Contacts of the strand formed by residues 47 - 53 (chain A) in PDB entry 4I0A
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 SER 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ILE* 5.0 0.9 - - - -
46A GLY* 1.3 72.5 - - - -
48A VAL* 1.3 65.7 + - - +
64A TYR* 6.1 0.9 - - - -
65A LEU 3.3 4.9 - - - -
66A ASN* 3.1 30.1 - - - -
90A LYS* 2.9 42.5 + - - +
91A THR* 3.2 19.7 + - - +
93A CYS* 3.4 11.5 - - - -
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Residues in contact with VAL 48 (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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30A LEU* 4.2 15.0 - - + -
43A ILE* 3.9 18.2 - - + -
47A SER* 1.3 80.9 - - - +
49A ALA* 1.3 62.7 + - - +
64A TYR* 3.3 11.4 - - - +
65A LEU* 2.9 57.2 + - + +
71A ILE* 4.3 2.7 - - + -
87A VAL* 3.6 28.3 - - + -
88A ARG 3.2 13.9 - - - +
89A ALA* 4.1 3.6 - - - -
90A LYS* 4.0 4.5 - - - +
93A CYS* 4.0 14.8 - - - -
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Residues in contact with ALA 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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48A VAL* 1.3 74.8 - - - +
50A VAL* 1.3 63.0 + - - +
51A LEU* 3.6 20.0 - - + +
61A ILE* 4.8 9.2 - - + -
63A SER 3.5 5.6 - - - +
64A TYR* 3.9 21.1 - - + -
87A VAL* 3.3 5.4 - - - +
88A ARG* 2.8 36.0 + - + +
90A LYS* 4.5 5.3 - - + +
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Residues in contact with VAL 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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48A VAL* 5.0 0.4 - - + -
49A ALA* 1.3 76.1 - - - +
51A LEU* 1.3 59.6 + - - +
61A ILE* 3.4 5.2 - - - -
62A LEU* 2.7 38.5 + - + -
63A SER 2.7 23.4 + - - +
65A LEU* 3.9 19.7 - - + -
85A ALA* 3.6 20.2 - - + -
86A TRP 3.4 3.4 - - - +
87A VAL* 4.2 10.3 - - + -
301A CMP 3.6 54.3 - - + +
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Residues in contact with LEU 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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49A ALA* 3.6 24.9 - - + +
50A VAL* 1.3 77.3 - - - +
52A ILE* 1.3 65.8 + - - +
53A LYS* 6.0 0.7 - - + -
59A GLU* 4.2 26.7 - - + +
60A MET 3.2 7.6 - - - +
61A ILE* 3.9 23.8 - - + -
62A LEU* 4.6 0.9 - - - +
85A ALA* 3.4 4.5 - - - +
86A TRP* 2.9 47.2 + - + +
88A ARG* 4.0 46.0 - - + +
175A GLN* 4.2 5.8 - - - +
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Residues in contact with ILE 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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33A GLN* 3.9 8.5 - - - +
51A LEU* 1.3 79.9 - - - +
53A LYS* 1.3 68.2 + - - +
59A GLU* 3.4 5.7 - - - +
60A MET* 2.9 45.3 + - + +
62A LEU* 3.8 27.8 - - + -
84A SER 3.7 21.8 - - - +
85A ALA* 3.9 0.9 - - + -
86A TRP* 4.1 5.8 - - - -
129B SER* 3.6 26.2 - - - +
130B GLU* 5.0 2.9 - - - -
133B GLY* 3.8 20.0 - - - -
137B PHE* 4.5 4.3 - - + -
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Residues in contact with LYS 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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33A GLN* 5.0 2.5 + - - +
51A LEU* 6.0 1.6 - - + -
52A ILE* 1.3 84.1 - - - +
54A ASP* 1.3 68.1 + - - +
57A GLY* 4.4 14.1 - - - +
58A LYS 3.1 11.7 - - - +
59A GLU* 3.5 31.1 + - + -
86A TRP* 3.7 51.3 - - + +
88A ARG* 5.0 4.8 - - - +
137B PHE* 3.6 7.4 - - - -
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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