Contacts of the strand formed by residues 32 - 38 (chain B) in PDB entry 2YZ5
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 GLY 32 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET 3.6 3.4 + - - -
2B VAL* 3.4 14.8 - - - +
3B ASP 3.1 19.2 + - - -
25B ALA* 5.5 0.2 - - - -
30B LEU* 3.4 8.9 - - - +
31B LYS* 1.3 81.3 - - - +
33B VAL* 1.3 68.2 + - - +
73B LEU* 4.1 6.2 - - - +
74B TYR* 3.1 19.7 - - - -
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Residues in contact with VAL 33 (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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2B VAL* 4.0 1.4 - - - +
3B ASP* 3.3 10.1 - - + +
6B VAL* 3.6 27.6 - - + -
21B TYR* 4.8 3.6 - - + +
22B LEU* 3.8 17.0 - - + +
25B ALA* 3.7 28.5 - - + -
32B GLY* 1.3 80.6 - - - +
34B VAL* 1.3 59.3 + - - +
35B PHE* 3.9 22.4 - - + -
73B LEU* 5.5 0.6 - - + +
74B TYR 2.8 8.6 + - - +
75B VAL* 3.2 6.4 - - - +
76B GLY 2.7 29.3 + - - +
231B VAL* 4.4 13.7 - - + -
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Residues in contact with VAL 34 (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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2B VAL* 4.2 4.5 - - + -
3B ASP 2.8 9.3 + - - -
4B SER* 3.5 35.7 - - - +
6B VAL* 3.4 10.7 - - - +
33B VAL* 1.3 73.3 - - - +
35B PHE* 1.3 65.5 + - - +
36B THR* 3.3 23.9 + - + +
74B TYR* 3.5 32.5 - - + +
76B GLY* 3.6 15.3 - - - -
77B ILE 4.5 0.2 - - - +
78B GLY 4.3 2.2 - - - +
101B ASP* 4.9 0.9 - - + -
102B TYR* 3.9 24.0 - - + +
252B TYR* 5.2 1.3 - - + -
253B PHE 4.3 5.8 - - - +
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Residues in contact with PHE 35 (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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6B VAL* 3.3 24.2 - - + +
7B HIS 4.1 8.3 - - - -
8B THR* 3.9 19.5 - - + -
18B PRO* 3.7 34.5 - - + -
21B TYR* 4.2 17.0 - + + -
22B LEU* 4.2 9.2 - - + -
33B VAL* 3.9 18.2 - - + -
34B VAL* 1.3 70.3 - - - +
36B THR* 1.3 58.1 + - - +
59B TYR* 3.5 6.3 - - + +
63B LEU* 3.7 36.8 - - + -
66B VAL* 4.8 2.9 - - + -
75B VAL* 4.0 20.2 - - + -
76B GLY 3.0 17.0 + - - +
78B GLY* 2.7 34.5 + - - +
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Residues in contact with THR 36 (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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4B SER 3.1 22.4 - - - +
5B HIS* 3.3 30.7 - - - -
6B VAL 2.8 11.9 + - - -
7B HIS* 3.5 8.0 - - - -
34B VAL* 3.3 13.6 + - + +
35B PHE* 1.3 79.7 - - - +
37B ASP* 1.3 66.8 + - - +
78B GLY 3.6 6.5 - - - -
79B LEU* 3.7 19.7 - - - +
80B GLU* 3.3 13.6 - - - +
102B TYR* 3.8 12.1 - - + +
104B ILE* 4.2 6.7 - - + -
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Residues in contact with ASP 37 (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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6B VAL 3.7 0.8 + - - -
7B HIS* 3.0 22.2 + - - +
8B THR* 2.7 39.8 + - + +
10B LEU* 3.6 7.1 - - - +
11B CYS* 3.3 27.9 + - - +
36B THR* 1.3 75.7 - - - +
38B HIS* 1.3 72.9 + - - +
39B SER 3.2 0.7 + - - -
51B MET* 3.9 10.0 - - + +
59B TYR* 3.0 30.9 + - + +
79B LEU* 3.4 8.7 - - - +
80B GLU 3.0 16.9 + - - -
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Residues in contact with HIS 38 (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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7B HIS* 3.1 18.1 + - - -
11B CYS* 3.5 13.5 - - + -
13B HIS* 3.3 2.0 + + - -
37B ASP* 1.3 75.9 + - - +
39B SER* 1.3 65.2 + - - +
49B SER* 3.5 28.5 - - - +
50B ARG* 3.7 24.4 + - + +
51B MET* 3.6 21.3 + - - +
80B GLU* 3.1 33.9 + - - +
82B ASP* 4.7 0.4 + - - -
108B HIS* 4.4 9.8 - + - -
1501B ZN 2.1 37.4 - - - -
2002B PO4 3.2 14.8 - - - -
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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