Contacts of the strand formed by residues 50 - 54 (chain C) in PDB entry 4JZJ
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 ILE 50 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ILE* 3.5 17.9 - - + -
41C TRP* 3.4 43.3 - - + +
43C LEU* 4.2 7.0 - - + -
47C VAL* 4.8 3.6 - - + -
49C ASP* 1.3 86.6 + - - +
51C GLU* 1.3 65.3 + - - +
61C PRO* 3.7 1.0 - - - +
62C ALA* 2.9 32.6 + - + +
65C ASN* 3.5 26.9 + - + +
83C VAL* 3.4 28.5 - - + -
84C ARG 3.6 3.8 - - - +
85C VAL* 4.1 14.6 - - + -
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Residues in contact with GLU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ASP 4.2 0.6 + - - +
50C ILE* 1.3 75.8 - - - +
52C CYS* 1.3 64.4 + - - +
53C VAL* 4.2 3.2 + - + +
59C SER* 2.9 24.9 + - - +
60C MET 3.5 10.5 - - - +
61C PRO* 4.3 0.2 - - - -
82C THR 3.8 0.5 - - - +
83C VAL* 3.3 3.3 - - - +
84C ARG* 3.0 64.9 + - + +
103H ARG* 4.3 17.6 + - - +
104H ALA* 4.6 5.8 + - + +
105H SER* 3.9 11.9 + - - -
98L TYR 5.9 0.4 - - - -
102L TYR* 2.1 37.8 + - - -
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Residues in contact with CYS 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 4.2 5.8 - - + -
41C TRP* 3.5 25.6 - - - -
50C ILE* 4.6 0.2 - - - -
51C GLU* 1.3 74.2 - - - +
53C VAL* 1.3 61.9 + - - +
59C SER* 3.0 3.9 - - - -
60C MET* 2.9 33.8 + - + +
68C CYS* 2.0 50.9 - - + -
70C PHE* 4.1 15.2 - - + -
82C THR 3.3 6.5 - - - +
83C VAL* 3.7 10.3 - - + -
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Residues in contact with VAL 53 (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* 4.5 13.9 - - + +
52C CYS* 1.3 79.6 - - - +
54C LYS* 1.3 61.7 + - - +
55C ASP 3.8 0.7 + - - -
56C ALA* 4.0 22.2 - - - +
58C TYR 3.8 9.2 - - - +
59C SER* 3.7 14.6 - - - -
70C PHE* 4.9 2.8 - - - -
81C TYR* 3.4 7.3 - - - +
82C THR* 2.6 56.5 + - + +
84C ARG* 5.1 9.6 - - + +
59H PHE* 5.5 5.8 - - + -
100L TYR* 4.7 11.7 - - + -
102L TYR* 5.1 2.7 - - - +
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Residues in contact with LYS 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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52C CYS 4.3 0.4 + - - -
53C VAL* 1.3 70.3 - - - +
55C ASP* 1.3 85.7 + - - +
56C ALA 3.3 1.3 - - - -
57C ASP* 3.1 41.7 + - + +
58C TYR* 2.9 48.5 + - + +
59C SER* 4.5 0.2 - - - +
70C PHE* 3.7 18.8 - - + -
79C THR* 3.6 24.2 - - + -
80C ASN 4.0 1.8 - - - -
81C TYR* 3.8 23.8 - - + +
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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