Contacts of the strand formed by residues 80 - 86 (chain L) in PDB entry 3J7Y
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 GLN 80 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2615A A 5.1 0.7 - - - +
46L LEU* 4.5 19.4 - - + +
75L LEU 3.3 0.7 - - - +
76L ALA* 3.7 3.3 - - - -
77L ILE* 2.7 43.2 + - + +
78L LYS* 3.2 4.5 + - + -
79L GLY* 1.3 74.9 - - - +
81L LYS* 1.3 61.4 + - - +
82L LYS* 3.9 32.3 - - + +
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Residues in contact with LYS 81 (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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2615A A 3.3 39.9 + - - +
2616A A 5.4 1.4 + - - -
3047A G 3.5 11.2 + - - +
3048A A 3.2 39.9 - - - -
58L ILE* 3.6 24.2 - - + -
74L LEU* 3.4 18.8 - - + +
75L LEU 3.3 5.6 - - - -
79L GLY 4.7 4.2 + - - +
80L GLN* 1.3 76.9 - - - +
82L LYS* 1.3 60.2 + - - +
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Residues in contact with LYS 82 (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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46L LEU* 3.7 30.9 - - + +
74L LEU* 3.4 4.3 - - - +
75L LEU* 2.8 37.0 + - + +
77L ILE* 5.4 2.5 - - + -
80L GLN* 3.9 23.3 - - + +
81L LYS* 1.3 75.5 - - - +
83L LYS* 1.3 65.9 + - - +
107L LEU* 4.2 16.8 - - + -
108L ILE 4.2 11.4 - - - +
109L GLU* 4.1 13.3 - - - +
115L VAL* 3.4 33.9 - - + +
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Residues in contact with LYS 83 (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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3049A U 4.9 2.5 - - - -
61L TYR* 3.5 33.5 + - + +
72L GLN* 4.1 20.2 + - - +
73L ILE 3.3 6.5 - - - +
74L LEU* 4.4 5.8 - - + -
82L LYS* 1.3 80.2 - - - +
84L ALA* 1.3 62.6 + - - +
107L LEU* 3.7 2.3 - - - +
108L ILE* 2.8 46.4 + - + +
110L ASP* 3.5 50.3 + - - +
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Residues in contact with ALA 84 (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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72L GLN* 3.2 7.4 - - - +
73L ILE* 2.8 48.3 + - + +
75L LEU* 3.8 17.5 - - + -
83L LYS* 1.3 79.1 - - - +
85L LEU* 1.3 57.6 + - - +
105L VAL* 3.3 30.1 - - + -
106L VAL 3.3 9.2 - - - +
107L LEU* 4.3 1.3 - - - -
108L ILE* 4.2 5.5 - - - +
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Residues in contact with LEU 85 (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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70L GLY* 3.2 36.6 - - - +
71L ASP 4.1 2.9 - - - +
72L GLN* 4.7 2.2 - - + +
84L ALA* 1.3 70.7 - - - +
86L ILE* 1.3 71.0 + - - +
87L VAL* 3.9 11.4 - - + +
105L VAL* 3.4 5.8 - - - +
106L VAL* 2.8 41.6 + - + +
108L ILE* 3.6 24.8 - - + +
127L LEU* 4.3 9.4 - - + -
134L TYR* 3.6 36.3 - - + +
137L VAL* 3.8 28.9 - - + -
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Residues in contact with ILE 86 (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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32L ILE* 3.5 44.0 - - + -
67L GLY* 4.2 16.2 - - - -
68L LYS* 3.9 18.4 - - - +
69L VAL* 3.7 7.0 - - + +
70L GLY 3.3 21.0 + - - -
71L ASP 3.2 19.5 + - - +
72L GLN 4.7 1.1 - - - +
73L ILE* 3.6 47.3 - - + -
85L LEU* 1.3 74.2 - - - +
87L VAL* 1.3 63.5 + - - +
88L GLY 3.9 11.7 - - - +
89L HIS* 4.9 1.6 - - + -
104L ASN 3.9 3.4 - - - +
105L VAL* 4.3 0.9 - - + -
127L LEU* 4.6 0.3 - - - +
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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