Contacts of the strand formed by residues 51 - 55 (chain L) 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 LYS 51 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110H TRP* 4.9 0.4 - - - -
42L TYR* 3.4 3.6 - - - -
43L GLN* 2.8 44.7 + - + +
49L PRO 3.4 3.5 + - - +
50L PRO* 1.3 73.7 - - - +
52L PRO* 1.3 81.8 - - + +
53L LEU* 3.9 16.8 - - + +
63L GLY 5.8 3.9 + - - -
64L VAL* 5.0 9.4 - - - -
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Residues in contact with PRO 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H PHE 3.9 12.3 - - - +
108H ALA 3.6 20.2 - - - +
109H TYR* 5.7 0.2 - - - -
110H TRP* 4.2 9.2 - - + +
41L TRP 3.9 0.9 - - - +
42L TYR* 3.6 22.0 - - + -
51L LYS* 1.3 94.6 - - + +
53L LEU* 1.3 60.4 + - - +
55L TYR* 3.1 37.0 - - + +
61L GLU* 3.8 20.1 - - + +
64L VAL* 4.5 2.4 - - - +
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Residues in contact with LEU 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L TRP* 2.8 20.6 + - + +
43L GLN* 3.5 40.8 - - + +
51L LYS* 3.5 17.4 + - + +
52L PRO* 1.3 76.9 - - - +
54L ILE* 1.3 69.7 + - + +
60L ARG 4.0 0.2 - - - -
61L GLU* 3.1 27.2 + - - +
64L VAL* 3.9 29.2 - - + +
68L PHE* 3.6 40.8 - - + -
79L LEU* 4.9 7.9 - - + -
92L TYR* 4.2 7.9 - - + -
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Residues in contact with ILE 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L THR* 3.2 10.4 - - - +
41L TRP* 2.7 54.4 + - + -
53L LEU* 1.3 89.0 - - + +
55L TYR* 1.3 65.5 + - - +
57L ALA* 3.4 36.6 - - - +
58L SER* 3.6 6.1 - - - +
59L THR 3.4 8.5 - - - +
60L ARG* 3.8 29.6 - - + -
64L VAL* 5.3 0.2 - - + -
68L PHE* 4.7 5.2 - - + +
69L SER* 4.6 4.7 - - - -
70L GLY 4.2 14.8 - - - +
79L LEU* 4.2 13.0 - - + -
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Residues in contact with TYR 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H HIS* 4.4 3.3 - + - -
106H TRP* 3.5 66.6 - + + -
107H PHE 5.4 0.2 - - - -
108H ALA* 3.7 19.8 + - - +
39L LEU 4.0 2.5 - - - -
40L THR* 3.7 27.4 - - + -
42L TYR* 5.2 1.6 - - - -
52L PRO* 3.1 32.3 - - + +
54L ILE* 1.3 72.4 - - - +
56L TRP* 1.3 74.5 + - + +
57L ALA 3.1 3.5 + - - -
58L SER 3.6 0.3 + - - -
59L THR* 2.9 33.7 + - + +
61L GLU* 3.1 41.6 - - + -
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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