Contacts of the strand formed by residues 67 - 72 (chain Q) in PDB entry 4R2G
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 ALA 67 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423K ILE* 4.0 4.2 - - - +
434K MET* 3.8 2.0 - - - +
48Q ILE* 4.5 10.1 - - + +
59Q TYR* 3.2 42.1 - - + -
63Q LEU* 4.7 9.0 - - + -
65Q SER* 3.3 3.9 - - - +
66Q ARG* 1.3 80.3 - - - +
68Q VAL* 1.3 64.7 + - - +
80Q LEU* 4.4 9.6 - - + -
81Q GLN 3.3 4.7 - - - +
82Q LEU* 4.0 14.8 - - + -
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Residues in contact with VAL 68 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120K VAL* 4.9 4.3 - - + -
122K LEU* 4.2 24.5 - - + -
423K ILE* 3.7 25.8 - - + -
432K LYS* 6.2 1.6 - - + -
434K MET* 3.5 38.6 - - + -
59Q TYR* 3.5 3.4 - - - +
67Q ALA* 1.3 77.4 - - - +
69Q ILE* 1.3 70.0 + - - +
70Q SER* 5.0 0.2 - - - -
79Q SER 3.7 0.2 - - - +
80Q LEU* 3.3 4.4 - - - -
81Q GLN* 2.9 52.6 + - + +
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Residues in contact with ILE 69 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Q TRP 5.2 0.7 - - - +
36Q TRP* 3.7 27.6 - - + +
48Q ILE 5.0 0.4 - - - -
49Q GLY* 3.3 40.8 - - - +
50Q TYR* 3.5 8.3 - - - +
51Q ILE* 3.6 29.8 - - + +
57Q THR* 3.8 13.8 - - + +
59Q TYR* 3.1 33.8 + - + +
68Q VAL* 1.3 78.5 - - - +
70Q SER* 1.3 66.4 + - - +
78Q LEU* 5.5 2.2 - - + -
79Q SER 3.5 5.6 - - - +
80Q LEU* 4.0 17.5 - - + -
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Residues in contact with SER 70 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122K LEU* 3.7 31.5 - - - +
51Q ILE* 4.1 8.4 - - - +
55Q GLU* 5.3 1.3 - - - -
68Q VAL* 5.0 1.8 - - - -
69Q ILE* 1.3 77.7 - - - +
71Q ARG* 1.3 64.2 + - - +
72Q ASP 4.2 0.4 + - - -
77Q GLN 4.0 0.2 - - - +
78Q LEU* 3.5 9.7 - - - +
79Q SER* 2.9 50.7 + - - +
81Q GLN* 4.4 1.7 + - - -
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Residues in contact with ARG 71 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29Q ILE* 3.6 44.0 + - + -
30Q SER* 3.4 31.3 + - - +
32Q TYR 5.1 0.2 + - - -
34Q TRP* 5.2 4.7 - - + -
51Q ILE* 3.9 13.1 - - + +
52Q SER 3.9 6.3 + - - -
53Q ASP* 2.7 34.2 + - - +
54Q ARG* 4.9 0.8 - - - +
55Q GLU* 2.7 59.0 + - - +
70Q SER* 1.3 77.6 - - - +
72Q ASP* 1.3 58.8 + - - +
73Q THR* 3.7 17.1 + - + +
77Q GLN 3.7 2.7 - - - -
78Q LEU* 5.9 0.7 - - + -
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Residues in contact with ASP 72 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197K GLY* 4.2 20.6 - - - -
198K GLY* 4.2 8.5 - - - -
29Q ILE* 4.8 0.2 - - - -
70Q SER* 4.2 1.0 + - - -
71Q ARG* 1.3 70.4 - - - +
73Q THR* 1.3 56.6 + - - +
74Q SER* 2.9 26.3 + - - -
75Q LYS* 2.9 28.5 + - - +
76Q ASN* 2.9 24.1 + - - -
77Q GLN* 2.9 39.2 + - + +
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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