Contacts of the strand formed by residues 97 - 100 (chain D) in PDB entry 5UQ9
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 ILE 97 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68D PRO* 4.6 4.5 - - + -
69D ARG 2.8 16.9 + - - +
70D ARG* 4.4 6.7 - - + -
71D ILE* 3.0 27.4 + - - +
95D GLY 3.8 8.7 - - - +
96D ASP* 1.3 81.9 - - - +
98D ILE* 1.3 68.0 + - - +
99D ILE* 3.7 25.8 - - + -
122D LEU* 3.2 12.8 - - + +
124D VAL* 4.1 5.6 - - + -
149D ALA* 3.7 34.3 - - + +
152D HIS* 3.6 36.8 - - + -
153D ILE* 4.2 7.9 - - + -
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Residues in contact with ILE 98 (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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71D ILE* 3.4 7.9 - - + +
73D LEU* 3.8 30.5 - - + -
85D ILE* 4.5 11.2 - - + +
88D LEU* 3.9 27.6 - - + -
89D VAL* 5.3 0.2 - - + -
92D LEU* 3.7 28.7 - - + -
96D ASP 4.4 0.2 + - - -
97D ILE* 1.3 77.3 - - - +
99D ILE* 1.3 64.0 + - - +
116D LEU* 4.5 12.3 - - + -
121D ILE* 4.4 13.2 - - + -
122D LEU 3.1 7.8 + - - +
123D PHE* 3.5 22.6 - - + -
124D VAL* 2.8 28.2 + - - +
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Residues in contact with ILE 99 (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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6D ILE* 5.1 0.4 - - + -
70D ARG* 4.4 5.4 - - + -
71D ILE 2.7 33.4 + - - +
72D ILE* 3.2 18.7 - - + -
73D LEU* 2.5 36.9 + - - +
97D ILE* 3.7 25.1 - - + -
98D ILE* 1.3 75.4 - - - +
100D ASP* 1.3 59.0 + - - +
101D GLY* 3.6 2.4 + - - +
124D VAL* 3.3 17.3 - - + +
126D SER* 4.1 17.3 - - - -
153D ILE* 4.1 15.3 - - + -
157D PHE* 3.5 31.0 - - + -
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Residues in contact with ASP 100 (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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73D LEU* 3.7 11.4 - - + +
75D VAL 5.6 0.5 + - - +
81D VAL* 3.6 31.0 - - + +
98D ILE 4.1 0.6 - - - -
99D ILE* 1.3 71.4 - - - +
101D GLY* 1.3 58.9 + - - +
102D GLY* 3.1 15.8 + - - -
104D SER* 2.7 30.6 + - - -
112D ARG* 3.7 5.5 + - - -
123D PHE* 3.6 25.2 - - + -
124D VAL 2.9 10.0 + - - +
126D SER 3.0 26.2 + - - +
181D HIS* 3.3 11.7 + - + -
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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