Contacts of the helix formed by residues 20 - 26 (chain H) in PDB entry 3F5O
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 ASN 20 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46G GLU* 3.2 26.0 - - + +
47G GLU 3.8 0.2 - - - -
49G THR* 3.3 17.3 - - - +
50G ASN 3.8 14.8 + - - -
51G ALA* 4.1 7.7 - - - +
15H MET 5.0 0.2 + - - -
18H ALA* 3.1 22.6 - - + +
19H ARG* 1.3 82.4 - - - +
21H PHE* 1.3 64.7 + - - +
22H GLU* 2.9 36.6 + - - +
23H ARG* 3.0 25.4 + - - +
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Residues in contact with PHE 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G PHE* 3.9 22.0 - + - -
24G VAL* 3.8 21.8 - - + -
47G GLU 3.3 20.9 + - - +
48G HIS* 4.0 2.9 - + - -
49G THR 2.8 19.6 + - - +
56G HIS* 3.5 34.5 - + + +
58G GLY 4.4 0.7 - - - -
59G LEU* 3.6 47.8 - - + -
62G THR* 4.7 0.2 - - - -
20H ASN* 1.3 67.3 - - - +
22H GLU* 1.3 61.7 + - - +
23H ARG* 2.9 11.5 + - - +
24H VAL* 3.0 36.0 + - + +
62H THR* 3.6 22.9 - - + -
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Residues in contact with GLU 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G ASN* 3.3 11.0 - - - +
51G ALA* 3.2 24.1 + - + +
56G HIS* 3.0 24.3 + - - -
15H MET* 3.5 43.1 - - + +
16H THR* 3.6 17.2 - - - +
20H ASN* 2.9 28.2 + - - +
21H PHE* 1.3 78.0 - - - +
23H ARG* 1.3 60.0 + - - +
24H VAL* 3.1 1.9 + - - -
25H LEU* 3.4 14.5 + - - +
66H ASN* 2.8 26.6 - - - +
149H UOC 5.2 3.1 - - - +
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Residues in contact with ARG 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G ARG* 5.3 10.6 - - - +
24G VAL* 4.2 25.5 + - - +
47G GLU* 2.7 49.4 + - - +
48G HIS* 6.3 0.2 - - - -
15H MET 4.7 0.2 + - - -
16H THR* 3.8 16.5 - - - +
18H ALA 3.3 16.1 + - - +
19H ARG* 3.5 14.4 + - - +
20H ASN* 3.0 26.5 + - - +
21H PHE* 2.9 5.5 - - - +
22H GLU* 1.3 78.1 - - - +
24H VAL* 1.3 68.7 + - + +
25H LEU 3.1 0.4 - - - -
26H GLY* 3.0 22.2 + - - -
47H GLU* 5.5 1.4 - - - +
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Residues in contact with VAL 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G PHE* 3.8 25.0 - - + -
23G ARG* 4.3 13.0 + - - +
24G VAL* 4.2 9.0 - - + -
21H PHE* 3.0 55.5 + - + +
22H GLU* 5.3 0.2 - - - -
23H ARG* 1.3 90.5 - - + +
25H LEU* 1.3 65.6 + - + +
26H GLY 3.3 2.3 + - - -
42H MET* 5.5 0.3 - - - +
47H GLU* 4.5 6.8 - - - +
48H HIS* 4.3 20.3 + - - -
59H LEU* 4.4 2.8 - - + +
62H THR* 4.0 16.8 - - + -
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Residues in contact with LEU 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H THR* 3.9 11.3 - - + +
22H GLU* 3.4 10.3 + - - +
23H ARG 3.0 1.6 + - - -
24H VAL* 1.3 85.4 - - + +
26H GLY* 1.3 64.6 + - - +
27H LYS 3.1 3.1 - - - -
28H ILE* 3.0 36.3 + - + +
42H MET* 5.3 2.9 - - - -
59H LEU* 3.6 31.0 - - + -
62H THR* 4.2 11.0 - - + +
63H LEU* 3.8 25.8 - - + -
66H ASN* 3.5 41.1 - - + +
67H ILE* 4.6 8.1 - - + -
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Residues in contact with GLY 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H THR* 3.8 22.7 + - - +
23H ARG 3.0 15.1 + - - -
24H VAL 3.3 2.2 + - - -
25H LEU* 1.3 76.7 - - - +
27H LYS* 1.3 63.2 + - - +
28H ILE 3.6 4.7 + - - +
47H GLU* 5.8 0.8 + - - -
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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