Contacts of the strand formed by residues 24 - 28 (chain B) in PDB entry 3A4Y
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 ARG 24 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU 4.4 0.4 - - - -
20B LEU* 3.7 3.6 - - - +
21B ALA 2.9 31.9 + - - +
22B GLY 4.1 1.7 + - - +
23B GLY* 1.3 106.9 + - - +
25B ARG* 1.3 67.7 + - - +
26B VAL* 4.1 12.3 - - + -
53B ASP* 3.0 40.6 + - + +
129B LEU* 3.6 24.5 - - + +
130B GLY* 3.7 13.7 - - - -
132B LEU* 5.3 0.7 - - + -
432B SO4 3.7 34.5 + - - -
445B SO4 2.6 47.3 + - - -
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Residues in contact with ARG 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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18B LEU* 3.5 34.5 - - + +
19B LEU 3.6 5.2 - - - -
20B LEU* 3.2 30.0 - - + +
24B ARG* 1.3 79.5 - - - +
26B VAL* 1.3 59.1 + - - +
47B PHE* 4.6 9.8 - - - +
48B ASP* 5.1 7.2 + - - +
51B GLU* 3.5 50.3 + - - +
52B VAL* 3.5 9.3 - - + +
53B ASP* 2.6 41.3 + - - +
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.6 3.1 - - - +
19B LEU* 2.7 51.5 + - + +
24B ARG* 4.6 4.0 - - + -
25B ARG* 1.3 81.1 - - - +
27B LEU* 1.3 63.5 + - - +
28B LEU* 3.7 17.4 - - + +
53B ASP* 5.0 0.2 - - + -
54B ALA* 3.3 18.6 - - + +
56B LEU* 4.2 16.4 - - + -
129B LEU* 3.3 29.6 - - + -
132B LEU* 4.2 17.0 - - + -
134B LEU* 4.5 7.6 - - + -
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Residues in contact with LEU 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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6B PHE* 5.8 0.2 - - + -
16B ALA* 4.2 6.3 - - + -
17B HIS 3.4 24.7 - - - +
18B LEU* 3.9 10.4 - - + +
25B ARG 4.2 0.2 - - - -
26B VAL* 1.3 70.9 - - - +
28B LEU* 1.3 68.9 + - - +
29B ASP 3.4 26.8 + - - +
30B CYS* 3.8 23.3 - - + -
47B PHE* 3.9 33.4 - - + -
52B VAL* 4.4 5.4 - - + +
54B ALA 2.9 15.1 + - - +
55B VAL* 3.4 9.2 - - + +
56B LEU 2.8 27.9 + - - -
71B LEU* 4.0 16.6 - - + -
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Residues in contact with LEU 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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3B ILE* 4.4 19.1 - - + -
17B HIS* 2.7 41.3 + - + +
19B LEU* 4.1 14.1 - - + -
26B VAL* 3.7 26.7 - - + +
27B LEU* 1.3 79.6 - - - +
29B ASP* 1.3 69.0 + - - +
56B LEU* 3.5 15.5 - - + -
58B THR* 6.1 0.2 - - + -
134B LEU* 5.1 2.0 - - + -
148B VAL* 4.6 15.5 - - + -
150B ALA* 5.9 0.2 - - + -
157B LEU* 4.5 11.7 - - + -
159B TYR* 3.8 38.8 - - + -
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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