Contacts of the helix formed by residues 273 - 283 (chain 5) 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 273 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1785 LEU* 4.6 1.6 - - - -
2615 LEU 3.8 11.2 - - - -
2625 PHE 4.0 11.9 + - - -
2645 PRO* 4.0 11.3 - - - +
2725 ALA* 1.3 77.3 - - - +
2745 ILE* 1.3 66.5 + - - -
2755 HIS* 3.3 6.0 - - - -
2765 GLU* 2.9 23.5 + - - +
2775 THR* 3.0 12.4 + - - -
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Residues in contact with ILE 274 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1535 LEU* 3.6 27.6 - - + +
1555 SER* 5.5 1.1 - - - +
1605 THR* 3.6 21.1 - - + -
1785 LEU* 3.4 26.0 - - + +
2615 LEU* 3.2 38.5 + - + +
2625 PHE* 3.6 26.0 - - + -
2735 GLY* 1.3 66.8 - - - -
2755 HIS* 1.3 59.1 + - - +
2775 THR* 3.3 7.3 + - + -
2785 THR* 2.9 31.6 + - - -
3095 ILE* 6.2 2.9 - - + -
3135 MET* 3.9 18.2 - - + -
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Residues in contact with HIS 275 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2625 PHE* 3.4 35.5 - + + -
2735 GLY* 2.9 8.6 + - - -
2745 ILE* 1.3 73.0 - - - +
2765 GLU* 1.3 97.0 + - + +
2785 THR* 3.5 3.5 - - - -
2795 TYR* 3.3 20.8 + - - +
3135 MET* 3.4 29.8 - - - -
3165 GLU* 3.2 54.6 + - + -
3175 ILE* 3.8 8.3 - - + +
3205 LEU* 4.9 8.0 - - + +
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Residues in contact with GLU 276 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2725 ALA* 4.1 20.6 - - + +
2735 GLY 2.9 12.9 + - - +
2755 HIS* 1.3 101.8 + - + +
2775 THR* 1.3 54.0 + - - +
2795 TYR* 3.2 7.6 - - - +
2805 ASN* 2.8 52.1 + - - +
3205 LEU* 4.5 13.7 - - + -
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Residues in contact with THR 277 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1605 THR* 6.1 0.4 - - + -
1625 ASN* 2.9 31.0 - - - +
1765 MET* 3.8 20.3 - - + +
1785 LEU* 5.2 17.1 - - + +
2725 ALA* 4.0 18.4 + - - +
2735 GLY 3.0 13.6 + - - -
2745 ILE* 3.5 11.9 - - + +
2765 GLU* 1.3 74.8 - - - +
2785 THR* 1.3 64.0 + - - +
2805 ASN* 3.8 8.2 + - - +
2815 SER* 3.1 23.7 + - - -
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Residues in contact with THR 278 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1515 ILE* 3.6 6.7 - - + +
1535 LEU* 3.9 2.6 - - - +
1625 ASN* 3.4 19.7 + - - +
2745 ILE 2.9 15.7 + - - -
2755 HIS 3.5 9.4 - - - -
2775 THR* 1.3 74.8 - - - +
2795 TYR* 1.3 63.5 + - - +
2815 SER* 3.4 4.2 - - - -
2825 ILE* 3.0 35.3 + - + +
2975 ASN* 3.2 34.1 + - - +
3135 MET* 3.0 17.9 - - + +
3175 ILE* 4.1 15.3 - - + -
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Residues in contact with TYR 279 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2755 HIS 3.3 10.5 + - - +
2765 GLU 3.2 8.5 + - - +
2785 THR* 1.3 79.5 - - - +
2805 ASN* 1.3 80.0 + - - +
2825 ILE* 2.9 24.6 + - - +
2835 MET* 2.9 56.1 + - + +
2945 TYR* 3.4 20.9 - + - -
3175 ILE* 5.1 6.3 - - + -
3205 LEU* 3.3 61.6 + - + +
3215 ALA* 4.4 0.4 - - - -
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Residues in contact with ASN 280 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1765 MET* 4.8 12.6 - - + -
2725 ALA* 4.9 4.9 - - - +
2765 GLU* 2.8 40.0 + - - +
2775 THR* 3.1 9.7 + - - +
2795 TYR* 1.3 92.1 - - - +
2815 SER* 1.3 62.3 + - - +
2835 MET* 3.2 6.5 + - - +
2845 LYS* 3.1 25.7 + - - +
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Residues in contact with SER 281 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1515 ILE* 3.6 13.0 - - - -
1625 ASN* 3.6 16.7 - - - +
1645 PRO* 3.4 11.8 - - - +
1745 ALA* 2.4 31.5 + - - +
1765 MET* 3.8 7.5 - - - +
2775 THR 3.1 12.0 + - - -
2785 THR 3.4 11.4 - - - -
2805 ASN* 1.3 75.0 - - - +
2825 ILE* 1.3 58.2 - - - +
2845 LYS* 3.1 24.4 + - - +
2855 CYS* 3.4 15.1 + - - -
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Residues in contact with ILE 282 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1515 ILE* 3.7 22.7 - - + -
2785 THR* 3.0 32.5 - - + +
2795 TYR* 2.9 10.7 + - - +
2815 SER* 1.3 81.0 - - - +
2835 MET* 1.3 55.6 + - - +
2845 LYS 3.0 5.3 + - - -
2855 CYS* 3.2 18.4 + - - +
2905 ARG* 3.4 28.4 + - + +
2935 LEU* 4.5 13.2 - - + -
2945 TYR* 3.6 57.9 - - + +
2975 ASN* 4.6 2.2 - - - +
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Residues in contact with MET 283 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2795 TYR* 2.9 55.3 + - + +
2805 ASN* 3.2 7.0 + - - +
2825 ILE* 1.3 69.6 - - - +
2845 LYS* 1.4 56.4 + - - +
2855 CYS 3.5 1.1 - - - +
2905 ARG* 3.9 41.8 + - - +
2945 TYR* 3.4 25.6 - - + +
3225 PRO* 4.0 24.5 - - + -
3255 MET* 6.0 0.7 - - + -
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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