Contacts of the helix formed by residues 51 - 56 (chain C) in PDB entry 5WYF
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 LEU 51 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ASP* 2.9 1.4 + - - +
50C LEU* 1.3 79.6 - - - +
52C ALA* 1.3 68.6 + - - +
53C SER 3.9 0.2 - - - +
54C ALA* 3.1 31.2 + - + +
55C SER 3.3 5.9 + - - -
398C VAL* 4.6 7.2 - - + +
399C ILE* 5.3 1.8 - - - -
400C ILE* 3.7 28.5 - - + +
408C ARG* 3.6 37.0 - - - +
410C GLN* 3.0 15.1 - - - +
80D TYR* 3.6 15.7 - - + +
84D TYR* 4.3 9.6 - - + -
85D PHE* 3.6 32.1 - - + -
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Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ASP* 2.8 28.6 + - - -
51C LEU* 1.3 73.9 - - - +
53C SER* 1.3 66.0 + - - +
55C SER 3.1 0.8 + - - +
56C ALA 2.8 17.3 + - - -
57C ILE* 3.1 27.2 + - + +
258C ARG* 3.8 14.6 - - - +
410C GLN 3.3 13.2 + - - +
412C PRO* 3.7 18.4 - - + +
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Residues in contact with SER 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 3.1 2.5 - - - -
52C ALA* 1.3 78.8 - - - +
54C ALA* 1.3 66.6 + - - +
56C ALA* 3.1 13.8 - - - +
57C ILE* 3.6 21.3 - - - -
79D HIS* 3.5 7.8 - - - -
80D TYR* 3.5 33.3 + - - -
81D THR* 2.8 37.7 + - - -
309D THR* 3.7 5.0 - - - +
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Residues in contact with ALA 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 3.1 17.6 + - - +
53C SER* 1.3 77.7 - - - +
55C SER* 1.3 61.4 + - - +
56C ALA 3.4 0.3 + - - -
280C LYS* 3.0 40.6 + - - +
408C ARG* 3.5 24.5 - - - +
1001C ILP 3.6 21.5 - - + +
81D THR* 4.9 0.4 - - + +
84D TYR* 4.1 11.4 - - + -
309D THR* 4.6 0.9 - - + -
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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
----------------------------------------------------------
51C LEU 3.3 6.6 + - - -
52C ALA 3.1 5.0 + - - -
54C ALA* 1.3 77.0 - - - +
56C ALA* 1.3 54.4 + - - +
57C ILE 3.5 1.6 - - - -
58C ASN* 3.3 4.8 + - - +
252C VAL 4.8 0.7 - - - +
253C ASN* 3.2 28.1 + - - +
258C ARG* 2.5 42.8 + - - +
280C LYS* 3.7 5.4 - - - +
281C SER* 2.8 25.8 + - - -
410C GLN* 3.8 15.3 + - - -
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Residues in contact with ALA 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ALA 2.8 2.3 + - - +
53C SER* 3.1 25.4 - - - +
54C ALA 3.3 0.2 - - - -
55C SER* 1.3 76.8 - - - +
57C ILE* 1.3 61.9 + - + +
280C LYS* 3.7 19.1 - - + +
281C SER* 3.2 27.8 - - - +
284C SER* 3.4 20.1 - - - -
285C GLY* 3.4 8.0 + - - -
79D HIS* 4.4 0.9 - - + -
309D THR* 4.2 10.1 - - + -
310D THR* 5.6 0.2 - - + -
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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
------------------------------------------------------------
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