Contacts of the strand formed by residues 45 - 51 (chain B) in PDB entry 2FHO
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 45 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TYR* 3.7 41.0 - - + +
39B PHE* 3.6 27.4 - - + +
40B GLY* 3.6 25.6 - - - +
43B GLY 4.2 0.2 - - - +
44B PRO* 1.3 76.3 - - - +
46B ARG* 1.3 67.5 + - - +
47B GLN* 4.2 2.9 - - - +
48B ILE* 3.8 27.1 - - + -
62B VAL* 4.0 11.0 - - + -
63B VAL 3.6 13.0 - - - +
64B TYR* 4.5 6.1 - - + -
65B GLU* 3.8 9.6 - - - +
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Residues in contact with ARG 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A ASP* 2.9 42.1 + - - +
404A LEU* 4.7 9.0 - - - +
45B ILE* 1.3 74.7 - - - +
47B GLN* 1.3 75.9 + - - +
63B VAL* 3.0 25.8 + - + +
64B TYR 3.5 22.0 - - - +
65B GLU* 3.7 25.2 + - + +
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Residues in contact with GLN 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A ASP* 3.8 21.9 + - - +
404A LEU* 4.2 20.2 - - + +
414A VAL* 4.0 21.4 - - + +
36B TYR* 5.4 5.4 - - - +
45B ILE* 3.7 2.1 - - - +
46B ARG* 1.3 91.1 - - - +
48B ILE* 1.3 74.9 + - - +
49B ARG* 4.1 24.1 - - + +
63B VAL* 3.0 32.9 + - + +
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Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A PHE* 5.6 0.7 - - - -
414A VAL* 3.7 6.8 - - - +
415A LEU* 2.9 54.0 + - + +
35B MET* 4.9 14.8 - - + +
36B TYR* 5.0 11.4 + - + +
39B PHE* 4.3 11.9 - - + -
45B ILE* 3.8 32.5 - - + -
47B GLN* 1.3 82.5 - - - +
49B ARG* 1.3 81.3 + - - +
50B VAL* 4.4 2.9 - - + -
60B ALA* 5.4 0.9 - - + -
61B TYR 4.3 7.2 - - - +
62B VAL* 3.8 30.5 - - + -
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Residues in contact with ARG 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A LEU* 4.9 3.4 - - - +
405A ASP* 2.7 58.2 + - - +
408A PHE* 3.5 44.8 - - + +
409A PRO 5.8 0.8 + - - -
412A TYR* 3.8 25.4 + - + -
413A LYS 3.1 12.3 - - - +
414A VAL* 3.8 26.3 - - + +
415A LEU 4.0 1.3 - - - +
47B GLN* 4.1 22.1 - - + +
48B ILE* 1.3 83.9 - - - +
50B VAL* 1.3 71.9 + - - +
60B ALA* 3.5 12.3 - - - +
61B TYR 3.9 8.7 + - - +
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Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A TYR* 3.3 8.2 - - - -
413A LYS* 2.8 35.1 + - + +
414A VAL 4.9 2.0 - - - +
415A LEU* 4.0 39.3 - - + -
26B LEU* 5.9 1.1 - - + -
30B ILE* 6.3 3.4 - - + -
35B MET* 5.1 7.0 - - + -
48B ILE* 4.4 2.2 - - + -
49B ARG* 1.3 80.8 - - - +
51B GLY* 1.3 67.5 + - - +
52B ASN* 3.4 14.9 + - - +
59B THR 5.1 0.4 - - - +
60B ALA* 4.2 14.1 - - + -
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Residues in contact with GLY 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A GLY 3.7 0.9 - - - -
412A TYR* 3.3 18.4 - - - -
50B VAL* 1.3 75.6 - - - +
52B ASN* 1.3 67.9 + - - -
56B THR* 3.2 31.4 - - - -
57B ARG* 3.5 19.1 - - - +
59B THR 3.6 6.1 + - - -
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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