Contacts of the strand formed by residues 85 - 90 (chain B) in PDB entry 3N2Z
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 SER 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79B TRP* 3.4 7.7 + - - +
84B GLY* 1.4 73.8 - - - -
86B ILE* 1.3 67.3 + - - +
87B LEU* 4.4 3.9 - - - +
113B LEU* 2.9 24.4 + - - +
114B LYS 3.2 4.6 + - - -
115B ALA* 3.2 12.2 - - - +
116B MET 3.0 22.7 + - - -
171B GLN* 3.7 7.5 - - - +
172B PRO* 3.6 13.0 - - - -
174B ILE* 5.3 1.3 - - - -
485B ILE* 3.7 29.0 - - - +
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B SER* 1.3 79.6 - - - +
87B LEU* 1.4 64.2 + - - +
88B PHE* 3.7 3.3 + - + +
116B MET* 3.6 20.2 - - + +
118B VAL* 3.9 28.9 - - + -
158B ILE* 6.1 1.6 - - + -
161B LEU* 5.3 9.4 - - + -
162B LYS* 5.2 7.0 - - + -
168B ALA* 4.2 23.8 - - + +
171B GLN* 3.7 25.4 - - + +
172B PRO 3.0 7.7 + - - +
173B VAL* 3.3 29.5 - - + +
174B ILE* 2.8 31.7 + - - +
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B SER* 4.2 5.8 - - - +
86B ILE* 1.4 74.7 - - - +
88B PHE* 1.3 55.3 + - - +
105B PHE* 6.1 0.2 - - + -
106B MET* 3.4 19.7 - - + +
109B VAL* 3.7 30.1 - - + -
110B ALA 5.1 1.1 - - - +
113B LEU* 4.5 12.3 - - + -
115B ALA* 4.2 17.2 - - + +
116B MET 2.9 7.6 + - - +
117B LEU* 3.6 27.8 - - + -
118B VAL 2.8 32.7 + - - +
174B ILE* 3.6 27.4 - - + -
176B ILE* 4.2 16.8 - - + -
481B MET* 4.7 3.1 - - - -
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Residues in contact with PHE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ILE* 3.7 4.0 + - + -
87B LEU* 1.3 70.1 - - - +
89B TYR* 1.3 64.3 + - - +
90B THR* 3.4 28.2 + - + -
106B MET* 4.7 0.9 - - - -
118B VAL* 3.5 23.8 - - + -
120B ALA* 3.5 20.2 - - + -
154B PHE* 3.6 33.4 - + + -
157B LEU* 3.8 21.3 - - + -
158B ILE* 3.7 30.1 - - + -
161B LEU* 4.9 2.7 - - + -
173B VAL* 3.8 21.3 - - + -
174B ILE 2.8 11.5 + - - +
175B ALA* 3.3 4.0 - - + -
176B ILE* 2.9 23.8 + - - +
188B PHE* 4.5 3.1 - + - -
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Residues in contact with TYR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LEU 4.0 1.2 + - - -
88B PHE* 1.3 69.3 - - - +
90B THR* 1.3 66.7 + - - +
91B GLY* 3.0 19.9 + - - -
92B ASN* 2.7 30.4 + - - -
96B ILE* 4.0 9.4 - - + -
99B PHE* 3.4 27.3 - + + -
103B THR* 3.9 24.6 + - + -
106B MET* 4.0 17.2 - - + +
118B VAL 2.8 12.1 + - - +
119B PHE* 3.6 26.7 - + + -
120B ALA* 3.2 23.2 + - - +
176B ILE* 3.2 17.9 - - + -
177B GLY* 3.7 17.0 - - - -
178B GLY* 3.6 18.2 + - - -
459B LEU* 4.9 2.0 - - + -
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Residues in contact with THR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B PHE* 3.4 25.8 + - + -
89B TYR* 1.3 70.7 - - - +
91B GLY* 1.3 68.0 + - - +
154B PHE* 3.7 26.2 - - + -
175B ALA* 4.3 5.8 - - + -
176B ILE 3.1 6.4 + - - -
181B GLY* 2.9 36.6 + - - -
184B LEU* 4.2 3.9 - - - +
185B ALA* 3.3 23.1 + - - +
188B PHE* 4.0 17.9 - - + -
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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