Contacts of the strand formed by residues 56 - 62 (chain C) in PDB entry 2H5X
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 SER 56 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C ILE 4.4 1.6 + - - -
52C VAL* 3.9 1.4 - - - +
53C ARG* 2.9 53.1 + - - +
54C GLU 3.5 1.6 - - - -
55C ASP* 1.3 82.5 - - - +
57C MET* 1.3 62.0 + - - +
58C THR* 4.1 10.8 - - - -
52D VAL* 3.9 10.3 - - - +
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Residues in contact with MET 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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57A MET* 5.0 0.9 - - + -
57B MET* 3.4 37.0 - - + +
50C MET* 4.6 7.6 - - + +
51C ILE 3.5 4.0 - - - -
52C VAL* 4.3 24.2 - - + -
56C SER* 1.3 74.7 - - - +
58C THR* 1.3 60.1 + - - +
1D MET* 3.1 50.4 + - - +
50D MET* 4.0 16.6 - - + -
52D VAL* 3.8 25.7 - - + +
57D MET* 4.2 22.7 - - - +
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Residues in contact with THR 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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27C ARG* 6.2 0.2 - - - -
29C ASN* 3.4 20.0 - - - +
49C ALA 3.7 0.9 - - - +
50C MET* 3.5 3.4 - - - -
51C ILE* 2.8 43.3 + - - +
56C SER* 4.5 8.7 + - - -
57C MET* 1.3 78.7 + - - +
59C LEU* 1.3 79.7 + - - +
60C TYR* 3.6 26.0 + - + +
1D MET* 5.0 1.6 - - - +
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Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C ILE* 3.9 6.1 - - + -
5C VAL* 4.2 14.1 - - + -
26C TYR* 3.9 29.4 - - + -
27C ARG 3.6 16.0 + - - +
28C VAL* 4.3 9.2 - - + -
29C ASN* 3.3 18.6 + - - -
48C THR* 3.9 22.4 - - + +
49C ALA 3.8 0.7 - - - -
50C MET* 3.7 36.1 - - + -
58C THR* 1.3 81.3 - - - +
60C TYR* 1.3 69.0 + - - +
1D MET* 3.9 29.4 - - + +
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Residues in contact with TYR 60 (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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28C VAL* 3.8 1.8 - - - -
29C ASN* 3.4 28.0 - - + +
48C THR* 2.9 4.3 - - - -
49C ALA* 2.8 47.4 + - + +
51C ILE* 3.4 27.6 - - + -
58C THR* 3.6 28.5 + - + +
59C LEU* 1.3 77.9 - - - +
61C GLY* 1.3 61.4 + - - +
62C PHE* 3.4 20.4 - - + -
71C PHE* 3.7 12.3 - + + -
82C PRO* 3.1 27.4 - - + +
83C ARG* 4.9 3.1 + - - +
86C MET* 3.9 29.4 - - + -
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Residues in contact with GLY 61 (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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28C VAL* 3.0 25.4 - - - +
29C ASN 3.1 10.5 + - - +
30C ALA* 4.0 11.0 - - - +
31C THR 5.1 0.2 + - - -
34C THR* 4.6 1.6 + - - +
46C LEU* 3.6 14.8 - - - -
47C ILE 3.2 6.3 - - - -
48C THR* 3.9 2.0 - - - -
60C TYR* 1.3 71.7 - - - +
62C PHE* 1.3 77.5 + - - -
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Residues in contact with PHE 62 (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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31C THR* 5.4 3.8 - - + -
34C THR* 4.5 3.6 - - - -
46C LEU* 3.3 13.5 - - - +
47C ILE* 2.7 39.4 + - - +
49C ALA* 4.4 0.4 - - + -
60C TYR* 3.4 22.7 - - + -
61C GLY* 1.3 81.1 - - - -
63C PRO* 1.3 73.9 - - + +
64C ASP 3.3 15.2 + - - +
67C THR* 3.7 19.1 - - + -
68C ARG* 3.5 25.6 - - + +
71C PHE* 3.3 37.0 - + + -
86C MET* 3.8 20.0 - - + -
89C LEU* 3.5 24.9 - - + -
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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