Contacts of the helix formed by residues 301 - 306 (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 GLY 301 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1546 ASP* 4.0 4.5 - - - -
1556 SER 3.2 16.2 - - - -
1566 GLY* 4.8 1.6 - - - -
3006 SER* 1.3 76.5 - - - +
3026 GLY* 1.3 67.3 + - - +
3046 THR* 2.9 20.1 + - - -
3056 MET* 3.9 5.2 + - - +
3356 ARG* 3.1 13.6 + - - +
3366 LYS* 4.2 8.3 - - - -
3396 VAL* 6.0 1.3 - - - +
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Residues in contact with GLY 302 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1556 SER 3.3 2.6 + - - -
1566 GLY* 4.4 6.4 - - - -
3016 GLY* 1.3 70.0 - - - -
3036 THR* 1.3 61.1 + - - +
3046 THR 3.2 1.7 + - - -
3056 MET* 3.2 27.8 + - - +
3066 TYR* 4.9 0.9 + - - -
3366 LYS* 4.2 16.2 + - - +
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Residues in contact with THR 303 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1556 SER* 3.1 29.7 + - - +
1566 GLY 2.9 18.5 + - - -
1816 ALA 4.3 1.8 - - - -
1826 GLY* 3.1 21.4 - - - +
1856 LEU* 3.8 26.7 - - + -
2136 LYS* 5.1 1.2 + - - -
2616 LEU* 4.1 11.6 - - + +
3026 GLY* 1.3 75.1 - - - +
3046 THR* 1.3 56.7 + - - +
3056 MET 3.2 1.6 - - - -
3066 TYR* 3.0 38.1 + - + -
3096 ILE* 3.9 2.8 - - - +
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Residues in contact with THR 304 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1536 LEU* 4.0 20.0 - - + -
1556 SER* 3.6 21.3 - - - -
2616 LEU* 6.5 0.2 - - + -
2996 MET* 3.8 15.4 - - + +
3006 SER 3.3 27.3 + - - +
3016 GLY 2.9 13.5 + - - +
3036 THR* 1.3 75.2 - - - +
3056 MET* 1.3 54.3 + - - +
3066 TYR 3.5 1.6 - - - -
3096 ILE* 3.2 23.4 - - + +
3356 ARG* 2.7 46.3 + - - -
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Residues in contact with MET 305 (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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3016 GLY 3.9 7.4 - - - +
3026 GLY* 3.2 23.6 - - - +
3036 THR 3.2 1.6 - - - -
3046 THR* 1.3 78.4 - - - +
3066 TYR* 1.4 65.3 + - - +
3076 PRO* 3.1 10.3 - - - +
3336 PRO 3.8 7.9 - - - +
3356 ARG* 3.3 44.3 + - + +
3366 LYS* 3.7 10.1 - - + -
410G ASN* 3.3 30.3 - - - +
411G GLU* 4.5 4.0 - - - +
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Residues in contact with TYR 306 (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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1856 LEU* 3.0 36.1 - - + +
2136 LYS* 3.7 42.9 + - + +
2146 GLU* 5.6 3.1 - - - -
2176 CYS* 4.0 16.6 - - + +
2196 VAL* 3.6 17.9 - - + +
2576 CYS* 5.1 0.8 - - - -
2586 PRO* 3.6 32.1 - - + -
2616 LEU* 4.0 9.9 - - + -
3026 GLY 4.9 0.4 + - - -
3036 THR* 3.0 38.6 + - + +
3046 THR 3.5 0.6 - - - -
3056 MET* 1.4 71.5 - - - +
3076 PRO* 1.3 72.3 - - + +
3096 ILE* 3.2 25.4 - - + +
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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