Contacts of the helix formed by residues 49 - 55 (chain C) in PDB entry 2O1S
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 HIS 49 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47C SER 2.5 12.5 + - - -
48C GLY* 1.3 66.9 - - - -
50C PHE* 1.3 64.8 + - - +
51C ALA 3.0 2.0 - - - -
52C SER* 2.9 19.8 + - - +
53C GLY* 3.2 8.5 + - - -
80C HIS* 3.4 34.0 - - + +
83C TYR* 3.5 27.1 + - + +
99C ARG* 3.5 29.4 + - - -
106C PRO 4.6 1.8 + - - -
107C PHE* 3.5 26.9 - + - -
288C TYR* 4.0 28.7 - + - -
289C GLU 4.8 5.1 + - - -
291C ALA* 6.1 3.1 + - + +
427C ASP* 4.4 2.9 - - - -
3002C TPP 6.3 0.2 - - - -
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Residues in contact with PHE 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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39C LEU* 3.6 30.1 - - + +
40C LEU* 3.7 31.9 - - + -
43C VAL* 4.4 8.3 - - + -
44C SER 4.6 2.0 - - - -
45C ARG* 3.9 50.7 - - + -
47C SER 4.8 0.4 - - - -
48C GLY* 2.9 25.3 + - - +
49C HIS* 1.3 77.6 - - - +
51C ALA* 1.3 73.3 + - + +
53C GLY* 3.4 2.6 + - - -
54C LEU* 3.1 35.8 + - + +
83C TYR* 3.8 20.4 - - + -
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Residues in contact with ALA 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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48C GLY 3.0 11.9 + - - +
49C HIS 3.0 0.2 - - - -
50C PHE* 1.3 97.8 - - + +
52C SER* 1.3 65.3 + - - +
53C GLY 3.1 1.3 - - - -
54C LEU* 3.0 28.5 + - + +
55C GLY 3.8 1.9 + - - -
284C LYS 5.0 7.6 - - - +
286C ARG 6.1 0.9 - - - +
287C GLY 3.5 28.0 - - - +
288C TYR* 4.5 0.4 - - + -
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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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48C GLY 4.3 0.6 + - - -
49C HIS* 2.9 13.6 + - - -
51C ALA* 1.3 77.6 - - - +
53C GLY* 1.3 61.0 + - - +
55C GLY* 3.2 13.3 + - - -
56C THR* 4.1 3.6 + - - +
80C HIS* 2.6 57.4 + - - -
81C GLN* 3.9 12.8 - - - +
284C LYS 5.8 2.2 - - - -
288C TYR* 3.9 16.0 - - - -
3002C TPP 4.2 3.8 - - - -
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Residues in contact with GLY 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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39C LEU* 4.1 2.7 - - - -
49C HIS 3.2 12.9 + - - -
50C PHE 3.7 5.4 - - - -
51C ALA 3.1 1.0 - - - -
52C SER* 1.3 77.2 + - - +
54C LEU* 1.3 64.2 + - - +
56C THR* 2.9 25.3 + - - -
57C VAL* 3.4 2.3 + - - +
81C GLN* 3.9 8.0 - - - +
83C TYR* 5.0 1.1 - - - -
84C PRO* 3.3 30.0 - - - +
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Residues in contact with LEU 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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36C ARG* 3.1 68.5 + - + +
39C LEU* 4.3 14.4 - - + -
40C LEU* 4.4 15.9 - - + -
50C PHE* 3.1 28.8 + - + +
51C ALA* 3.0 25.9 + - + +
53C GLY* 1.3 78.0 - - - +
55C GLY* 1.3 58.0 + - - +
56C THR 3.2 1.2 + - - -
57C VAL* 3.6 7.3 + - - +
257C HIS* 4.3 0.2 - - - -
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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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51C ALA 3.8 2.2 + - - -
52C SER 3.2 8.6 + - - -
53C GLY 3.1 1.4 - - - -
54C LEU* 1.3 80.2 - - - +
56C THR* 1.3 62.4 - - - +
57C VAL 3.7 0.4 - - - -
58C GLU* 4.9 0.2 - - - +
59C LEU* 5.2 0.2 - - - +
179C ASN* 5.5 0.2 - - - -
256C GLY 5.0 1.6 - - - +
257C HIS* 3.6 18.9 + - - -
282C THR* 3.2 31.5 - - - +
283C LYS* 4.1 17.9 + - - -
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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