Contacts of the strand formed by residues 28 - 34 (chain J) in PDB entry 6VVT
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 GLN 28 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27J ARG 1.3 68.7 - - - +
29J VAL* 1.3 62.0 + - - +
30J ALA 3.9 0.4 - - - +
42J VAL 3.7 0.5 - - - +
43J PRO* 2.9 5.9 - - - +
44J PHE* 2.3 61.0 + - + +
45J ALA 3.4 9.4 - - - +
46J ASP* 2.6 45.6 + - + +
48J ALA 3.9 3.5 + - - +
50J ILE* 2.9 39.8 - - + +
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Residues in contact with VAL 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J ARG* 4.4 21.1 - - + +
28J GLN* 1.3 78.4 - - - +
30J ALA* 1.3 61.2 + - - +
31J ARG* 5.3 4.4 - - + +
41J ASP* 4.4 26.5 - - + +
42J VAL 4.3 2.7 - - - +
43J PRO* 4.4 9.9 - - + -
50J ILE* 6.2 0.9 - - - -
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Residues in contact with ALA 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J GLN 3.9 0.4 + - - -
29J VAL* 1.3 74.0 - - - +
31J ARG* 1.3 61.0 + - - +
32J TYR* 4.2 4.2 + - + -
40J PHE 3.8 0.3 - - - +
41J ASP* 3.5 3.1 - - - +
42J VAL* 2.8 46.8 + - - +
44J PHE* 3.9 19.5 - - + -
50J ILE* 4.1 11.0 - - + -
64J LEU* 3.8 26.2 - - + -
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Residues in contact with ARG 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J VAL* 5.3 5.4 - - + +
30J ALA* 1.3 77.0 - - - +
32J TYR* 1.3 63.5 + - - +
39J GLU* 2.2 43.0 + - + +
40J PHE 3.2 5.8 - - - +
41J ASP* 3.0 47.1 + - - +
64J LEU* 3.4 10.4 - - - +
65J ILE* 3.3 42.9 + - + +
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Residues in contact with TYR 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J ALA* 4.2 9.6 - - + -
31J ARG* 1.3 75.9 - - - +
33J ARG* 1.3 60.0 + - - +
34J THR 4.3 0.2 - - - -
38J GLU 4.2 0.2 - - - +
39J GLU* 3.4 8.8 - - - +
40J PHE* 3.0 32.7 + - - +
42J VAL* 4.0 16.6 - - + -
44J PHE* 4.0 19.8 - + - -
51J PRO* 2.8 38.7 + - - +
52J GLY 3.5 20.2 - - - -
54J TRP* 3.4 31.9 - + + +
56J CYS* 4.1 15.0 - - - -
62J GLY 3.0 26.7 - - - -
63J THR 3.5 2.7 - - - -
64J LEU* 3.3 27.0 - - + +
65J ILE* 4.9 2.9 - - - +
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Residues in contact with ARG 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32J TYR* 1.3 74.2 - - - +
34J THR* 1.3 73.6 + - - +
35J ASP* 5.3 1.0 - - - +
37J GLY* 5.3 7.3 + - - -
38J GLU 3.9 5.6 - - - +
39J GLU* 2.4 34.1 + - + +
61J GLU 4.2 0.2 - - - +
62J GLY* 3.2 4.9 - - - -
63J THR* 2.9 34.5 + - - +
65J ILE* 3.9 27.9 - - + +
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Residues in contact with THR 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J ARG* 1.3 87.9 - - - +
35J ASP* 1.3 66.1 + - - +
36J ASN* 2.4 26.0 + - - -
37J GLY* 3.3 9.5 + - - -
38J GLU* 2.7 24.2 + - - +
40J PHE* 3.3 32.1 - - + -
56J CYS* 4.3 11.0 - - + -
58J ASN* 4.0 12.6 - - + +
60J LEU* 4.6 8.3 - - + +
61J GLU 3.9 14.6 - - - +
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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