Contacts of the strand formed by residues 90 - 94 (chain B) in PDB entry 1YZH
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 90 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B TYR* 3.3 32.5 - - + -
35B PHE* 3.7 2.2 - - - -
53B VAL* 3.5 46.2 - - + +
54B SER* 3.7 11.0 - - - +
57B ALA* 3.9 5.6 - - + -
65B TYR* 3.1 13.5 - - + +
82B VAL* 3.9 27.4 - - + +
87B VAL* 3.5 32.5 - - + +
88B PRO 3.0 4.8 + - - +
89B ASN* 1.3 79.8 - - - +
91B LYS* 1.3 81.2 - - - +
92B LEU* 5.1 0.4 - - + -
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Residues in contact with LYS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PRO 5.1 1.0 + - - -
18B GLN* 2.7 28.3 + - - +
19B TYR* 3.2 15.7 - - - +
21B VAL* 4.7 4.9 - - + -
31B TRP* 3.8 28.5 - - + -
34B LEU* 3.6 37.4 + - + +
35B PHE* 3.3 31.9 - - + +
65B TYR 2.8 5.8 + - - +
66B ILE* 3.2 5.2 - - + -
67B GLY 3.0 23.4 + - - -
88B PRO 4.9 6.2 + - - -
90B ILE* 1.3 82.9 + - - +
92B LEU* 1.3 67.3 + - - +
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TYR* 2.7 11.0 + - + +
20B VAL* 3.3 15.4 - - + -
21B VAL* 2.8 34.5 + - - +
47B SER* 5.5 1.1 - - - -
53B VAL* 4.5 9.6 - - + -
67B GLY* 3.4 18.6 - - - +
75B LEU* 3.9 25.4 - - + +
78B ALA* 3.8 12.8 - - + -
79B LEU* 3.5 42.0 - - + +
82B VAL* 4.0 23.3 - - + -
90B ILE* 5.1 0.7 - - + -
91B LYS* 1.3 82.2 - - - +
93B LEU* 1.3 57.6 + - - +
94B TRP 4.3 0.2 - - - -
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Residues in contact with LEU 93 (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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21B VAL* 3.5 34.5 - - + +
23B ASN 4.7 1.3 - - - +
27B ALA* 4.4 0.4 - - + -
31B TRP* 4.1 10.8 - - + -
66B ILE* 4.0 10.8 - - + -
67B GLY 2.7 14.4 + - - +
68B ILE* 3.4 11.7 - - + -
69B ASP 3.1 25.1 + - - +
75B LEU* 3.9 5.9 - - - +
91B LYS 4.4 0.2 + - - -
92B LEU* 1.3 74.9 - - - +
94B TRP* 1.3 65.3 + - - +
95B VAL* 3.7 25.0 + - + -
103B TYR* 3.8 30.7 - - + -
104B PHE* 4.1 24.9 - - + -
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Residues in contact with TRP 94 (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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21B VAL 3.1 9.7 + - - +
22B LEU* 3.5 48.0 - - + +
69B ASP 3.6 15.0 - - - -
70B ILE 2.9 23.6 + - - -
71B GLN 4.0 1.6 - - - -
72B LYS* 3.3 62.6 - - + +
75B LEU* 3.7 10.8 - - + +
93B LEU* 1.3 83.0 - - - +
95B VAL* 1.3 71.0 + - - +
96B ASP* 4.0 24.0 - - + -
103B TYR* 4.0 6.2 + - - -
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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