Contacts of the helix formed by residues 56 - 63 (chain R) in PDB entry 5A31
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 ASN 56 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54R GLY 2.8 18.0 - - - +
55R ALA* 1.3 69.2 - - - +
57R TRP* 1.3 71.2 + - - +
58R SER* 3.2 3.4 - - - +
59R VAL* 3.5 37.6 - - + +
60R ASN* 2.9 36.0 + - - +
100R LEU 5.4 4.8 + - - -
101R GLY* 5.8 2.8 - - - +
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Residues in contact with TRP 57 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407C GLN* 4.1 20.7 - - + +
410C GLU* 4.2 22.0 - - + -
411C ILE* 3.1 38.7 - - + +
441C GLU* 5.1 3.8 - - - -
50R PRO* 3.9 9.4 - - + -
51R SER 4.0 21.1 - - - -
52R ARG* 4.1 28.0 - - + +
55R ALA* 3.1 23.0 + - + -
56R ASN* 1.3 78.2 - - - +
58R SER* 1.3 65.4 + - - +
60R ASN* 4.2 0.7 - - - +
61R PHE* 3.1 25.5 + - - +
127R LEU* 4.0 10.8 - - + +
128R PHE* 3.4 46.9 - + + -
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Residues in contact with SER 58 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1191A LEU* 3.4 13.0 - - - +
411C ILE 5.3 4.3 - - - -
413C LYS* 4.1 28.9 + - - +
56R ASN* 4.7 2.9 - - - +
57R TRP* 1.3 79.6 - - - +
59R VAL* 1.3 77.5 + - - +
61R PHE* 3.7 4.6 - - - +
62R HIS* 3.1 18.4 + - - +
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Residues in contact with VAL 59 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190A THR* 5.5 10.8 - - + -
1191A LEU* 3.7 12.8 - - + -
56R ASN* 3.5 32.4 + - + +
57R TRP 3.3 0.4 - - - -
58R SER* 1.3 88.3 + - - +
60R ASN* 1.3 72.3 + - - +
62R HIS* 3.0 14.6 + - - +
63R ARG* 3.1 17.3 + - - +
99R LEU 5.6 0.7 - - - +
100R LEU* 3.7 47.3 - - + +
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Residues in contact with ASN 60 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55R ALA* 5.0 4.3 - - - +
56R ASN* 2.9 36.5 + - - +
57R TRP* 5.6 0.2 - - - -
59R VAL* 1.3 93.0 - - - +
61R PHE* 1.3 56.3 + - - +
63R ARG* 3.4 17.4 + - - +
64R ILE* 3.1 29.5 + - - +
100R LEU 5.3 2.0 + - - -
125R LYS 5.2 4.2 + - - +
126R GLY* 4.5 7.9 - - - -
127R LEU* 3.8 31.4 + - + +
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Residues in contact with PHE 61 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C MET* 4.0 15.0 - - + -
379C LYS* 2.8 66.2 + - + +
381C THR* 5.1 2.0 - - - -
411C ILE* 3.3 35.9 - - + -
412C LEU* 4.1 17.5 - - + -
413C LYS* 5.6 5.8 - - - -
296O TYR* 3.8 28.7 - + - -
57R TRP 3.1 19.6 + - - +
58R SER* 3.7 3.8 - - - +
60R ASN* 1.3 76.5 - - - +
62R HIS* 1.3 62.5 + - - +
64R ILE* 3.4 9.7 - - + +
127R LEU* 3.4 24.8 - - + +
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Residues in contact with HIS 62 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1191A LEU* 3.1 63.0 + - + +
1192A ASN* 5.5 2.2 - - - -
1194A HIS* 4.6 15.1 + + - -
1195A ASP* 4.7 14.1 - - + +
379C LYS* 3.5 17.6 + - - +
413C LYS* 6.0 1.1 - - - +
296O TYR* 5.9 0.4 + - - -
58R SER 3.1 5.7 + - - +
59R VAL 3.0 4.7 + - - +
61R PHE* 1.3 79.4 - - - +
63R ARG* 1.3 63.7 + - + +
64R ILE 3.2 1.5 + - - -
65R ASN 3.6 11.1 - - - +
100R LEU* 5.0 6.1 - - + -
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Residues in contact with ARG 63 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59R VAL* 3.1 29.3 + - - +
60R ASN* 3.7 17.8 - - - +
62R HIS* 1.3 80.5 - - + +
64R ILE* 1.3 63.4 + - - +
65R ASN 3.3 3.4 - - - -
66R GLU* 3.3 37.3 + - - +
96R LYS* 4.0 21.8 - - - +
100R LEU* 4.1 26.2 + - + +
102R ALA* 3.9 27.5 - - - +
104R ILE* 4.2 7.9 - - - +
125R LYS* 5.2 13.3 + - - +
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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