Contacts of the strand formed by residues 30 - 35 (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 MET 30 (chain g).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23g THR* 4.9 1.7 - - - +
24g THR* 4.1 16.2 + - + +
27g PHE* 3.2 56.7 + - + +
28g PRO 4.6 1.4 - - - +
29g ASP* 1.3 81.6 - - + +
31g ILE* 1.3 66.6 + - - +
32g LEU* 6.4 0.2 - - - -
42g MET* 3.6 35.7 - - + -
43g TRP 3.1 12.6 - - - +
44g LYS* 4.9 3.4 - - - +
56g GLN* 5.8 3.1 - - - +
75g GLY* 5.0 9.4 - - - +
92g LEU* 5.1 6.3 - - - -
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Residues in contact with ILE 31 (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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11g LEU* 4.2 6.3 - - + -
21g ILE* 3.7 23.3 - - + -
22g ALA 3.5 13.7 - - - +
23g THR* 3.7 18.4 - - + -
28g PRO 6.0 0.2 - - - +
30g MET* 1.3 79.6 - - - +
32g LEU* 1.3 66.7 + - - +
33g SER* 4.1 0.9 - - - +
42g MET* 3.7 6.6 - - - +
43g TRP* 2.9 56.6 + - + +
45g LEU* 4.1 15.5 - - + -
299g PHE* 3.5 45.3 - - + -
307g VAL* 5.6 1.1 - - + -
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Residues in contact with LEU 32 (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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21g ILE* 3.5 2.5 - - - -
22g ALA* 2.8 47.5 + - + +
30g MET* 6.4 0.2 - - - -
31g ILE* 1.3 80.1 - - - +
33g SER* 1.3 60.3 + - - +
34g ALA 4.1 0.2 - - - -
40g ILE* 3.9 18.2 - - + -
41g ILE 3.9 9.0 - - - +
42g MET* 4.0 14.1 - - + -
59g LEU* 5.6 0.4 - - + -
69g VAL* 3.8 20.4 - - + +
71g ILE* 3.8 20.4 - - + -
78g ALA* 3.7 30.1 - - + -
92g LEU* 3.7 31.4 - - + -
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Residues in contact with SER 33 (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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14g HIS* 3.5 22.8 + - - -
18g VAL* 4.0 7.6 - - - -
20g GLN 3.9 3.8 - - - -
21g ILE* 3.7 20.9 - - - +
31g ILE* 4.1 1.5 - - - +
32g LEU* 1.3 72.6 - - - +
34g ALA* 1.3 60.7 + - - +
40g ILE* 3.6 3.3 - - - -
41g ILE 2.8 36.5 + - - -
43g TRP* 3.0 30.9 + - - -
307g VAL* 4.2 3.2 - - - +
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Residues in contact with ALA 34 (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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18g VAL* 3.3 8.1 - - - +
19g THR* 2.8 34.6 + - - +
20g GLN 2.9 17.3 + - - +
32g LEU 4.0 1.2 + - - -
33g SER* 1.3 73.0 - - - +
35g SER* 1.3 58.5 + - - +
39g THR 4.0 3.6 - - - -
40g ILE* 4.4 7.4 - - + +
66g VAL* 3.9 21.3 - - + +
69g VAL* 3.7 24.8 - - + +
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Residues in contact with SER 35 (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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14g HIS* 3.5 36.0 - - - -
16g GLY 3.5 5.2 + - - -
17g TRP 2.5 21.9 + - - -
18g VAL* 4.2 0.2 - - - +
19g THR* 4.2 5.6 - - - +
34g ALA* 1.3 75.0 - - - +
36g ARG* 1.3 62.2 + - - +
37g ASP* 3.1 28.7 + - - +
38g LYS 3.4 9.2 + - - -
39g THR 3.0 12.7 + - - +
66g VAL* 3.8 16.7 + - - +
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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