Contacts of the strand formed by residues 87 - 91 (chain N) 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 PHE 87 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82N PHE* 3.5 5.9 - - - -
86N ASN* 1.3 94.4 - - + +
88N ALA* 1.3 65.0 + - - +
118N MET* 5.5 1.6 - - + -
162N GLU* 3.4 3.3 - - - +
163N MET* 2.8 39.9 + - + +
164N GLY* 5.1 2.5 - - - -
165N GLY 5.3 2.5 - - - -
167N CYS* 3.4 42.4 - - + -
169N PHE* 3.9 31.0 - + + -
172N VAL* 3.6 43.7 - - + -
173N GLN* 6.4 1.8 - - + -
176N LEU* 4.1 1.8 - - + -
190N VAL 3.4 7.6 - - - +
191N SER* 4.1 22.4 - - - +
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Residues in contact with ALA 88 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82N PHE* 3.3 22.9 - - + -
87N PHE* 1.3 78.6 - - - +
89N ILE* 1.3 63.5 + - - +
90N LEU 3.9 0.2 - - - -
159N LEU* 4.1 21.5 - - + -
161N VAL 3.1 16.2 - - - +
162N GLU* 4.1 2.5 - - + +
163N MET 4.5 0.2 - - - +
176N LEU* 3.6 9.8 - - - +
189N ALA* 3.5 4.9 - - - -
190N VAL* 2.7 37.1 + - + +
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Residues in contact with ILE 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88N ALA* 1.3 79.0 - - - +
90N LEU* 1.3 59.4 + - - +
91N ALA 3.7 0.3 + - - -
109N ILE* 4.4 1.1 - - + -
159N LEU* 3.5 1.1 - - - -
160N VAL* 2.8 34.0 + - + +
161N VAL* 2.8 36.7 + - + +
176N LEU* 3.7 34.1 - - + +
179N VAL* 3.3 32.5 - - + -
180N ALA* 4.1 19.1 - - + -
183N LEU* 3.8 27.1 - - + -
187N ALA* 4.3 4.0 - - + -
188N LYS 3.5 4.7 - - - +
189N ALA* 5.0 0.7 - - - -
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Residues in contact with LEU 90 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88N ALA 3.9 1.0 - - - -
89N ILE* 1.3 71.1 - - - +
91N ALA* 1.3 88.1 + - - +
92N LEU* 3.4 12.4 + - + +
157N GLY* 3.7 28.0 - - - +
158N ARG 3.8 0.4 - - - +
159N LEU* 3.6 21.5 - - + +
187N ALA* 3.3 4.2 - - - +
188N LYS* 2.7 44.2 + - + +
190N VAL* 3.7 18.8 - - + -
195N LEU* 3.5 29.6 - - + -
198N MET* 4.2 13.2 - - + -
199N ARG* 5.8 1.3 - - - +
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Residues in contact with ALA 91 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89N ILE 3.7 1.6 + - - -
90N LEU* 1.3 74.3 - - - +
92N LEU* 1.3 60.7 + - - +
93N GLY 3.9 0.9 - - - +
154N VAL* 3.8 8.7 - - + -
155N LYS 3.5 17.7 - - - +
156N ALA* 4.3 0.2 - - - -
157N GLY 2.8 29.5 + - - -
158N ARG 2.8 20.2 + - - +
160N VAL* 4.1 3.3 - - + +
185N PHE* 3.3 35.0 - - + -
186N ALA 4.1 0.4 - - - -
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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