Contacts of the strand formed by residues 29 - 36 (chain B) in PDB entry 4B3E
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 VAL 29 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B PHE* 4.0 28.7 - - + -
21B GLU 3.4 11.0 - - - +
22B GLN* 3.6 28.9 - - + +
28B PRO* 1.3 72.3 - - - +
30B LYS* 1.3 72.4 + - - +
31B VAL* 3.8 7.7 + - + +
100B GLU* 3.5 2.0 - - - -
101B ASP 2.8 35.9 + - - +
104B ILE* 3.5 34.1 - - + +
105B SER* 4.0 6.5 - - - -
106B LEU* 4.3 8.7 - - + +
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Residues in contact with LYS 30 (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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20B PHE* 3.1 6.9 - - - -
21B GLU* 2.7 63.5 + - + +
23B LYS* 4.8 14.9 - - + +
28B PRO* 5.3 4.5 - - + +
29B VAL* 1.3 73.4 - - - +
31B VAL* 1.3 59.0 + - - +
32B TRP* 3.5 17.7 - - + -
99B ILE 3.6 6.7 - - - +
100B GLU* 3.7 29.4 - - + +
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Residues in contact with VAL 31 (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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18B ILE* 3.6 28.3 - - + -
19B ASN 3.3 4.5 - - - +
20B PHE* 3.9 23.3 - - + -
29B VAL* 3.9 11.9 - - + +
30B LYS* 1.3 76.5 - - - +
32B TRP* 1.3 61.7 + - - +
45B PHE* 4.3 18.2 - - + -
84B LEU* 5.0 4.5 - - + -
97B VAL* 3.9 3.6 - - + +
98B SER* 3.3 1.4 + - - -
99B ILE* 2.7 56.6 + - + +
101B ASP* 5.2 1.3 - - + -
104B ILE* 4.2 16.4 - - + -
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Residues in contact with TRP 32 (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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3B LYS* 6.0 3.1 - - + -
18B ILE* 4.4 5.4 - - - -
19B ASN* 2.7 73.4 + - + +
20B PHE 4.5 2.0 - - - -
21B GLU* 3.7 35.2 - - + -
30B LYS* 3.5 32.3 - - + -
31B VAL* 1.3 77.0 - - - +
33B GLY* 1.3 59.9 + - - +
97B VAL* 3.3 17.5 - - - +
98B SER* 4.2 11.0 - - - +
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Residues in contact with GLY 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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17B ILE 3.4 12.6 - - - -
18B ILE* 4.1 5.4 - - - -
19B ASN* 4.4 4.3 - - - -
32B TRP* 1.3 85.3 - - - +
34B SER* 1.3 61.2 + - - -
96B ASP* 3.7 2.1 - - - +
97B VAL* 2.8 29.1 + - - +
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Residues in contact with SER 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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16B GLY* 3.3 3.3 - - - -
17B ILE* 3.1 29.5 + - - +
18B ILE* 4.7 0.2 - - - -
33B GLY* 1.3 74.0 - - - -
35B ILE* 1.3 65.6 + - - +
94B VAL* 4.4 9.0 - - - -
95B ALA 3.2 13.7 - - - -
96B ASP* 3.5 18.8 + - - -
97B VAL 4.6 0.4 - - - +
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Residues in contact with ILE 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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8B LEU* 3.5 30.1 - - + -
14B VAL* 3.8 20.2 - - + -
15B GLN 3.5 13.7 - - - +
18B ILE* 4.2 10.3 - - + -
34B SER* 1.3 81.0 - - - +
36B LYS* 1.3 62.2 + - - +
38B LEU* 3.4 23.2 - - + +
45B PHE* 4.0 21.5 - - + -
87B VAL* 4.5 5.8 - - + -
93B GLY 3.8 0.9 - - - +
94B VAL* 3.5 2.4 - - - +
95B ALA* 2.8 35.0 + - + +
97B VAL* 4.5 10.5 - - + -
119B VAL* 4.1 16.2 - - + -
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Residues in contact with LYS 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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14B VAL* 3.4 7.1 - - - +
15B GLN* 2.7 71.5 + - + +
16B GLY* 5.6 1.1 - - - -
34B SER* 4.3 0.6 + - - -
35B ILE* 1.3 74.5 - - - +
37B GLY* 1.3 65.7 + - - +
38B LEU 3.3 3.6 + - - -
92B ASP 6.0 0.2 - - - +
93B GLY 3.5 5.6 - - - +
94B VAL* 4.4 16.6 - - + +
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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