Contacts of the strand formed by residues 81 - 89 (chain D) in PDB entry 4J1R
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 LEU 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72D GLN* 3.3 28.3 - - - +
73D ALA 3.4 8.3 - - - +
74D LYS* 3.7 26.9 - - + -
79D GLY 4.6 2.2 - - - +
80D GLU* 1.3 75.3 - - - +
82D VAL* 1.3 65.4 + - - +
113D ARG* 4.2 7.1 + - - -
133D ASP* 4.6 0.3 - - - +
134D TYR* 3.6 41.9 + - + +
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Residues in contact with VAL 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D TYR* 5.5 0.4 - - + -
72D GLN* 3.5 5.0 - - - +
73D ALA* 3.0 45.4 + - + +
75D LEU* 4.0 32.5 - - + -
81D LEU* 1.3 79.2 - - - +
83D ALA* 1.3 59.2 + - - +
84D ILE* 4.4 14.1 - - + -
113D ARG* 3.8 21.5 - - + +
131D VAL* 3.7 27.6 - - + -
132D LEU 3.2 14.4 - - - +
134D TYR* 3.5 11.8 - - - +
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Residues in contact with ALA 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ILE* 4.5 1.3 - - + -
70D VAL* 4.3 12.3 - - + -
71D TYR 3.2 9.6 - - - +
72D GLN* 4.6 0.7 - - - +
82D VAL* 1.3 75.2 - - - +
84D ILE* 1.3 63.0 + - - +
85D LYS 4.0 0.7 - - - +
130D LEU 3.2 2.4 - - - +
131D VAL* 3.4 3.6 - - - -
132D LEU* 2.8 37.4 + - + +
133D ASP 4.5 0.4 - - - +
134D TYR* 3.8 6.8 - - + +
502D I5R 4.1 37.5 - - + +
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Residues in contact with ILE 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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56D TYR* 3.9 39.5 - - + +
59D THR* 5.5 0.4 - - + -
70D VAL* 3.3 4.4 - - - -
71D TYR* 2.8 57.3 + - + +
73D ALA* 4.0 16.4 - - + -
82D VAL* 4.4 13.2 - - + -
83D ALA* 1.3 77.2 - - - +
85D LYS* 1.3 60.8 + - - +
86D LYS 3.4 2.1 + - - -
116D PHE* 4.4 8.3 - - + -
129D ASN* 3.8 34.8 - - + +
130D LEU 3.2 5.4 - - - +
131D VAL* 4.5 10.1 - - + -
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Residues in contact with LYS 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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67D PHE* 3.7 45.5 - - + +
69D VAL 3.5 3.6 - - - -
70D VAL* 4.1 9.6 - - + +
83D ALA 4.0 1.2 - - - -
84D ILE* 1.3 70.4 - - - +
86D LYS* 1.3 60.8 + - - +
87D VAL* 3.6 17.8 + - + +
97D GLU* 3.1 37.7 + - - +
128D LEU 3.3 5.9 - - - +
129D ASN* 4.4 0.9 - - - -
130D LEU* 2.9 46.6 + - + +
132D LEU* 4.7 9.2 - - + +
200D ASP* 3.4 24.0 + - - -
202D GLY* 3.8 7.5 - - - -
502D I5R 4.3 15.7 + - + +
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Residues in contact with LYS 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D PHE* 3.5 0.5 - - - +
68D GLY* 3.4 8.8 - - - -
69D VAL* 2.7 41.1 + - + +
71D TYR* 4.0 32.2 + - + +
84D ILE 3.4 1.0 + - - -
85D LYS* 1.3 69.4 - - - +
87D VAL* 1.3 62.2 + - - +
88D LEU 4.2 0.4 + - - -
118D SER* 3.6 20.3 + - - -
119D SER 5.3 2.0 + - - -
127D TYR* 3.6 43.6 - - + -
128D LEU 3.6 2.5 - - - -
129D ASN* 3.6 20.6 - - - +
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Residues in contact with VAL 87 (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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67D PHE* 3.5 21.1 - - + +
85D LYS* 3.8 38.4 - - + +
86D LYS* 1.3 78.1 - - - +
88D LEU* 1.3 75.5 + - - +
89D GLN* 3.3 1.3 + - - +
95D ASN* 4.3 19.7 - - - +
97D GLU* 5.0 4.7 - - - +
127D TYR* 3.9 2.7 - - - -
128D LEU* 2.7 48.3 + - + +
130D LEU* 5.4 5.6 - - + -
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Residues in contact with LEU 88 (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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67D PHE 3.7 9.3 + - - +
87D VAL* 1.3 82.9 - - - +
89D GLN* 1.3 66.7 + - - +
125D GLU* 3.5 33.2 - - + -
126D VAL 3.3 18.4 - - - +
127D TYR* 3.4 32.1 - - + +
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Residues in contact with GLN 89 (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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87D VAL* 4.1 7.8 - - - +
88D LEU* 1.3 86.7 - - - +
90D ASP* 1.3 73.4 + - - +
91D LYS* 4.0 1.7 + - - -
93D PHE* 2.5 33.4 + - - +
94D LYS 3.8 10.1 + - - -
95D ASN* 3.4 31.9 + - + +
117D TYR* 5.3 7.4 - - + -
125D GLU* 5.4 0.3 - - - -
126D VAL* 2.7 41.9 + - + +
128D LEU* 4.3 15.0 - - + +
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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