Contacts of the helix formed by residues 53 - 58 (chain C) in PDB entry 6BAA
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 GLY 53 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C GLU* 3.3 4.9 - - - +
52C GLN* 1.3 79.9 - - - +
54C ARG* 1.3 59.8 + - - +
55C PHE* 2.9 8.8 + - - +
56C LEU* 3.1 16.2 + - - +
57C GLN* 3.1 18.7 + - - +
130G SER* 4.0 13.4 + - - -
131G ASN 3.2 12.2 + - - -
132G PHE* 3.9 13.9 - - - -
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Residues in contact with ARG 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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50C ARG 4.9 0.8 + - - -
52C GLN* 3.0 44.4 - - + +
53C GLY* 1.3 76.7 - - - +
55C PHE* 1.3 62.4 + - - +
56C LEU 3.4 0.5 + - - -
57C GLN* 3.3 26.3 - - - +
58C ASP* 3.4 22.2 + - - +
176D ARG 5.3 1.7 - - - +
179D GLU* 2.9 48.9 + - + +
180D THR* 4.5 9.6 - - + +
182D ILE* 4.2 11.3 - - - +
205D LEU* 3.8 26.1 - - - +
206D ARG* 4.3 9.7 + - - +
401D ATP 4.3 8.7 + - - -
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Residues in contact with PHE 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 GLU* 5.0 20.2 - - + +
53C GLY* 2.9 4.4 - - - +
54C ARG* 1.3 81.2 - - - +
56C LEU* 1.3 77.6 + - + +
58C ASP* 4.0 5.2 - - - +
62C THR* 3.6 26.4 + - + -
206D ARG* 3.2 56.5 - - - +
53G SER* 3.8 32.1 - - - -
56G SER* 6.0 0.7 - - - -
57G LYS* 5.0 15.9 - - + -
60G ILE* 5.9 6.1 - - + -
130G SER* 5.2 4.5 - - - +
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Residues in contact with LEU 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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53C GLY* 3.1 9.3 + - - +
55C PHE* 1.3 103.0 - - + +
57C GLN* 1.3 66.3 + - - +
58C ASP 3.1 2.4 + - - -
59C VAL* 2.9 26.0 + - - +
62C THR* 5.2 2.7 - - + -
46G ILE* 5.2 11.4 - - + +
49G ILE* 4.6 20.6 - - + -
50G GLY* 5.1 13.5 - - - +
53G SER* 5.2 0.2 - - - +
126G ASN 5.9 2.7 - - - +
130G SER* 5.8 10.5 - - - +
132G PHE* 5.7 11.2 - - + -
135G LEU* 5.0 15.7 - - + -
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Residues in contact with GLN 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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52C GLN 5.4 1.3 - - - -
53C GLY 3.1 15.7 + - - +
54C ARG* 3.3 31.9 + - + +
56C LEU* 1.3 77.1 - - - +
58C ASP* 1.3 53.1 + - - +
59C VAL* 2.8 19.7 + - - +
60C PHE* 5.8 0.9 - - - -
176D ARG* 4.2 32.1 + - - +
179D GLU* 4.0 9.8 - - - +
132G PHE* 3.0 38.4 - - + -
134G LYS* 4.4 16.6 - - - +
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Residues in contact with ASP 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 ARG 3.4 12.6 + - - +
55C PHE 4.0 4.2 - - - +
56C LEU 3.1 3.7 - - - -
57C GLN* 1.3 75.0 - - - +
59C VAL* 1.3 55.3 + - - +
60C PHE* 4.1 1.7 + - - +
61C THR* 2.6 44.0 + - - +
62C THR* 2.7 30.1 + - - +
176D ARG* 4.1 30.3 - - + +
177D ARG* 3.1 25.5 + - - +
180D THR* 5.2 2.2 - - + +
206D ARG* 5.6 3.5 - - - +
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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