Contacts of the helix formed by residues 359 - 366 (chain 6) in PDB entry 1O1F
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 LYS 359 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1246 PHE* 3.8 13.5 - - + -
1296 VAL 4.9 2.2 - - - +
1306 PRO* 3.1 27.7 + - + +
3586 THR* 1.3 74.6 - - - +
3606 GLN* 1.4 79.7 + - + +
3626 TYR* 3.7 9.9 - - + -
3636 ASP* 2.7 51.5 + - - +
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Residues in contact with GLN 360 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3586 THR* 3.0 12.1 - - - +
3596 LYS* 1.4 96.8 - - + +
3616 GLU* 1.4 72.9 + - - +
3626 TYR 3.1 0.2 + - - -
3636 ASP* 4.0 2.6 - - - +
3646 GLU* 3.1 57.1 + - - +
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Residues in contact with GLU 361 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3566 TRP 4.2 9.9 - - - +
3576 ILE* 4.1 10.7 - - + +
3586 THR* 2.7 47.4 + - - +
3606 GLN* 1.4 83.6 + - - +
3626 TYR* 1.3 50.5 + - - +
3646 GLU* 3.5 2.7 - - - +
3656 ALA* 2.7 40.1 + - - +
3696 ILE* 3.6 33.4 - - + -
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Residues in contact with TYR 362 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1206 THR* 4.3 7.6 - - + -
1216 GLN* 3.6 15.2 - - - +
1246 PHE* 3.6 47.6 - + + -
1256 GLU* 3.5 36.6 + - + -
3586 THR 2.9 10.5 + - - +
3596 LYS* 3.8 7.4 - - + +
3606 GLN 3.1 0.2 + - - -
3616 GLU* 1.3 72.2 - - - +
3636 ASP* 1.3 70.0 + - - +
3646 GLU 2.8 11.2 + - - -
3656 ALA 3.0 10.6 + - - -
3666 GLY* 3.0 24.5 + - - -
3676 PRO* 3.3 44.5 - - + +
3696 ILE* 4.1 11.0 - - + +
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Residues in contact with ASP 363 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3596 LYS* 2.7 41.1 + - - +
3606 GLN* 4.2 3.3 - - - +
3626 TYR* 1.3 81.9 - - - +
3646 GLU* 1.3 63.4 + - + +
3666 GLY 5.2 0.3 + - - -
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Residues in contact with GLU 364 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3606 GLN* 3.1 53.8 + - - +
3616 GLU* 3.8 3.1 - - - +
3626 TYR 2.8 1.6 + - - -
3636 ASP* 1.3 84.8 - - + +
3656 ALA* 1.4 57.0 + - + +
3666 GLY 3.8 0.9 - - - -
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Residues in contact with ALA 365 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3616 GLU* 2.7 20.6 + - - +
3646 GLU* 1.4 73.7 - - + +
3666 GLY* 1.3 61.5 + - - +
3686 SER* 4.0 13.2 - - - -
3696 ILE* 3.5 30.1 - - + -
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Residues in contact with GLY 366 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3626 TYR* 3.0 20.8 + - - -
3636 ASP 5.1 0.2 - - - -
3646 GLU 3.8 1.0 - - - -
3656 ALA* 1.3 74.9 - - - +
3676 PRO* 1.3 68.1 - - - +
3686 SER* 2.8 11.3 + - - -
3696 ILE* 3.0 22.0 + - - +
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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