Contacts of the helix formed by residues 47 - 52 (chain C) in PDB entry 1SZU
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 ALA 47 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C ASP* 2.8 1.9 + - - +
46C PHE* 1.3 80.9 - - - +
48C GLY* 1.3 53.3 + - - +
49C GLY 4.4 0.2 - - - +
50C ILE* 2.7 31.5 + - - +
51C ALA 3.4 4.7 + - - -
386C ILE* 4.0 17.3 - - + +
388C LEU* 3.7 31.9 - - + -
400C LEU* 3.5 12.1 - - - +
1029C EDO 3.0 18.8 - - - +
80D VAL* 4.4 1.8 - - + -
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Residues in contact with GLY 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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45C ASP* 2.9 20.8 + - - -
46C PHE 3.8 0.4 - - - -
47C ALA* 1.3 75.9 - - - +
49C GLY* 1.3 61.0 + - - +
51C ALA 4.1 0.7 - - - -
52C VAL* 3.0 5.0 + - - -
53C LEU* 2.9 45.6 + - - +
400C LEU 3.7 13.6 + - - -
402C PRO* 4.5 6.3 - - - -
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Residues in contact with GLY 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C GLY* 1.3 72.3 - - - -
50C ILE* 1.3 70.2 + - - +
52C VAL* 3.2 10.2 - - - +
1029C EDO 2.9 19.4 + - - -
75D HIS* 3.0 28.4 + - - -
76D THR 3.2 27.8 - - - -
77D CYS* 3.8 3.2 - - - +
297D THR* 4.1 1.2 - - - +
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Residues in contact with ILE 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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47C ALA 2.7 11.7 + - - -
49C GLY* 1.3 80.8 - - - +
51C ALA* 1.3 67.8 + - - +
52C VAL* 3.1 4.8 + - - +
211C GLU* 4.0 21.5 - - - +
242C GLN* 4.6 2.7 - - - +
268C LYS* 3.3 26.2 - - - +
388C LEU* 3.8 15.7 - - + +
398C ARG* 4.1 15.0 - - - +
400C LEU* 4.0 4.9 - - + -
1029C EDO 4.6 0.2 + - - -
1468C PLP 5.7 0.7 - - + -
77D CYS* 3.5 26.0 - - - -
79D GLN* 4.8 7.9 - - - +
80D VAL* 3.7 22.0 - - + -
297D THR* 5.3 4.7 - - + +
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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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47C ALA 3.4 8.5 + - - -
48C GLY 3.7 0.8 + - - -
50C ILE* 1.3 74.8 - - - +
52C VAL* 1.3 54.1 + - - +
53C LEU 3.5 1.6 - - - +
54C ASN* 4.1 11.3 + - - +
241C ALA 5.1 0.3 - - - +
242C GLN* 3.6 37.3 - - + +
247C ARG* 5.2 1.8 - - - -
268C LYS* 3.6 6.3 - - + +
269C SER* 2.7 30.6 + - - -
400C LEU* 3.6 27.5 - - + +
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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
----------------------------------------------------------
48C GLY 3.0 3.7 + - - +
49C GLY 3.2 11.2 - - - +
50C ILE 3.5 5.4 - - - +
51C ALA* 1.3 76.1 - - - +
53C LEU* 1.3 57.5 + - - +
268C LYS* 3.6 21.1 - - + +
269C SER* 3.3 24.2 + - - +
272C GLY* 3.7 3.1 - - - -
273C GLY* 3.6 29.5 + - - +
75D HIS* 3.5 30.3 - - + +
297D THR* 3.2 34.1 - - + -
298D TYR* 4.3 6.1 - - + -
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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