Contacts of the strand formed by residues 23 - 27 (chain B) in PDB entry 1HYH
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 23 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ALA* 5.3 0.9 - - + +
22B ARG* 1.3 74.5 - - - +
24B ILE* 1.3 69.3 + - - +
48B ASP* 3.3 38.3 - - + +
50B VAL* 4.3 9.1 - - + +
86B ALA* 2.9 37.4 + - - +
89B ASP* 3.1 30.2 + - - +
90B ALA* 3.6 27.7 - - + -
91B ASP* 2.9 37.3 + - - +
92B VAL 3.7 0.7 + - - -
264B MET* 5.0 0.2 - - - -
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Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LYS* 1.3 82.6 - - - +
25B GLY* 1.3 75.4 + - - +
26B ILE* 4.3 7.1 - - + +
40B LEU* 3.7 43.5 - - + -
45B VAL* 4.6 0.2 - - + -
46B ALA* 4.0 18.4 - - + -
48B ASP 3.1 7.3 + - - -
49B TYR* 3.3 15.2 - - + +
50B VAL* 3.0 22.7 + - - +
92B VAL* 3.5 14.6 - - + +
94B ILE* 4.2 15.3 - - + -
260B ALA* 4.8 8.1 - - + -
264B MET* 4.2 26.5 - - + -
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Residues in contact with GLY 25 (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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24B ILE* 1.3 77.2 - - - +
26B ILE* 1.3 66.6 + - - +
27B ILE* 4.2 0.7 - - - -
50B VAL* 3.3 8.5 - - - -
87B LEU* 3.9 23.6 - - - -
90B ALA* 4.5 1.4 - - - +
92B VAL 3.1 11.8 + - - -
93B VAL* 3.4 6.2 - - - +
94B ILE 2.8 26.0 + - - -
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Residues in contact with ILE 26 (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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24B ILE* 4.3 9.6 - - + +
25B GLY* 1.3 79.4 - - - +
27B ILE* 1.3 64.3 + - - +
28B GLY 3.9 0.8 + - - +
29B LEU* 3.5 23.5 - - + +
33B GLY* 4.1 9.4 - - - +
36B VAL* 4.2 14.1 - - + -
37B ALA* 4.0 26.7 - - + +
40B LEU* 4.6 9.0 - - + -
49B TYR* 4.9 3.4 - - + -
50B VAL 2.8 9.2 + - - +
51B PHE* 3.7 26.7 - - + -
52B ILE* 2.8 28.8 + - - +
87B LEU* 5.4 0.2 - - - +
94B ILE* 3.5 9.6 - - + +
96B THR* 3.7 20.9 - - + +
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Residues in contact with ILE 27 (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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26B ILE* 1.3 73.9 - - - +
28B GLY* 1.3 61.5 + - - +
52B ILE* 3.4 20.6 - - + +
84B TRP* 4.3 17.3 - - + -
87B LEU* 5.0 2.5 - - + -
93B VAL* 3.5 30.1 - - + -
94B ILE 2.9 12.7 + - - +
95B SER* 4.3 11.4 - - - +
96B THR* 2.8 31.6 + - - -
97B LEU* 3.2 28.4 + - + -
125B VAL* 4.2 23.1 - - + -
129B LEU* 4.4 8.5 - - + -
138B LEU* 5.0 0.2 - - + -
330B NAD 4.1 14.6 - - + +
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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