Contacts of the strand formed by residues 38 - 45 (chain B) in PDB entry 5VT2
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ARG* 3.2 47.7 + - + +
22B ALA 3.2 15.4 - - - +
23B SER* 4.0 9.7 - - - +
24B LEU 4.8 0.2 - - - +
36B PRO* 3.3 17.8 - - - +
37B ARG* 1.3 84.5 - - + +
39B VAL* 1.3 67.3 + - - +
40B GLN* 3.7 10.5 + - - +
86B MET* 5.4 0.2 - - - +
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Residues in contact with VAL 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ILE* 6.0 0.2 - - + -
21B ARG* 3.7 0.5 - - - -
22B ALA 2.7 36.7 + - - +
24B LEU* 4.9 6.1 - - + -
27B LEU* 3.5 30.5 - - + -
29B TRP* 4.3 14.8 - - + -
36B PRO* 4.8 4.5 - - + -
38B GLU* 1.3 78.5 - - - +
40B GLN* 1.3 67.3 + - - +
41B VAL* 3.1 27.6 + - + +
86B MET* 4.0 33.0 - - + -
88B LEU* 6.3 0.2 - - + -
104B LEU* 4.8 5.4 - - + -
105B LEU* 4.2 6.5 - - + -
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Residues in contact with GLN 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR* 3.7 24.8 - - + +
20B VAL 4.1 2.9 - - - -
21B ARG* 3.4 36.6 + - - +
38B GLU* 3.7 13.5 + - - +
39B VAL* 1.3 73.9 - - - +
41B VAL* 1.3 64.4 + - - +
42B THR* 3.3 9.3 + - + +
86B MET* 5.4 2.0 - - - +
105B LEU* 3.8 11.1 - - - +
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Residues in contact with VAL 41 (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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58A HIS* 4.3 9.0 - - + +
61A ILE* 3.9 26.7 - - + -
65A LEU* 4.3 2.9 - - + -
18B HIS 3.5 0.7 - - - +
19B THR* 3.3 3.3 - - - -
20B VAL* 2.9 44.6 + - - +
22B ALA* 4.2 15.0 - - + -
27B LEU* 4.9 2.0 - - + -
39B VAL* 3.7 23.1 - - + +
40B GLN* 1.3 67.9 - - - +
42B THR* 1.3 73.1 + - - +
43B MET* 3.8 27.1 + - + +
104B LEU 4.7 1.6 - - - +
105B LEU* 4.0 8.7 - - + -
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Residues in contact with THR 42 (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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58A HIS* 3.0 12.5 + - - -
17B LEU* 4.0 19.3 - - + -
18B HIS 3.2 3.4 - - - +
19B THR* 4.0 19.1 - - + +
40B GLN* 3.3 9.2 + - + +
41B VAL* 1.3 72.1 - - - +
43B MET* 1.3 62.2 + - - +
84B ASN* 5.6 0.5 + - - -
105B LEU* 3.3 16.1 - - + +
106B ALA* 2.7 52.8 + - - +
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Residues in contact with MET 43 (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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58A HIS* 3.9 17.0 - - + +
61A ILE* 4.4 3.8 - - + -
62A LYS* 4.3 20.2 - - + -
65A LEU* 3.8 29.6 - - + -
73A VAL* 3.8 31.0 - - + -
74A PRO* 4.5 2.5 - - - -
17B LEU* 3.6 3.7 - - - +
18B HIS* 2.8 37.8 + - - +
20B VAL* 4.5 9.9 - - + -
41B VAL* 3.8 19.3 - - + +
42B THR* 1.3 76.9 - - - +
44B CYS* 1.3 73.0 + - - +
45B ILE* 3.7 16.2 + - + -
106B ALA* 4.0 2.2 - - - -
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Residues in contact with CYS 44 (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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58A HIS* 4.7 2.6 - - - -
62A LYS* 5.3 3.1 + - - -
74A PRO* 4.2 10.4 - - - +
16B ARG 3.5 0.2 - - - -
43B MET* 1.3 77.0 - - - +
45B ILE* 1.3 64.0 + - - +
78B CYS* 3.6 25.3 - - - +
79B VAL* 3.9 13.2 - - - -
80B PRO* 3.7 15.9 - - + -
106B ALA* 4.0 12.2 - - - +
108B ASP 3.5 8.5 - - - -
109B CYS* 2.1 54.3 - - + -
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Residues in contact with ILE 45 (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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72A THR* 3.8 28.3 - - + +
73A VAL* 4.8 0.2 - - - -
74A PRO* 4.1 17.3 - - + -
14B CYS 3.5 2.4 - - - +
15B CYS* 3.4 0.2 - - - -
16B ARG 3.0 27.2 + - - +
18B HIS* 3.6 45.8 - - + +
20B VAL* 4.5 9.0 - - + -
43B MET* 4.1 24.9 - - + +
44B CYS* 1.3 80.3 - - - +
46B GLY* 1.3 63.5 + - - +
78B CYS* 3.6 7.1 - - - -
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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