Contacts of the strand formed by residues 24 - 32 (chain B) in PDB entry 5A72
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 24 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B PHE 3.8 0.2 + - - -
20B VAL* 3.0 29.5 + - - -
22B ALA 3.4 1.1 - - - +
23B ASP* 1.3 80.6 - - - +
25B CYS* 1.3 65.0 + - - +
47B THR 3.1 12.1 - - - -
48B VAL* 4.3 2.0 - - - -
49B PHE* 4.3 1.8 - - - -
102B LYS* 3.1 17.1 + - - -
615D G 3.5 12.0 - - - +
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Residues in contact with CYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 4.2 4.6 - - - +
24B GLY* 1.3 76.4 - - - +
26B ILE* 1.3 62.7 + - - +
27B ASN* 3.8 23.3 - - - -
45B SER* 3.6 1.9 + - - +
46B LEU* 3.5 2.3 - - - -
47B THR* 2.8 34.7 + - - +
49B PHE* 3.6 20.9 - - + -
102B LYS* 4.3 2.4 - - - +
139B THR* 5.7 1.1 - - - -
615D G 4.0 1.1 - - + -
616D A 3.4 48.2 - - - +
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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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20B VAL* 4.2 10.8 - - + -
25B CYS* 1.3 72.2 - - - +
27B ASN* 1.3 63.1 + - - +
45B SER 3.5 8.1 - - - +
46B LEU* 3.9 20.9 - - + -
92B LEU* 4.0 22.9 - - + -
99B LEU* 3.8 29.6 - - + -
102B LYS* 3.9 23.5 - - + +
105B GLN* 3.5 29.4 + - + +
106B ALA* 4.0 19.3 - - + +
109B VAL* 4.0 20.9 - - + -
135B VAL* 4.0 1.6 - - - +
139B THR* 4.5 4.3 - - - +
616D A 4.9 0.2 + - - -
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Residues in contact with ASN 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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25B CYS* 3.8 17.2 - - - -
26B ILE* 1.3 77.0 - - - +
28B ALA* 1.3 78.6 + - - +
29B GLN* 3.7 20.2 - - + +
44B VAL* 3.6 2.3 - - - -
45B SER* 2.9 40.5 + - - +
109B VAL* 3.7 10.3 - - - +
135B VAL* 3.9 11.2 - - - +
139B THR* 4.2 3.8 - - - +
144B ARG* 3.4 18.0 + - - -
616D A 3.8 11.5 - - - +
617D C 3.1 30.8 + - - -
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Residues in contact with ALA 28 (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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27B ASN* 1.3 84.5 + - - +
29B GLN* 1.3 53.7 - - - +
42B VAL* 4.8 0.4 - - + -
43B ARG 3.2 11.0 - - - +
44B VAL* 4.1 4.3 - - + -
109B VAL* 4.3 2.0 - - + -
112B ILE* 3.6 32.1 - - + -
132B ALA* 3.7 17.2 - - + +
135B VAL* 4.1 11.3 - - + +
144B ARG* 2.2 30.2 + - - -
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Residues in contact with GLN 29 (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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27B ASN* 3.7 21.9 - - - +
28B ALA* 1.3 77.3 - - - +
30B ILE* 1.3 64.5 + - - +
31B VAL* 3.8 14.5 - - + +
41B GLN 3.4 0.2 - - - +
42B VAL* 3.3 8.0 - - - +
43B ARG* 2.9 52.9 + - + +
45B SER* 4.6 9.6 + - - +
132B ALA* 4.7 0.9 - - - -
144B ARG* 3.2 9.0 - - - +
617D C 3.7 27.9 - - - +
618D G 3.1 46.1 + - - +
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Residues in contact with ILE 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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29B GLN* 1.3 76.5 - - - +
31B VAL* 1.3 58.7 + - - +
40B TYR* 3.6 22.2 - - + -
41B GLN 3.4 7.6 - - - +
42B VAL* 5.0 3.1 - - + -
125B LEU* 6.5 0.2 - - + -
129B ALA* 3.8 25.1 - - + +
132B ALA* 4.2 13.0 - - + -
133B ASP* 3.8 9.4 - - - +
144B ARG* 4.3 3.5 - - - +
146B ILE* 3.3 51.8 + - + +
147B LEU 3.5 31.4 - - - +
148B ALA* 3.6 4.5 - - - +
151B VAL* 3.6 11.9 - - + -
618D G 4.1 7.5 + - - -
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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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29B GLN* 4.1 11.9 - - + +
30B ILE* 1.3 77.3 - - - +
32B SER* 1.3 64.4 + - - +
33B ARG* 3.5 33.0 - - + +
40B TYR* 3.4 6.4 - - - -
41B GLN* 2.9 42.6 + - + +
43B ARG* 3.7 47.3 - - + +
146B ILE* 4.6 1.6 - - - -
618D G 5.8 0.4 - - - +
619D T 4.2 18.2 - - + -
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Residues in contact with SER 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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30B ILE 4.1 1.4 + - - -
31B VAL* 1.3 76.4 - - - +
33B ARG* 1.3 68.8 + - - +
34B GLU* 4.3 14.9 + - - +
39B LYS 3.8 1.1 - - - -
40B TYR* 3.7 22.6 - - - -
146B ILE* 4.1 14.0 - - - +
619D T 4.4 13.4 + - - +
620D T 5.2 8.5 - - - +
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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