Contacts of the strand formed by residues 90 - 96 (chain D) in PDB entry 4A12
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 LYS 90 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84D GLN* 3.2 13.7 + - - +
86D ASN* 2.8 30.5 + - + +
89D VAL* 1.4 88.1 - - + +
91D ALA* 1.3 63.8 + - - +
92D GLN* 3.5 34.3 + - - +
125D LEU* 3.5 2.9 - - - -
153D GLU* 4.0 23.5 + - - -
154D ALA 3.3 14.4 - - - +
155D ARG* 3.7 19.5 - - + +
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Residues in contact with ALA 91 (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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84D GLN* 3.3 13.5 - - - +
85D VAL* 3.8 17.3 - - + -
90D LYS* 1.3 76.4 - - - +
92D GLN* 1.3 65.0 + - - +
121D LEU* 3.8 17.1 - - + +
125D LEU* 3.8 24.2 - - + +
153D GLU* 3.4 1.9 - - - +
154D ALA 2.8 33.5 + - - +
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Residues in contact with GLN 92 (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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82D LEU* 3.7 2.4 - - - +
83D ILE* 2.8 41.4 + - + +
84D GLN* 2.9 54.5 + - + +
90D LYS* 3.5 24.4 + - - +
91D ALA* 1.3 73.8 - - - +
93D SER* 1.3 53.9 + - - +
94D ILE* 5.8 0.4 - - + -
121D LEU* 3.8 4.0 - - - -
151D ARG* 3.4 30.9 + - + +
152D ALA 3.2 13.2 - - - +
153D GLU* 3.8 7.3 - - + +
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Residues in contact with SER 93 (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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78D PHE* 4.0 13.2 - - - -
79D ILE 4.5 0.9 + - - -
81D ASP 3.1 20.9 - - - -
82D LEU* 4.2 0.4 - - - -
83D ILE 4.2 0.7 - - - +
92D GLN* 1.3 74.3 - - - +
94D ILE* 1.3 63.2 + - - +
117D GLN* 3.1 30.0 + - - +
121D LEU* 3.7 16.9 - - - +
151D ARG* 3.7 2.8 - - - +
152D ALA* 2.9 36.0 + - - +
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Residues in contact with ILE 94 (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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80D GLY* 3.5 0.5 - - - -
81D ASP* 2.8 37.5 + - + +
83D ILE* 3.6 36.6 - - + -
92D GLN* 5.8 0.4 - - + -
93D SER* 1.3 77.7 - - - +
95D LEU* 1.3 58.6 + - - +
96D ASP* 4.5 8.4 + - - +
117D GLN* 3.7 0.7 - - - -
149D THR* 3.2 32.5 - - + -
150D VAL 3.4 3.4 - - - +
151D ARG* 4.2 24.5 - - + -
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Residues in contact with LEU 95 (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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79D ILE* 4.2 8.1 - - + -
80D GLY* 3.8 24.0 - - - +
94D ILE* 1.3 74.6 - - - +
96D ASP* 1.3 69.9 + - - +
97D ILE* 3.5 24.4 + - + -
101D SER* 5.7 2.7 - - - +
113D VAL* 3.9 23.8 - - + +
114D LEU* 5.3 1.3 - - - +
117D GLN* 3.5 39.7 - - + +
148D ASP 3.8 0.2 - - - +
149D THR* 3.4 2.1 - - - -
150D VAL* 2.8 41.5 + - + +
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Residues in contact with ASP 96 (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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81D ASP* 6.1 0.9 - - - +
94D ILE* 4.5 7.2 - - - +
95D LEU* 1.3 82.2 - - - +
97D ILE* 1.3 60.9 + - - +
98D THR* 3.3 21.0 + - + +
101D SER* 4.8 2.3 + - - -
147D ASN 6.1 0.4 - - - +
148D ASP 3.8 5.2 - - - +
149D THR* 3.3 28.0 + - - +
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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