Contacts of the helix formed by residues 264 - 268 (chain 4) 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 PRO 264 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1784 LEU* 5.2 0.2 - - + -
1804 LEU* 3.7 19.1 - - + -
2604 THR 3.7 6.5 - - - +
2614 LEU 4.7 1.3 - - - +
2624 PHE 3.6 7.2 - - - +
2634 GLN* 1.3 85.3 - - - +
2654 SER* 1.4 55.8 + - - +
2664 PHE 3.2 3.6 - - - -
2674 ILE* 3.0 22.7 + - + +
2694 MET* 2.9 42.5 + - + +
2714 SER* 3.5 25.8 - - - +
2724 ALA* 3.6 15.7 - - - +
2734 GLY* 4.0 8.7 - - - +
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Residues in contact with SER 265 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2634 GLN* 3.6 19.4 - - - +
2644 PRO* 1.4 73.9 - - - +
2664 PHE* 1.4 61.4 + - - +
2674 ILE 3.0 6.4 + - - -
2684 GLY* 3.4 10.2 + - - +
2694 MET 3.3 13.6 + - - -
2704 GLU* 5.4 4.9 - - - -
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Residues in contact with PHE 266 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1884 TYR* 3.1 36.4 + + + +
1914 LYS* 5.0 3.5 + - - -
2274 MET* 5.6 5.2 - - + -
2564 ARG* 3.3 28.5 - - + -
2594 GLU* 3.6 38.6 - - + -
2604 THR* 3.9 15.3 - - + -
2634 GLN* 3.6 37.7 - - + +
2644 PRO 3.2 0.2 - - - -
2654 SER* 1.4 77.8 - - - +
2674 ILE* 1.3 63.4 + - - +
2684 GLY 3.7 0.4 - - - -
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Residues in contact with ILE 267 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1733 HIS* 4.6 10.3 - - - +
1804 LEU* 3.8 25.1 - - + -
1844 ASP* 5.0 15.0 - - + +
1854 LEU* 5.7 0.4 - - + -
1884 TYR* 3.5 31.2 - - + -
2604 THR* 3.6 24.5 - - + -
2644 PRO 3.0 17.0 + - - +
2664 PHE* 1.3 86.7 - - - +
2684 GLY* 1.3 62.8 + - - +
2694 MET* 3.0 28.3 + - + +
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Residues in contact with GLY 268 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1733 HIS* 4.1 33.1 + - - +
2654 SER* 3.4 12.6 + - - -
2664 PHE 3.7 0.4 - - - -
2674 ILE* 1.3 77.3 - - - +
2694 MET* 1.3 61.5 + - - +
2704 GLU* 3.9 9.1 + - - +
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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