Contacts of the strand formed by residues 64 - 69 (chain A) in PDB entry 1VQ9
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 ASP 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ARG* 3.8 19.6 + - - +
59A GLU* 4.9 0.4 - - - -
60A PHE* 3.2 35.8 + - - -
62A ASP* 2.7 28.5 - - - +
63A GLY* 1.3 76.7 - - - +
65A ARG* 1.3 60.7 + - - +
66A ARG* 3.6 14.6 + - - +
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Residues in contact with ARG 65 (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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43A VAL* 4.7 10.6 - - - +
44A ASP* 5.0 4.9 + - - +
46A GLU* 3.8 11.9 + - - -
57A ALA* 3.3 33.9 - - - +
58A VAL 3.3 19.5 - - - -
59A GLU* 3.8 33.3 + - + +
63A GLY 3.6 6.8 + - - +
64A ASP* 1.3 69.5 - - - +
66A ARG* 1.3 71.5 + - - +
67A LEU* 5.3 1.6 - - - +
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Residues in contact with ARG 66 (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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28A GLU* 3.4 25.1 + - - +
29A HIS 4.2 1.6 + - - -
30A ARG* 3.2 41.8 - - - +
31A LYS 5.3 0.2 - - - +
57A ALA* 3.8 1.6 - - - -
58A VAL* 3.0 33.1 + - - +
60A PHE* 4.5 7.8 - - + -
64A ASP* 3.6 28.8 + - + +
65A ARG* 1.3 84.3 - - - +
67A LEU* 1.3 72.0 + - - +
68A ILE* 3.9 1.3 + - - +
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Residues in contact with LEU 67 (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 LYS* 4.1 35.7 - - + -
25A ALA* 4.3 18.9 - - + +
26A ASP 4.6 3.2 - - - +
27A LEU* 3.9 22.6 - - + +
28A GLU 5.4 1.7 - - - +
46A GLU* 4.0 18.4 - - - +
55A VAL* 3.8 26.0 - - + +
56A ALA 3.5 0.7 - - - -
57A ALA* 3.6 30.7 - - + +
65A ARG* 5.3 2.0 - - - +
66A ARG* 1.3 83.9 + - - +
68A ILE* 1.3 60.0 + - - +
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Residues in contact with ILE 68 (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* 4.1 7.2 - - - +
29A HIS* 6.0 3.8 - - - +
55A VAL* 3.2 16.5 - - - +
56A ALA* 2.7 38.8 + - + +
58A VAL* 3.7 17.5 - - + -
60A PHE* 5.5 10.1 - - + -
66A ARG* 5.0 0.9 - - - +
67A LEU* 1.3 74.1 - - - +
69A LEU* 1.3 73.8 + - + +
70A ALA* 2.9 9.9 + - - +
71A PRO* 5.6 4.3 - - + -
80A LEU* 3.9 23.1 - - + -
82A VAL* 5.8 5.2 - - + -
91A GLY 4.6 7.9 - - - +
93A THR* 5.2 9.0 - - - +
107A ASN* 6.3 0.7 - - - +
155A THR* 5.6 5.8 - - + +
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Residues in contact with LEU 69 (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* 3.4 27.6 + - + +
51A ARG* 3.2 44.4 - - - +
55A VAL* 4.5 0.2 - - - -
68A ILE* 1.3 78.9 - - + +
70A ALA* 1.3 58.4 + - - +
71A PRO* 3.0 18.5 - - - +
106A CYS* 4.7 4.6 - - - -
107A ASN* 3.4 43.1 - - + +
119A ALA 4.2 2.0 - - - +
120A ARG* 3.9 27.4 - - + +
155A THR* 4.9 4.9 + - - +
159A VAL* 4.4 16.6 - - + -
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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