Contacts of the helix formed by residues 2285 - 2290 (chain F) in PDB entry 6X34
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 ASN2285 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2245F ARG* 4.8 2.9 - - - +
2284F ASN* 1.3 75.4 + - - +
2286F GLU* 1.3 69.0 + - - +
2287F LEU 3.5 0.4 - - - -
2288F ALA* 3.8 4.8 - - - +
2289F LEU* 3.5 20.7 + - - +
2342F VAL* 3.5 28.7 - - + +
2347F VAL* 5.1 4.7 - - - +
3848F ALA* 5.6 7.1 + - - +
3851F LEU* 3.5 29.9 - - + +
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Residues in contact with GLU2286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2245F ARG* 3.4 25.7 - - - +
2249F ARG* 4.5 11.4 - - - +
2284F ASN* 2.9 3.2 + - - +
2285F ASN* 1.3 81.5 - - - +
2287F LEU* 1.3 62.4 + - - +
2288F ALA 3.4 0.5 + - - -
2289F LEU* 3.4 10.4 + - - +
2290F ALA* 3.4 12.8 + - - +
3848F ALA* 5.5 8.2 - - + +
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Residues in contact with LEU2287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2248F GLN* 3.9 17.3 - - + +
2249F ARG* 5.5 2.5 - - - +
2252F PHE* 3.8 45.9 - - + -
2280F SER 3.6 26.2 - - - +
2281F VAL* 3.8 27.8 - - + +
2284F ASN* 3.0 33.4 + - + +
2286F GLU* 1.3 74.6 - - - +
2288F ALA* 1.3 64.8 + - + +
2290F ALA* 3.6 5.5 - - - +
2291F LEU* 3.0 29.8 + - + +
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Residues in contact with ALA2288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2281F VAL* 5.2 7.0 - - + +
2284F ASN 3.7 19.1 - - - +
2285F ASN* 3.6 9.3 + - - +
2286F GLU 3.2 1.0 - - - -
2287F LEU* 1.3 88.5 - - + +
2289F LEU* 1.3 61.1 + - - +
2291F LEU* 3.5 21.3 + - + +
2339F ALA 5.3 7.6 - - - +
2342F VAL* 4.9 14.1 - - + -
2347F VAL* 5.1 9.4 - - + +
2350F ASN* 5.1 10.4 - - - +
3844F ARG* 4.8 3.3 + - - -
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Residues in contact with LEU2289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2285F ASN* 3.5 11.4 + - - +
2286F GLU 3.4 9.0 + - - +
2287F LEU 3.3 0.2 - - - -
2288F ALA* 1.3 78.2 - - - +
2290F ALA* 1.3 55.8 + - - +
2291F LEU 3.2 4.2 + - - -
2347F VAL* 5.5 10.7 - - + +
2349F GLU* 5.9 1.6 - - - +
3844F ARG* 3.0 49.1 + - + +
3847F LYS* 6.1 2.2 - - + -
3848F ALA* 4.4 21.8 - - + +
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Residues in contact with ALA2290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2252F PHE* 5.0 9.4 - - + -
2286F GLU 3.4 13.3 + - - +
2287F LEU* 3.5 7.8 + - - +
2288F ALA 3.4 0.2 - - - -
2289F LEU* 1.3 75.4 - - - +
2291F LEU* 1.3 62.5 + - - +
2292F GLN* 3.4 7.2 + - - +
3844F ARG* 5.2 4.7 - - - +
3868F LYS* 3.1 36.3 + - + +
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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