Contacts of the strand formed by residues 67 - 72 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423E ILE* 4.6 1.2 - - - +
434E MET* 3.8 5.5 - - - +
48J ILE* 3.9 22.4 - - + +
59J TYR* 3.8 31.5 - - + -
63J LEU* 4.8 7.6 - - + +
65J SER* 5.0 1.6 - - - -
66J ARG* 1.3 82.5 + - - +
68J VAL* 1.3 65.3 + - - +
69J ILE* 5.3 0.2 - - + -
80J LEU* 4.0 5.4 - - + -
81J GLN 3.0 10.3 - - - +
82J LEU* 3.8 16.6 - - + -
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Residues in contact with VAL 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E VAL* 4.6 10.1 - - + -
122E LEU* 4.6 19.3 - - + -
423E ILE* 3.6 26.5 - - + -
434E MET* 3.4 42.0 - - + -
59J TYR* 3.8 4.0 - - - +
67J ALA* 1.3 76.5 - - - +
69J ILE* 1.3 70.7 + - - +
70J SER* 5.1 1.6 - - - +
79J SER 3.4 4.3 - - - +
80J LEU* 3.5 0.7 - - - -
81J GLN* 2.9 44.6 + - + +
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Residues in contact with ILE 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36J TRP* 3.5 35.0 - - + +
48J ILE* 5.1 1.8 - - + -
49J GLY* 3.6 36.1 - - - +
50J TYR* 3.9 4.7 - - - +
51J ILE* 3.9 30.1 - - + -
57J THR* 3.1 24.1 - - + +
59J TYR* 3.3 25.4 + - + -
67J ALA* 5.3 0.7 - - + -
68J VAL* 1.3 79.0 - - - +
70J SER* 1.3 68.6 + - - +
78J LEU* 4.9 1.8 - - + -
79J SER 3.3 6.5 - - - +
80J LEU* 4.3 10.8 - - + -
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Residues in contact with SER 70 (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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122E LEU* 4.0 30.2 - - - +
200E VAL* 5.6 0.5 - - - +
51J ILE* 4.1 9.6 - - - -
68J VAL* 4.1 2.7 + - - -
69J ILE* 1.3 75.2 - - - +
71J ARG* 1.3 65.8 + - - +
78J LEU* 3.6 8.3 - - - +
79J SER* 2.9 46.5 + - - +
81J GLN* 4.5 1.9 + - - -
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Residues in contact with ARG 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J ILE* 3.4 24.0 + - + -
30J SER* 3.4 41.2 + - - +
32J TYR 4.4 2.4 + - - -
34J TRP* 4.8 5.4 - - - +
51J ILE* 4.1 9.2 - - + +
52J SER 3.7 4.2 + - - -
53J ASP* 3.0 38.4 + - - +
55J GLU* 2.8 48.0 + - + +
70J SER* 1.3 80.2 - - - +
72J ASP* 1.3 59.9 + - - +
73J THR* 4.0 7.4 + - + +
77J GLN 3.4 11.4 - - - +
78J LEU* 3.9 13.0 - - + -
79J SER* 4.9 0.4 - - - +
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Residues in contact with ASP 72 (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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198E GLY* 4.4 18.2 + - - -
29J ILE* 4.9 0.9 - - - -
71J ARG* 1.3 74.1 - - - +
73J THR* 1.3 62.9 + - - +
74J SER* 2.6 32.5 + - - -
75J LYS* 3.2 26.4 - - + +
76J ASN 2.8 23.2 + - - -
77J GLN* 2.9 33.2 + - + +
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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