0.8 - - - -
50C PRO* 3.5 19.2 - - - +
51C PRO* 1.3 76.4 - - - +
53C LYS* 1.3 72.2 + - - +
55C GLY* 4.6 0.7 + - - -
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Residues in contact with LYS 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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143A LYS* 3.9 17.9 - - - +
50C PRO* 3.2 40.4 + - + +
51C PRO 3.1 0.4 - - - -
52C ASP* 1.3 88.3 + - - +
54C TYR* 1.3 84.9 + - + +
55C GLY 3.7 1.5 + - - -
56C GLN 5.3 0.3 + - - -
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Residues in contact with TYR 54 (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 ASN* 3.6 17.2 + - - -
12C ASN* 4.0 4.3 - - + +
13C PRO* 3.4 32.5 - - + +
49C LEU* 3.8 30.3 - - + -
50C PRO* 3.3 34.0 + - + +
51C PRO 3.2 3.9 + - - -
53C LYS* 1.3 100.7 - - + +
55C GLY* 1.3 63.6 + - - +
56C GLN 3.1 3.8 - - - -
57C ASN* 3.0 28.0 + - + +
60C PHE* 3.3 35.6 - - + -
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Residues in contact with GLY 55 (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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143A LYS* 5.3 4.9 - - - +
51C PRO 3.1 11.3 + - - -
52C ASP 4.6 2.0 + - - -
53C LYS 3.7 1.6 - - - -
54C TYR* 1.3 76.7 - - - +
56C GLN* 1.3 63.1 + - - +
57C ASN 3.7 0.2 + - - -
60C PHE* 4.8 1.1 - - - -
89C ASN 3.3 26.4 - - - +
90C CYS* 3.9 13.4 - - - +
91C LYS 5.0 0.3 + - - -
92C LYS* 4.4 4.0 - - - +
93C PHE* 4.1 8.1 - - - -
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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