Contacts of the strand formed by residues 38 - 45 (chain A) in PDB entry 5VZ4
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 GLU 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ARG* 3.3 44.3 + - + +
22A ALA 3.4 20.0 - - - +
23A SER* 4.6 4.5 - - - +
36A PRO* 3.4 17.2 - - - +
37A ARG* 1.3 79.5 - - + +
39A VAL* 1.3 63.4 + - - +
40A GLN* 3.7 10.7 + - - +
140B GLY 5.1 3.3 - - - +
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Residues in contact with VAL 39 (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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20A VAL 3.6 0.2 - - - +
21A ARG* 3.6 0.7 - - - -
22A ALA* 2.7 36.7 + - - +
24A LEU* 5.0 2.7 - - + -
27A LEU* 3.9 22.4 - - + -
29A TRP* 4.4 10.1 - - + -
36A PRO* 4.0 11.2 - - + +
38A GLU* 1.3 77.4 - - - +
40A GLN* 1.3 69.6 + - - +
41A VAL* 3.2 26.7 + - + +
86A MET* 4.0 37.0 - - + -
104A LEU* 4.8 4.9 - - + -
105A LEU* 4.2 5.4 - - + -
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Residues in contact with GLN 40 (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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19A THR* 3.5 26.2 - - + -
20A VAL 4.2 2.0 - - - -
21A ARG* 3.1 53.8 + - + +
38A GLU* 3.7 12.2 + - - +
39A VAL* 1.3 71.8 - - - +
41A VAL* 1.3 63.9 + - - +
42A THR* 3.3 8.2 + - + +
105A LEU* 3.5 14.6 - - - +
142B VAL* 3.5 32.0 - - + +
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Residues in contact with VAL 41 (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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18A HIS 3.4 1.2 - - - +
19A THR* 3.3 3.2 - - - -
20A VAL* 2.9 45.1 + - + +
22A ALA* 4.3 11.4 - - + -
27A LEU* 4.9 11.0 - - + -
39A VAL* 3.6 25.1 - - + +
40A GLN* 1.3 70.3 - - - +
42A THR* 1.3 68.4 + - - +
43A MET* 3.7 28.5 + - + +
104A LEU* 4.8 14.4 - - + +
105A LEU* 4.0 5.6 - - + -
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Residues in contact with THR 42 (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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17A LEU* 4.0 17.9 - - + -
18A HIS 3.2 3.8 - - - +
19A THR* 3.8 21.1 - - + +
40A GLN* 3.3 8.7 + - + +
41A VAL* 1.3 76.4 - - - +
43A MET* 1.3 61.5 + - - +
84A ASN* 5.0 3.3 + - - +
104A LEU 4.7 0.9 - - - +
105A LEU* 3.5 16.2 - - + +
106A ALA* 2.7 54.9 + - - +
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Residues in contact with MET 43 (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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17A LEU* 3.4 4.7 - - - +
18A HIS* 2.6 48.4 + - - +
20A VAL* 4.2 21.8 - - + -
41A VAL* 3.7 28.9 - - + +
42A THR* 1.3 73.2 - - - +
44A CYS* 1.3 64.5 - - - +
45A ILE* 3.8 28.8 + - + -
80A PRO* 5.9 0.4 - - - -
106A ALA* 4.1 5.6 - - - -
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Residues in contact with CYS 44 (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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16A ARG 3.5 0.2 - - - -
43A MET* 1.3 76.6 - - - +
45A ILE* 1.3 63.2 + - - +
78A CYS* 3.5 26.3 - - - +
79A VAL* 3.9 13.0 - - - -
80A PRO* 3.6 18.9 - - + +
106A ALA* 4.0 9.4 - - - +
108A ASP 3.6 8.3 - - - -
109A CYS* 2.1 53.4 - - + -
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Residues in contact with ILE 45 (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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14A CYS 3.7 1.0 - - - +
15A CYS* 3.6 0.2 - - - -
16A ARG 3.0 26.5 + - - +
18A HIS* 3.3 48.5 - - + +
20A VAL* 5.1 5.8 - - + -
43A MET* 3.8 26.4 + - + -
44A CYS* 1.3 78.2 - - - +
46A GLY* 1.3 63.3 - - - +
78A CYS* 3.6 6.5 - - - -
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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