Contacts of the strand formed by residues 95 - 99 (chain D) in PDB entry 3H2U
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 THR 95 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62D LEU* 4.1 15.0 - - + -
63D ILE 2.9 7.9 - - - -
64D ARG* 3.5 36.8 - - + +
66D LEU* 4.1 2.5 - - - -
89D VAL* 3.5 6.9 - - - +
90D ASP* 2.9 45.1 + - - +
93D LYS* 3.6 29.3 - - + +
94D GLY* 1.3 81.0 - - - +
96D ALA* 1.3 62.1 + - - +
97D PHE* 3.6 9.2 - - - -
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Residues in contact with ALA 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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61D ILE 3.7 1.0 - - - +
62D LEU* 3.6 6.5 - - - +
63D ILE* 2.8 36.5 + - + +
66D LEU* 3.9 13.9 - - + -
75D VAL* 4.4 6.5 - - + -
88D PHE 3.0 10.8 - - - +
89D VAL* 3.6 18.2 - - + -
95D THR* 1.3 77.9 - - - +
97D PHE* 1.3 65.1 + - - +
98D VAL* 3.8 14.9 + - + -
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Residues in contact with PHE 97 (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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61D ILE 3.8 4.0 - - - -
62D LEU* 3.8 22.2 - - + -
64D ARG* 6.2 0.7 - - - -
86D TYR* 3.8 12.4 - - + +
87D CYS* 3.4 1.7 - - - -
88D PHE* 2.5 66.9 + + + +
90D ASP* 4.0 19.5 - - + -
93D LYS* 6.4 1.3 - - + -
95D THR* 3.6 22.0 - - - -
96D ALA* 1.3 75.0 - - - +
98D VAL* 1.3 60.3 + - - +
128D GLN* 2.9 35.2 - - + +
129D PRO* 5.6 3.8 - - + -
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Residues in contact with VAL 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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59D ARG 3.8 0.9 - - - +
60D LYS* 3.6 4.3 - - - -
61D ILE* 3.0 45.9 + - + +
63D ILE* 4.5 5.4 - - + -
75D VAL* 4.3 10.3 - - + -
79D LEU* 4.1 10.1 - - + -
84D LEU* 4.0 30.1 - - + -
86D TYR 3.1 8.7 - - - +
87D CYS* 4.3 13.7 - - - -
96D ALA* 4.2 21.5 - - + +
97D PHE* 1.3 79.6 - - - +
99D THR* 1.3 65.8 + - - +
100D LEU* 4.0 12.7 + - + -
128D GLN* 3.9 3.7 + - - +
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Residues in contact with THR 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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59D ARG* 3.6 35.2 - - + +
60D LYS* 3.4 32.6 + - + +
84D LEU* 3.3 3.8 - - - -
85D LYS* 2.5 36.5 + - + -
86D TYR* 2.4 51.8 + - + +
98D VAL* 1.3 75.1 - - - +
100D LEU* 1.3 58.8 + - - +
159D GLU* 4.3 3.6 - - - +
181D MET* 6.1 0.2 - - - -
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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