Contacts of the helix formed by residues 86 - 93 (chain Y) 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 THR 86 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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809 GLU* 3.9 31.1 + - - +
819 SER* 6.0 0.2 - - - +
839 GLU* 5.2 6.6 + - - +
84Y ALA 3.3 6.6 + - - -
85Y TRP* 1.3 76.6 - - - +
87Y CYS* 1.3 75.1 + - - +
88Y GLN* 3.9 6.2 + - + +
89Y GLN* 3.5 43.5 + - + +
90Y LEU* 3.2 20.5 + - - +
141Y ALA* 4.8 0.7 - - - -
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Residues in contact with CYS 87 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839 GLU* 4.5 23.3 - - + +
85Y TRP 4.1 0.4 + - - -
86Y THR* 1.3 81.4 + - - +
88Y GLN* 1.3 51.7 + - - +
90Y LEU* 3.2 7.5 + - - +
91Y ARG* 2.7 55.2 + - - +
141Y ALA* 4.5 12.7 - - - +
144Y LYS* 3.5 32.8 - - - +
145Y VAL* 4.0 6.2 - - + +
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Residues in contact with GLN 88 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809 GLU* 5.2 1.1 - - - +
819 SER* 3.5 25.1 + - - +
829 GLU 3.0 22.4 - - - +
839 GLU* 3.8 13.9 - - + +
849 THR* 2.6 44.8 + - - +
86Y THR* 3.3 9.2 + - + +
87Y CYS* 1.3 77.8 - - - +
89Y GLN* 1.3 64.6 + - + +
91Y ARG* 3.2 18.0 + - - +
92Y ASN* 3.0 27.3 + - - +
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Residues in contact with GLN 89 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749 VAL* 3.6 27.9 - - - +
789 ALA* 4.2 14.8 + - - +
799 PRO 4.5 11.4 + - - +
809 GLU* 6.1 0.2 - - - +
182V ALA* 4.6 13.2 - - + +
183V LEU* 4.5 19.8 - - + +
84Y ALA 4.7 1.2 + - - +
85Y TRP* 3.4 29.8 - - + -
86Y THR* 3.5 31.2 + - + +
87Y CYS 3.3 0.2 - - - -
88Y GLN* 1.3 78.6 - - + +
90Y LEU* 1.3 63.3 + - - +
92Y ASN* 3.2 14.9 + - - +
93Y LYS* 3.3 17.3 + - - +
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Residues in contact with LEU 90 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85Y TRP* 4.0 21.5 - - + -
86Y THR 3.2 7.2 + - - +
87Y CYS 3.4 8.1 - - - +
89Y GLN* 1.3 80.0 - - - +
91Y ARG* 1.3 64.0 + - - +
93Y LYS* 3.1 14.8 + - - +
98Y LEU* 3.3 58.4 - - + +
101Y LEU* 4.6 9.0 - - + -
105Y LEU* 6.0 0.2 - - + -
138Y SER 3.8 8.3 - - - +
141Y ALA* 3.8 8.5 - - + -
142Y LEU* 3.3 53.2 - - + +
145Y VAL* 3.8 9.9 - - + -
149Y ARG* 3.7 2.3 + - - -
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Residues in contact with ARG 91 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839 GLU* 4.9 5.3 + - - +
849 THR* 2.7 40.6 + - - +
859 PRO* 3.5 10.1 - - - +
869 LEU* 4.2 25.4 - - + +
187V TYR* 3.8 9.7 - - - -
87Y CYS* 2.7 55.3 + - - +
88Y GLN* 3.4 24.9 - - - +
90Y LEU* 1.3 71.8 - - - +
92Y ASN* 1.3 58.1 + - - +
93Y LYS 3.5 0.2 - - - +
144Y LYS* 4.7 5.7 - - - +
145Y VAL* 3.7 33.4 - - + +
148Y GLU* 3.5 22.8 + - - -
149Y ARG* 2.5 23.4 + - - -
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Residues in contact with ASN 92 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182V ALA 6.0 1.6 - - - +
183V LEU* 6.5 0.7 - - - -
185V ARG* 3.1 57.4 + - + +
186V THR 3.7 5.4 + - - -
187V TYR* 3.1 24.9 + - - +
88Y GLN* 3.0 16.1 + - - +
89Y GLN* 3.7 9.6 - - - +
90Y LEU 3.1 0.6 - - - -
91Y ARG* 1.3 74.3 - - - +
93Y LYS* 1.3 60.6 + - - +
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Residues in contact with LYS 93 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709 LEU* 3.8 22.3 - - + +
181V ASP 3.3 26.0 + - - -
182V ALA 4.0 11.4 - - - +
184V GLU* 3.5 24.0 + - - +
185V ARG 4.3 8.1 - - - +
186V THR* 3.9 13.1 - - - +
187V TYR* 3.4 2.8 - - - +
85Y TRP* 5.3 5.8 - - + -
89Y GLN 3.3 11.9 + - - +
90Y LEU* 3.1 7.7 + - - +
92Y ASN* 1.3 79.0 - - - +
94Y SER* 1.3 57.7 + - - +
97Y ASP* 3.7 31.6 + - + +
98Y LEU* 3.4 23.5 - - + +
101Y LEU* 5.9 3.8 - - + -
149Y ARG* 2.7 31.7 + - - -
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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