Contacts of the strand formed by residues 48 - 54 (chain A) in PDB entry 3A4I
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 LEU 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ALA* 3.6 13.0 - - + +
25A ILE* 3.9 21.8 - - + -
37A ALA* 3.3 35.4 - - + +
40A ALA* 3.8 16.8 - - + -
41A HIS* 3.6 19.4 + - + +
44A ILE* 3.6 15.3 - - + +
45A GLY 2.9 15.2 + - - +
46A ASP 3.6 0.2 - - - +
47A ARG* 1.3 78.4 - - - +
49A HIS* 1.3 64.3 + - - +
50A ALA* 3.9 2.5 + - + +
76A MET* 4.5 8.5 - - + -
77A ASN* 3.2 25.6 + - - +
125A ILE* 3.9 17.9 - - + -
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Residues in contact with HIS 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LYS* 3.5 28.4 - - + +
23A ALA 2.8 16.5 + - - +
24A ILE* 3.3 7.6 - - + +
25A ILE* 3.0 24.3 + - - +
46A ASP 3.8 4.4 + - - -
47A ARG* 3.5 17.0 - - - -
48A LEU* 1.3 75.0 - - - +
50A ALA* 1.3 61.6 + - - +
51A VAL* 4.0 0.4 - - - -
77A ASN* 3.3 27.4 + - - -
79A HIS* 2.9 32.0 + + + +
119A ILE* 3.6 33.8 - - + +
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ILE* 3.5 15.5 - - + -
27A LEU* 3.8 29.2 - - + -
48A LEU* 3.9 4.1 + - + +
49A HIS* 1.3 72.3 - - - +
51A VAL* 1.3 55.8 + - - +
52A PHE 4.0 0.2 - - - -
76A MET* 4.4 17.7 - - + -
77A ASN 2.9 12.2 + - - +
78A LEU* 3.3 11.4 - - + +
79A HIS* 2.7 31.4 + - - -
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 3.7 34.5 - - + -
25A ILE 2.8 13.3 + - - +
26A ALA* 3.5 4.7 - - - +
27A LEU* 2.8 27.3 + - - +
49A HIS 4.4 0.4 - - - +
50A ALA* 1.3 75.1 - - - +
52A PHE* 1.3 61.2 + - - +
53A VAL* 4.0 17.0 + - + +
79A HIS* 3.6 5.8 - - + -
81A VAL* 3.8 25.1 - - + -
108A PHE* 5.8 0.3 - - - -
112A PHE* 4.0 17.5 - - + -
115A VAL* 4.1 14.4 - - + -
119A ILE* 4.1 13.9 - - + -
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Residues in contact with PHE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 3.3 23.6 - - + +
28A SER* 4.6 10.1 - - - -
50A ALA 3.9 0.8 + - - -
51A VAL* 1.3 73.4 - - - +
53A VAL* 1.3 66.7 + - - +
54A ASN 3.8 1.6 + - - -
58A LEU* 3.6 31.2 - - + -
62A GLU* 5.0 1.6 - - + -
63A PRO* 3.8 25.1 - - + -
66A VAL* 3.8 39.0 - - + -
67A VAL* 4.4 4.5 - - + -
78A LEU* 3.8 20.4 - - + -
79A HIS 2.9 10.0 + - - +
80A TYR* 3.5 33.7 - + - -
81A VAL* 2.9 27.8 + - - +
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Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU 4.5 2.0 + - - -
51A VAL* 4.0 19.7 + - + +
52A PHE* 1.3 87.2 - - - +
54A ASN* 1.3 62.1 + - - +
55A THR* 3.4 16.9 + - + +
58A LEU* 4.2 4.7 - - - +
81A VAL* 3.6 7.2 - - + +
83A ALA* 4.0 13.2 - - + -
87A PHE* 3.9 27.8 - - + -
108A PHE* 3.7 32.6 - - + -
111A VAL* 3.8 22.2 - - + -
112A PHE* 5.2 3.1 - - - +
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Residues in contact with ASN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A PHE* 3.8 2.4 + - + -
53A VAL* 1.3 68.3 - - - +
55A THR* 1.3 63.4 + - - +
56A GLY* 3.0 22.9 + - - +
58A LEU* 3.7 23.5 - - + +
63A PRO* 3.6 15.8 - - - +
80A TYR* 2.8 34.5 + - + +
81A VAL 2.8 16.3 + - - +
82A ASP* 4.3 5.8 - - - -
83A ALA* 3.0 27.4 + - - +
84A GLN* 3.2 20.3 + - - +
210A ARG* 5.9 0.2 - - - +
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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