Contacts of the helix formed by residues 273 - 283 (chain 2) 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 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1782 LEU* 4.6 1.3 - - - -
2612 LEU 3.8 10.5 - - - -
2622 PHE 4.0 11.9 + - - -
2642 PRO* 4.0 11.6 - - - +
2722 ALA* 1.3 76.3 - - - +
2742 ILE* 1.3 66.0 - - - -
2752 HIS* 3.3 6.4 - - - -
2762 GLU* 2.9 23.9 + - - +
2772 THR* 3.0 12.4 + - - -
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Residues in contact with ILE 274 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1532 LEU* 3.6 27.3 - - + +
1552 SER* 5.5 1.3 - - - +
1602 THR* 3.6 20.9 - - + -
1782 LEU* 3.4 25.4 - - + -
2612 LEU* 3.2 40.3 + - + +
2622 PHE* 3.6 25.8 - - + -
2732 GLY* 1.3 66.8 - - - -
2752 HIS* 1.3 57.2 + - - +
2772 THR* 3.3 7.5 + - + -
2782 THR* 2.9 31.0 + - - -
3092 ILE* 6.2 2.9 - - + -
3132 MET* 3.9 18.8 - - + -
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Residues in contact with HIS 275 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2622 PHE* 3.4 34.7 - + + -
2732 GLY* 2.9 8.2 + - - -
2742 ILE* 1.3 71.2 - - - +
2762 GLU* 1.3 98.6 + - + +
2782 THR* 3.5 3.5 - - - -
2792 TYR* 3.3 21.1 + - - +
3132 MET* 3.4 30.1 - - - -
3162 GLU* 3.2 54.0 + - + -
3172 ILE* 3.8 7.9 - - + +
3202 LEU* 4.9 7.3 - - + +
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Residues in contact with GLU 276 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2722 ALA* 4.1 21.0 - - + +
2732 GLY 2.9 12.2 + - - +
2752 HIS* 1.3 100.4 + - + +
2772 THR* 1.3 52.3 + - - +
2792 TYR* 3.2 7.9 - - - +
2802 ASN* 2.8 52.0 + - - +
3202 LEU* 4.5 14.1 - - + -
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Residues in contact with THR 277 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1602 THR* 6.1 0.2 - - + -
1622 ASN* 2.9 31.4 - - - +
1762 MET* 3.8 19.2 - - + +
1772 ARG 6.0 0.2 - - - -
1782 LEU* 5.2 16.1 - - + +
2722 ALA* 4.0 18.5 + - - +
2732 GLY 3.0 13.6 + - - -
2742 ILE* 3.5 12.1 - - + +
2762 GLU* 1.3 74.8 - - - +
2782 THR* 1.3 64.5 + - - +
2802 ASN* 3.8 8.2 + - - +
2812 SER* 3.1 24.1 + - - -
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Residues in contact with THR 278 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1512 ILE* 3.6 6.0 - - + +
1532 LEU* 3.9 2.8 - - - +
1622 ASN* 3.4 19.6 + - - +
2742 ILE 2.9 15.1 + - - -
2752 HIS 3.5 9.4 - - - -
2772 THR* 1.3 71.8 - - - +
2792 TYR* 1.3 62.7 + - - +
2812 SER* 3.4 4.2 - - - -
2822 ILE* 3.0 36.3 + - + +
2972 ASN* 3.2 34.0 + - - +
3132 MET* 3.0 18.0 - - + +
3172 ILE* 4.1 16.4 - - + -
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Residues in contact with TYR 279 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2752 HIS 3.3 10.1 + - - +
2762 GLU 3.2 7.8 + - - +
2782 THR* 1.3 80.6 - - - +
2802 ASN* 1.3 78.3 + - - +
2822 ILE* 2.9 26.0 + - - +
2832 MET* 2.9 55.6 + - + +
2942 TYR* 3.4 21.3 - + - -
3172 ILE* 5.1 5.4 - - + -
3202 LEU* 3.3 63.9 + - + +
3212 ALA 4.5 0.4 - - - -
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Residues in contact with ASN 280 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1762 MET* 4.8 13.2 - - - -
2722 ALA* 4.9 5.2 - - - +
2762 GLU* 2.8 40.0 + - - +
2772 THR* 3.1 9.6 + - - +
2792 TYR* 1.3 92.8 - - - +
2812 SER* 1.3 61.5 - - - +
2832 MET* 3.2 6.1 + - - +
2842 LYS* 3.1 26.4 + - - +
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Residues in contact with SER 281 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1512 ILE* 3.6 12.6 - - - -
1622 ASN* 3.6 17.4 - - - +
1642 PRO* 3.4 12.2 - - - +
1742 ALA* 2.4 31.4 + - - +
1762 MET* 3.8 8.3 - - - +
2772 THR 3.1 11.6 + - - -
2782 THR 3.4 11.2 - - - -
2802 ASN* 1.3 74.8 - - - +
2822 ILE* 1.3 59.2 + - - +
2842 LYS* 3.1 24.8 + - - +
2852 CYS* 3.4 14.6 + - - -
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Residues in contact with ILE 282 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1512 ILE* 3.7 23.1 - - + -
2782 THR* 3.0 32.3 - - + +
2792 TYR* 2.9 11.8 + - - +
2812 SER* 1.3 80.1 - - - +
2832 MET* 1.3 55.1 + - - +
2842 LYS 3.0 5.3 + - - -
2852 CYS* 3.2 19.2 + - - +
2902 ARG* 3.4 28.4 + - + +
2932 LEU* 4.5 13.2 - - + -
2942 TYR* 3.6 59.0 - - + +
2972 ASN* 4.6 2.0 - - - +
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Residues in contact with MET 283 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2792 TYR* 2.9 57.9 + - + +
2802 ASN* 3.2 6.8 + - - +
2822 ILE* 1.3 69.3 - - - +
2842 LYS* 1.4 55.5 + - - +
2852 CYS 3.5 0.8 - - - +
2902 ARG* 3.9 42.8 + - - +
2942 TYR* 3.4 24.5 - - + +
3222 PRO* 4.0 24.9 - - + -
3252 MET* 6.0 0.4 - - + -
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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