Contacts of the strand formed by residues 54 - 59 (chain g) in PDB entry 5OA3
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 ILE 54 (chain g).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101Q ASP* 5.1 1.3 - - + +
103Q ALA* 3.5 30.5 - - + -
43g TRP* 3.5 4.7 - - - -
44g LYS* 2.7 44.0 + - + +
46g THR* 4.3 14.8 - - - +
48g ASP* 5.7 1.1 - - - +
51g ASN* 3.5 27.6 - - + +
53g GLY* 1.3 78.6 - - - +
55g PRO* 1.3 86.3 - - + +
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Residues in contact with PRO 55 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Q ASP* 4.6 2.6 - - - +
102Q GLU* 3.6 40.7 + - + +
103Q ALA* 5.2 0.7 - - - -
106Q LYS* 5.8 7.9 - - + -
12g LYS 5.0 3.8 - - - +
13g GLY* 4.7 10.8 - - - -
41g ILE* 3.9 27.6 - - + -
42g MET 3.6 6.1 - - - +
43g TRP* 3.6 16.6 - - + -
44g LYS* 5.4 0.3 - - - +
53g GLY 4.5 0.7 - - - +
54g ILE* 1.3 105.0 - - + +
56g GLN* 1.3 60.4 + - - +
57g ARG 6.3 0.2 - - - -
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Residues in contact with GLN 56 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97Q GLN 4.4 0.3 - - - +
100Q VAL 4.0 3.3 - - - +
101Q ASP* 3.6 18.0 - - + +
102Q GLU* 3.3 24.8 + - - +
30g MET* 5.8 3.0 - - - +
42g MET* 2.7 40.1 + - + +
44g LYS* 3.2 37.5 - - + +
55g PRO* 1.3 76.4 - - - +
57g ARG* 1.3 76.2 + - + +
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Residues in contact with ARG 57 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97Q GLN 4.8 6.7 - - - +
98Q LYS* 3.2 26.7 + - - +
99Q TYR* 4.9 7.1 - - - +
100Q VAL 5.3 2.8 + - - +
102Q GLU* 4.7 1.3 - - - -
40g ILE 3.1 14.2 - - - +
41g ILE* 3.7 2.0 - - - -
42g MET* 3.2 33.4 + - + +
55g PRO* 6.3 0.2 - - - -
56g GLN* 1.3 97.5 - - + +
58g ALA* 1.3 60.7 + - - +
59g LEU* 3.8 13.6 + - + +
92g LEU 3.6 15.3 - - - +
93g THR 2.5 29.3 + - - -
94g THR* 2.9 28.1 + - - +
95g GLY* 3.2 7.0 - - - +
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Residues in contact with ALA 58 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97Q GLN* 3.1 38.5 + - - +
102Q GLU* 3.5 27.4 + - - +
105Q LYS* 5.2 0.2 - - - +
39g THR* 3.5 19.7 - - + -
40g ILE 3.6 4.3 - - - -
41g ILE* 4.6 5.6 - - + -
57g ARG* 1.3 71.2 - - - +
59g LEU* 1.3 64.2 + - - +
60g ARG* 3.8 2.1 + - - +
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Residues in contact with LEU 59 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32g LEU* 5.6 0.2 - - + -
38g LYS 3.7 2.8 - - - +
39g THR* 3.7 6.1 - - - +
40g ILE* 3.0 55.1 + - + +
42g MET* 6.4 0.7 - - + -
57g ARG* 4.3 15.7 - - + +
58g ALA* 1.3 75.2 - - - +
60g ARG* 1.3 61.9 + - - +
61g GLY 3.9 2.1 + - - -
62g HIS* 5.8 0.7 - - - -
78g ALA* 5.9 0.4 - - + -
90g TRP* 3.8 44.3 - - + -
91g ASP 4.9 1.6 - - - +
92g LEU* 3.9 28.7 - - + -
95g GLY* 3.7 32.8 - - - +
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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