Contacts of the strand formed by residues 68 - 73 (chain I) in PDB entry 5G04
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 VAL 68 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I ILE* 4.1 17.5 - - - +
38I ALA* 4.0 19.2 - - + +
39I ASN 5.1 0.7 - - - +
42I GLY* 4.1 27.8 - - - +
44I VAL* 4.2 11.0 - - + -
67I GLU* 1.3 74.6 - - - +
69I THR* 1.3 61.3 + - - +
70I CYS 3.4 21.8 - - - +
71I LEU* 4.7 4.5 - - + -
82I PHE* 3.9 19.1 - - + -
83I ALA 3.2 20.2 - - - +
84I LEU* 4.1 11.7 - - + -
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Residues in contact with THR 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I ILE* 5.6 7.4 - - - +
25I PHE* 4.4 15.7 - - - +
67I GLU* 4.3 0.9 + - + -
68I VAL* 1.3 76.4 - - - +
70I CYS* 1.3 69.1 + - - +
71I LEU* 5.0 2.7 - - - -
83I ALA* 3.4 7.8 + - - +
85I ALA* 3.7 25.7 - - + +
110I VAL 2.6 28.5 + - - +
111I SER* 4.3 3.1 - - - -
570I PHE* 5.3 11.6 - - + -
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Residues in contact with CYS 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I PHE* 5.0 7.6 - - + -
68I VAL* 3.4 3.1 - - - +
69I THR* 1.3 91.4 + - - +
71I LEU* 1.3 69.9 + - - +
82I PHE* 3.3 21.0 - - - +
83I ALA* 3.3 13.0 + - + -
110I VAL 4.1 1.1 - - - -
111I SER* 3.2 39.0 - - - -
112I CYS* 3.3 11.9 - - - -
113I MET* 3.6 26.2 - - + +
570I PHE* 5.4 2.0 - - - -
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Residues in contact with LEU 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I PHE* 3.5 46.5 - - + -
26I LEU* 4.0 0.2 - - - -
27I VAL* 4.4 8.8 - - + +
36I ALA* 3.4 40.8 - - + +
37I LEU* 3.6 14.6 - - - +
38I ALA* 3.5 26.2 - - + -
44I VAL* 4.5 11.4 - - + -
68I VAL* 4.7 2.2 - - + -
69I THR 5.0 0.2 - - - -
70I CYS* 1.3 86.9 - - - +
72I ALA* 1.3 62.9 + - - +
80I LEU* 4.5 9.9 - - + -
81I ALA 3.8 3.8 - - - -
82I PHE* 4.4 4.3 - - + -
113I MET* 4.4 9.0 - - - +
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Residues in contact with ALA 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71I LEU* 1.3 78.2 - - - +
73I TRP* 1.3 62.2 + - - +
80I LEU* 2.9 10.3 - - - +
81I ALA* 2.6 46.6 + - - +
113I MET* 3.7 33.0 - - + +
115I TRP* 4.3 18.1 - - + +
176I LEU* 4.5 2.5 - - + -
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Residues in contact with TRP 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I VAL* 3.5 42.6 + - + +
28I TRP 3.8 4.3 - - - +
29I SER* 3.7 19.9 - - - +
30I PRO* 3.6 21.8 - - + -
32I ARG* 5.3 0.4 - - - -
34I LEU* 3.9 18.4 - - + -
36I ALA* 3.7 5.9 - - + +
46I LEU* 3.7 23.1 - - + -
71I LEU* 5.8 0.2 - - + -
72I ALA* 1.3 74.5 - - - +
74I ARG* 1.3 62.6 + - - +
75I PRO* 3.9 1.9 - - - +
77I GLY* 3.1 38.4 - - - -
79I LEU 3.6 2.2 - - - -
80I LEU* 3.1 48.5 - - + +
95I VAL* 3.5 20.6 - - + -
115I TRP* 3.5 19.3 + - - +
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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