Contacts of the strand formed by residues 86 - 91 (chain X) 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 ILE 86 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54H VAL* 4.1 3.6 - - + +
56H VAL* 3.6 26.2 - - + -
80H TYR* 4.1 15.3 - - + -
42X HIS* 3.3 52.0 - - + +
67X ILE* 4.1 22.0 - - + -
68X PRO* 6.4 0.2 - - + -
69X ILE* 5.1 5.2 - - + +
70X TYR 5.1 0.4 - - - +
84X GLY 3.4 0.2 + - - -
85X TRP* 1.3 73.4 - - - +
87X LEU* 1.3 65.2 + - - +
103X LYS 4.0 0.5 - - - +
104X VAL* 3.4 6.2 - - - +
105X TRP* 2.8 64.9 + - + +
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Residues in contact with LEU 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1715A C 3.6 11.9 - - - +
1716A U 3.2 52.5 - - + +
78H ARG* 3.0 28.7 + - - +
80H TYR* 3.6 8.2 + - - -
68X PRO* 5.0 0.9 - - - +
69X ILE* 5.7 1.4 - - - +
70X TYR* 3.9 33.1 - - + +
85X TRP* 4.0 6.8 + - + +
86X ILE* 1.3 74.7 - - - +
88X GLY* 1.3 57.3 + - - +
103X LYS 3.7 1.6 - - - -
104X VAL* 3.4 40.2 - - + -
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Residues in contact with GLY 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1716A U 3.3 12.6 - - - -
78H ARG* 3.6 5.4 - - - -
80H TYR* 3.4 22.2 - - - -
86X ILE* 4.0 2.2 - - - +
87X LEU* 1.3 73.5 - - - +
89X GLN* 1.3 64.1 + - - +
102X LYS* 3.5 2.1 - - - -
103X LYS* 2.8 34.2 + - - +
105X TRP* 5.3 3.0 - - - -
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Residues in contact with GLN 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1716A U 4.9 8.1 + - + -
1718A A 4.2 11.4 + - - -
75H ARG* 3.4 19.9 - - - +
78H ARG* 3.2 28.3 + - + +
79H VAL* 3.4 8.8 - - + +
80H TYR* 2.9 29.6 + - - +
88X GLY* 1.3 79.2 - - - +
90X ILE* 1.3 63.4 + - - +
100X ARG* 3.7 44.3 + - + +
101X LEU* 3.5 6.8 - - - +
102X LYS* 4.1 19.3 - - + +
103X LYS 4.3 0.2 - - - +
105X TRP* 5.1 1.1 - - - -
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Residues in contact with ILE 90 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2745A A 5.5 7.9 - - - -
79H VAL* 4.7 0.4 - - - -
80H TYR 4.0 11.9 - - - +
81H LYS* 5.3 3.1 - - - -
82H LEU* 5.9 1.8 - - + +
89X GLN* 1.3 76.3 - - - +
91X TYR* 1.3 82.0 + - - +
92X ALA* 5.3 1.6 - - - +
94X ASN* 4.2 12.3 - - - +
100X ARG* 3.5 3.8 - - - -
101X LEU* 2.8 42.2 + - + +
103X LYS* 3.3 57.0 - - + +
105X TRP* 4.3 13.7 - - + -
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Residues in contact with TYR 91 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1728A U 2.9 28.9 + - - -
1729A U 2.7 23.9 + - - -
59H TRP* 3.7 31.6 - + + -
60H TRP* 2.8 30.3 + - - -
79H VAL* 3.9 17.5 - - + +
80H TYR 4.7 1.0 + - - -
90X ILE* 1.3 91.3 - - - +
92X ALA* 1.3 67.7 + - - +
93X ASN 3.6 1.1 - - - -
94X ASN* 3.4 15.9 + - - +
95X ASP 3.4 16.8 - - - +
96X LYS* 3.6 30.1 - - + -
98X SER 4.1 0.9 - - - -
99X LYS 3.5 5.6 - - - -
100X ARG* 3.9 22.2 - - + -
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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