Contacts of the strand formed by residues 79 - 85 (chain D) 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 THR 79 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D LYS* 3.7 24.6 + - + -
55D ASP* 3.3 20.6 + - - +
74D SER* 4.7 6.6 + - - -
77D GLU* 3.2 19.6 + - - -
78D VAL* 1.3 73.5 + - - +
80D ASN* 1.3 64.0 + - - +
81D TYR* 3.4 34.9 + - + +
95D LEU* 3.4 5.3 - - - -
96D PHE 2.9 40.6 + - - +
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Residues in contact with ASN 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D VAL 3.8 0.2 - - - +
55D ASP* 3.2 39.8 + - - +
78D VAL 4.4 0.2 + - - -
79D THR* 1.3 75.8 - - - +
81D TYR* 1.3 62.0 + - - +
82D THR* 3.7 10.1 + - - -
93D TRP* 3.7 26.6 - - - +
94D ILE 3.4 10.3 - - - +
95D LEU* 3.6 17.9 - - + +
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Residues in contact with TYR 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 5.0 0.2 - - - +
32D MET* 3.5 21.5 - - + -
39D LEU* 4.0 21.3 - - + -
53D VAL 3.7 4.5 - - - +
54D LYS* 3.9 17.8 - - + -
70D PHE* 3.9 20.0 - + + -
73D ILE* 3.2 47.4 - - + +
74D SER 4.5 2.4 + - - -
79D THR* 3.4 32.4 + - + +
80D ASN* 1.3 71.7 - - - +
82D THR* 1.3 60.2 + - - +
83D VAL* 4.2 2.7 + - - +
93D TRP* 3.4 1.6 - - - +
94D ILE* 2.9 43.6 + - + +
96D PHE* 3.5 38.5 + - + -
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Residues in contact with THR 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PHE* 4.0 27.6 - - + -
51D GLU 3.8 0.7 - - - +
52D CYS* 3.5 1.7 - - - -
53D VAL* 2.7 53.4 + - + +
55D ASP 5.7 0.3 + - - -
80D ASN* 3.7 18.2 + - - -
81D TYR* 1.3 72.1 - - - +
83D VAL* 1.3 71.5 + - - +
91D SER* 4.7 4.9 - - - +
92D THR 3.6 12.3 - - - +
93D TRP* 3.7 8.1 - - + +
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Residues in contact with VAL 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ILE* 4.6 14.6 - - + -
30D LEU* 3.6 26.2 - - + -
39D LEU* 3.5 30.5 - - + -
41D TRP* 4.5 10.3 - - + -
50D ILE* 3.5 28.7 - - + -
51D GLU 3.5 6.1 - - - +
52D CYS* 4.5 2.5 - - + -
81D TYR 4.8 0.4 - - - +
82D THR* 1.3 80.3 - - - +
84D ARG* 1.3 66.0 + - - +
85D VAL* 5.7 0.4 - - + -
90D PHE* 5.7 0.2 - - - -
91D SER* 3.3 4.5 - - - -
92D THR* 2.8 36.2 + - + +
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Residues in contact with ARG 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A TYR* 3.6 29.8 - - + +
47A TRP* 5.4 1.2 - - - -
50A ASP* 2.6 32.5 + - - -
59A PHE* 3.8 28.4 - - + +
104A ALA* 3.6 28.3 - - + +
105A SER* 4.3 2.6 - - - +
102B TYR* 3.3 23.5 + - - -
50D ILE* 3.4 5.5 - - - +
51D GLU* 2.9 70.0 + - + +
53D VAL* 5.0 7.1 - - + +
82D THR* 5.3 0.2 - - + -
83D VAL* 1.3 78.0 - - - +
85D VAL* 1.3 66.0 + - - +
90D PHE* 3.4 8.3 - - - +
91D SER* 4.0 7.6 - - - -
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Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A TYR* 3.2 18.0 + - - -
104A ALA* 5.0 0.9 - - - -
26D PRO* 4.9 5.4 - - + -
27D ILE* 4.8 11.9 - - + -
47D VAL* 3.7 22.4 - - + -
49D ASP 3.2 5.4 - - - +
50D ILE* 3.7 26.0 - - + -
83D VAL* 5.7 0.4 - - + -
84D ARG* 1.3 82.2 - - - +
86D ALA* 1.3 69.0 + - - +
88D PRO* 3.1 28.5 - - + +
89D PRO* 3.9 0.2 - - - +
90D PHE* 3.0 35.4 + - + +
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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