Contacts of the helix formed by residues 51 - 59 (chain C) in PDB entry 3SR2
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 THR 51 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C GLN* 2.9 40.7 + - + +
50C ASP* 1.3 75.1 - - - +
52C SER* 1.3 67.1 + - - +
54C VAL* 3.0 12.8 + - + +
55C SER* 3.0 25.3 + - - -
69C PRO* 4.4 20.9 - - + -
70C ALA* 5.5 4.0 - - + +
73C LEU* 6.0 0.9 - - + -
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Residues in contact with SER 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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50C ASP* 2.6 26.0 + - - -
51C THR* 1.3 82.1 + - - +
53C VAL* 1.3 64.2 + - - +
55C SER* 3.4 6.1 + - - -
56C GLN* 3.0 27.7 + - - +
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Residues in contact with VAL 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C VAL* 3.3 40.2 - - + -
50C ASP* 3.4 12.6 - - - +
52C SER* 1.3 78.6 + - - +
54C VAL* 1.3 68.7 + - - +
56C GLN* 4.2 7.9 - - + +
57C ARG* 2.9 63.2 + - + +
119C TRP* 4.3 0.6 - - + -
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Residues in contact with VAL 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C GLY* 5.2 0.7 - - - -
34C TYR* 5.9 2.5 - - + -
49C VAL* 3.5 15.5 - - + +
50C ASP 3.0 23.1 - - - +
51C THR* 3.2 10.5 - - - +
53C VAL* 1.3 81.4 - - - +
55C SER* 1.3 54.9 + - - +
58C ALA* 2.7 33.9 + - - +
69C PRO* 4.0 12.1 - - + +
72C PHE* 3.8 36.3 - - + -
73C LEU* 4.9 16.2 - - + +
76C LEU* 6.1 1.6 - - + -
119C TRP* 3.8 19.6 - - + -
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Residues in contact with SER 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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51C THR 3.0 8.3 + - - -
52C SER* 3.6 9.9 - - - -
54C VAL* 1.3 79.7 - - - +
56C GLN* 1.3 63.1 + - - +
58C ALA* 3.7 6.4 + - - +
59C LYS* 3.8 22.1 + - - +
67C ALA 5.0 3.9 + - - -
69C PRO* 3.0 37.5 - - - +
72C PHE* 5.5 2.9 - - - -
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Residues in contact with GLN 56 (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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52C SER 3.0 18.0 + - - +
53C VAL* 3.3 7.4 + - + +
55C SER* 1.3 79.9 - - - +
57C ARG* 1.3 64.2 + - + +
59C LYS* 3.6 12.3 + - - +
60C GLU* 3.3 30.9 + - - +
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Residues in contact with ARG 57 (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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34C TYR* 4.3 2.2 + - - -
47C GLU* 3.4 24.4 + - - -
49C VAL* 4.7 0.6 - - - +
53C VAL* 2.9 45.8 + - + +
56C GLN* 1.3 77.5 - - + +
58C ALA* 1.3 60.2 + - - +
60C GLU* 2.9 34.1 + - + +
61C LEU* 3.5 22.2 - - + +
119C TRP* 3.6 31.0 - - + +
120C ASN* 3.5 22.5 + - - -
122C HIS* 3.6 33.1 + - + +
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Residues in contact with ALA 58 (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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54C VAL 2.7 22.6 + - - +
55C SER 4.1 2.9 - - - +
56C GLN 3.3 0.4 - - - -
57C ARG* 1.3 77.1 - - - +
59C LYS* 1.3 56.2 + - - +
60C GLU 3.3 1.2 + - - -
61C LEU* 4.3 2.8 + - - +
62C ASN* 3.2 28.5 + - - +
65C LEU 4.5 1.7 - - - +
72C PHE* 3.1 42.6 - - + -
117C PHE* 5.8 0.2 - - - -
118C TYR 5.8 1.8 - - - -
119C TRP* 3.7 17.0 - - + -
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Residues in contact with LYS 59 (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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55C SER* 3.8 14.2 + - - +
56C GLN* 3.6 14.8 + - - +
57C ARG 3.1 1.0 - - - -
58C ALA* 1.3 76.1 - - - +
60C GLU* 1.3 61.1 + - + +
61C LEU 3.6 0.2 - - - -
62C ASN 3.2 21.2 - - - +
63C LYS* 3.4 15.7 - - - +
65C LEU 4.0 14.8 - - - +
66C THR* 5.0 13.1 - - - +
67C ALA 6.1 0.2 - - - +
1H MET* 4.7 17.6 - - - -
48H GLN* 5.0 10.8 - - - +
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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