Contacts of the strand formed by residues 46 - 51 (chain C) in PDB entry 4JHN
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 HIS 46 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C GLY* 2.8 25.0 + - - -
44C ASP 3.8 0.2 - - - -
45C GLU* 1.3 83.0 + - - +
47C SER* 1.3 62.8 + - - +
58C MET* 3.8 18.8 - - + -
59C PHE 3.5 13.7 - - - +
60C GLY* 4.2 0.7 - - - -
61C SER 3.7 8.5 - - - +
66C GLN* 3.6 27.3 + - + +
67C LEU* 3.6 10.3 - - + -
94C CYS* 3.4 18.6 - - + +
95C GLY 3.2 27.1 + - - -
96C ARG 4.6 2.4 + - - -
98C HIS 3.4 12.7 + - - -
99C THR* 2.7 28.7 + - - -
360C HIS* 3.1 10.0 + - - -
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Residues in contact with SER 47 (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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20C SER* 5.0 0.5 + - - -
41C SER 3.4 10.5 - - - -
42C CYS* 3.6 3.5 - - - -
46C HIS* 1.3 71.5 - - - +
48C ALA* 1.3 60.1 + - - +
58C MET* 3.4 9.9 - - - +
59C PHE* 2.9 64.1 + - - +
94C CYS* 4.1 4.9 - - - -
360C HIS* 2.9 31.4 + - - -
362C VAL* 3.7 9.4 - - - +
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Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C HIS* 4.6 0.4 - - - -
40C LEU* 3.6 4.2 - - - +
41C SER* 2.8 33.6 + - - +
47C SER* 1.3 74.0 - - - +
49C VAL* 1.3 67.1 + - - +
50C VAL 4.2 0.4 - - - -
56C LEU* 4.2 1.3 - - + -
57C TYR 3.4 4.9 - - - -
58C MET* 3.5 20.9 - - - -
92C ALA* 3.9 24.7 - - + -
94C CYS* 3.6 17.2 - - - -
99C THR* 5.1 0.2 - - + -
362C VAL* 5.9 0.3 - - - +
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Residues in contact with VAL 49 (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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14C VAL* 4.9 2.5 - - + -
30C PHE* 4.3 15.0 - - + -
32C PHE* 3.9 20.4 - - + -
37C PRO* 3.9 28.9 - - + -
39C HIS 3.6 2.5 - - - -
40C LEU* 3.7 16.6 - - + -
47C SER* 5.9 0.2 - - - -
48C ALA* 1.3 78.3 - - - +
50C VAL* 1.3 67.8 + - - +
51C THR* 4.1 1.1 + - + -
55C LYS 3.7 1.2 - - - +
56C LEU* 3.5 3.4 - - - +
57C TYR* 2.8 49.6 + - + +
59C PHE* 4.1 22.7 - - + -
362C VAL* 5.0 1.8 - - + -
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Residues in contact with VAL 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C PRO* 3.5 4.3 - - - +
38C VAL* 2.8 29.0 + - + -
39C HIS* 2.9 24.1 + - + +
48C ALA 5.7 0.2 - - - -
49C VAL* 1.3 75.9 - - - +
51C THR* 1.3 69.1 + - - +
55C LYS 3.4 4.7 - - - +
56C LEU* 3.9 18.6 - - + -
89C VAL* 3.5 33.0 - - + +
90C LYS* 3.6 14.1 - - - +
91C LEU* 3.9 26.5 - - - -
92C ALA* 3.9 7.2 - - + +
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Residues in contact with THR 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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32C PHE* 3.9 24.5 - - + -
35C ASP* 2.7 28.7 + - - +
36C VAL 3.3 8.5 - - - +
38C VAL* 3.6 10.2 - - - +
49C VAL* 4.4 2.5 - - + -
50C VAL* 1.3 78.0 - - - +
52C GLY* 1.3 56.3 + - - +
53C ASN 3.6 1.4 + - - -
54C ASN* 2.8 27.0 + - - -
55C LYS* 3.0 25.4 + - - +
57C TYR* 3.7 31.4 - - + -
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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