Contacts of the strand formed by residues 85 - 90 (chain D) in PDB entry 3AB0
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 ALA 85 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D LEU* 3.4 2.2 - - - +
84D PRO* 1.3 85.7 - - + +
86D GLY* 1.3 57.1 + - - +
114D PHE* 3.4 17.2 - - - +
115D GLY* 4.2 1.3 - - - -
116D THR 4.3 0.4 - - - +
117D ALA* 3.7 37.7 - - + +
118D ILE* 4.0 8.5 - - + +
130D GLU* 5.5 0.7 - - - +
211D GLU* 3.4 3.8 - - - +
212D LYS* 2.7 39.9 + - + +
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Residues in contact with GLY 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D ALA* 1.3 75.9 - - - +
87D LEU* 1.3 61.9 + - - +
112D SER 4.2 0.4 - - - +
113D LYS* 3.8 2.9 - - - +
114D PHE* 2.9 56.3 + - - +
118D ILE* 4.2 4.6 - - - +
210D ILE 3.3 10.3 - - - -
211D GLU* 4.0 5.2 - - - -
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D GLY* 1.3 75.0 - - - +
88D TYR* 1.3 74.2 + - - +
89D ALA* 4.1 3.8 - - + +
110D VAL* 4.2 12.3 - - + -
112D SER 3.6 9.2 - - - +
113D LYS* 3.9 12.3 - - + -
118D ILE* 3.6 26.2 - - + +
119D SER* 3.8 29.2 - - - -
120D GLN* 3.8 13.9 - - + +
126D PHE* 3.7 29.8 - - + -
208D ILE* 3.8 1.8 - - + +
209D ILE* 3.4 6.0 - - - +
210D ILE* 2.7 39.4 + - + +
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Residues in contact with TYR 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D LEU* 1.3 75.5 - - - +
89D ALA* 1.3 70.1 + - - +
90D PHE* 3.5 23.8 - + - +
110D VAL* 3.7 3.1 - - - +
111D GLY* 2.8 53.1 + - - -
112D SER* 3.1 23.5 + - - +
207D SER* 4.2 15.2 - - - -
208D ILE 3.4 11.9 - - - -
209D ILE* 3.8 25.8 - - + -
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Residues in contact with ALA 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D LEU* 4.1 4.9 - - + +
88D TYR* 1.3 76.8 - - - +
90D PHE* 1.3 66.0 + - - +
107D PHE* 4.0 5.2 - - + -
109D THR 3.4 11.7 - - - +
110D VAL* 4.4 4.5 - - - -
111D GLY 4.3 0.9 - - - +
120D GLN* 4.4 2.7 - - - +
126D PHE* 3.7 35.2 - - + -
207D SER* 3.4 4.5 - - - -
208D ILE* 2.9 39.9 + - + +
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Residues in contact with PHE 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D TYR* 3.5 31.2 - + - +
89D ALA* 1.3 75.7 - - - +
91D ASN* 1.3 70.8 + - - +
92D SER* 4.9 7.9 - - - -
107D PHE* 3.3 7.2 - - - -
108D ASN* 3.3 4.7 + - - +
109D THR* 2.8 70.5 + - + +
111D GLY* 4.1 19.1 - - - -
206D ALA 3.3 13.9 - - - +
207D SER* 4.4 5.8 - - - -
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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