Contacts of the helix formed by residues 252 - 257 (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 ASN 252 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1962 ARG* 3.5 19.1 + - - -
2272 MET* 5.7 1.3 - - - -
2302 ALA* 3.3 41.6 + - + +
2332 SER* 5.0 2.2 + - - -
2362 LEU* 3.9 12.6 - - - +
2372 GLU* 4.0 9.8 + - - +
2512 GLY* 1.3 75.8 - - - +
2532 GLU* 1.4 58.8 + - - +
2542 ARG* 2.8 15.7 + - - +
2552 PHE* 3.1 35.7 + - + -
2562 ARG* 3.8 12.8 - - - +
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Residues in contact with GLU 253 (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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1892 LEU* 4.6 5.4 - - + +
1922 ILE* 3.6 27.8 - - + +
1932 LEU* 4.1 17.0 - - + -
1962 ARG* 3.3 40.2 + - - +
2502 ILE* 3.5 12.2 - - + -
2512 GLY 3.0 28.6 + - - -
2522 ASN* 1.4 70.3 + - - +
2542 ARG* 1.3 65.3 + - - +
2552 PHE 3.1 0.9 - - - -
2562 ARG* 3.0 44.6 + - - +
2572 CYS* 3.1 17.7 + - - +
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Residues in contact with ARG 254 (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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1892 LEU* 5.7 0.4 - - - -
2152 LYS 5.4 0.2 + - - -
2162 LEU* 2.9 34.2 + - + +
2172 CYS* 2.9 29.9 - - - +
2182 TYR* 3.1 59.1 + - + +
2362 LEU 3.1 21.7 + - - -
2382 LYS* 3.5 31.3 - - - +
2502 ILE* 3.6 24.6 - - + +
2512 GLY 3.1 26.5 - - - +
2522 ASN 3.5 1.1 - - - +
2532 GLU* 1.3 75.0 - - - +
2552 PHE* 1.4 59.2 + - + +
2582 PRO* 3.7 1.7 - - - +
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Residues in contact with PHE 255 (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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2182 TYR* 3.4 22.7 - - + +
2202 ALA* 4.4 3.6 - - + -
2232 PHE* 3.0 50.3 - + + -
2262 GLU* 3.4 55.0 - - + -
2272 MET* 3.3 36.3 - - + -
2302 ALA* 4.8 1.3 - - + -
2362 LEU* 4.5 8.7 - - + -
2512 GLY 5.1 1.1 - - - -
2522 ASN* 3.1 30.9 + - - -
2532 GLU 3.1 0.4 - - - -
2542 ARG* 1.4 78.9 - - + +
2562 ARG* 1.3 69.4 + - + +
2572 CYS 3.1 2.2 - - - -
2582 PRO* 3.6 1.6 - - - +
2592 GLU* 3.1 17.3 + - - +
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Residues in contact with ARG 256 (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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1882 TYR* 3.3 22.2 + - - +
1912 LYS* 5.9 0.2 - - - +
1922 ILE* 3.6 43.7 + - + +
1952 GLU* 3.7 13.9 + - - -
1962 ARG* 6.2 0.6 - - - +
2272 MET* 3.7 33.2 - - + +
2522 ASN* 3.8 10.3 - - - +
2532 GLU* 3.0 45.7 + - - +
2552 PHE* 1.3 84.6 - - + +
2572 CYS* 1.3 60.6 + - - +
2592 GLU* 4.2 7.2 - - - +
2602 THR* 3.4 2.3 + - - -
2662 PHE* 3.3 21.6 - - + -
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Residues in contact with CYS 257 (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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1852 LEU* 3.2 40.4 - - - +
1882 TYR* 3.8 9.9 - - - -
1892 LEU* 3.8 17.5 - - + -
1922 ILE* 4.0 7.6 - - + +
2132 LYS* 4.2 17.3 - - - -
2172 CYS* 4.2 8.3 - - - -
2532 GLU 3.1 13.3 + - - +
2552 PHE 3.1 0.6 - - - -
2562 ARG* 1.3 75.2 - - - +
2582 PRO* 1.3 70.9 - - + +
2602 THR* 2.6 27.5 + - - -
3062 TYR* 5.1 0.2 - - - -
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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