Contacts of the helix formed by residues 4544 - 4556 (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 VAL4544 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4543F GLU* 1.3 78.7 - - + +
4545F GLN* 1.3 63.5 + - - +
4546F ARG 3.2 0.2 - - - -
4547F VAL* 3.3 14.9 - - + +
4548F LYS* 3.3 22.7 + - - +
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Residues in contact with GLN4545 (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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4543F GLU 3.2 7.0 - - - +
4544F VAL* 1.3 76.7 - - - +
4546F ARG* 1.3 60.0 + - - +
4548F LYS* 3.8 6.9 - - - +
4549F PHE* 3.0 28.6 + - - +
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Residues in contact with ARG4546 (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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4543F GLU* 3.4 16.0 + - - +
4544F VAL 3.2 1.0 - - - -
4545F GLN* 1.3 76.6 - - - +
4547F VAL* 1.3 67.0 + - + +
4549F PHE* 3.4 10.5 + - - +
4550F LEU* 3.3 24.9 + - - +
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Residues in contact with VAL4547 (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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4543F GLU 4.3 8.3 - - - +
4544F VAL* 3.3 21.5 - - + +
4546F ARG* 1.3 77.6 - - + +
4548F LYS* 1.3 58.4 + - + +
4550F LEU* 3.8 12.9 + - + +
4551F ASN* 2.6 36.7 + - - +
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Residues in contact with LYS4548 (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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4544F VAL 3.3 14.6 + - - +
4545F GLN* 4.0 6.7 - - - +
4546F ARG 3.2 0.6 - - - -
4547F VAL* 1.3 82.5 - - + +
4549F PHE* 1.3 63.3 + - - +
4550F LEU 3.2 0.7 - - - -
4551F ASN* 3.5 6.4 + - - +
4552F TYR* 3.1 23.9 + - - +
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Residues in contact with PHE4549 (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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4545F GLN 3.0 18.4 + - - +
4546F ARG* 3.4 6.9 + - - +
4548F LYS* 1.3 74.5 - - - +
4550F LEU* 1.3 75.2 + - + +
4552F TYR* 3.9 19.0 - + - +
4553F LEU* 3.2 32.0 + - + +
4654F LEU* 5.4 12.8 - - + -
4657F ILE* 5.0 14.6 - - + -
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Residues in contact with LEU4550 (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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4546F ARG 3.3 18.4 - - - +
4547F VAL* 4.1 12.6 - - + +
4548F LYS 3.2 0.8 - - - -
4549F PHE* 1.3 92.1 - - + +
4551F ASN* 1.3 62.7 + - - +
4553F LEU* 4.1 3.6 - - - +
4554F SER* 2.9 26.0 + - - -
4657F ILE* 5.5 11.6 - - + +
4658F GLY* 5.4 1.2 - - - -
4661F CYS* 4.2 31.8 - - - +
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Residues in contact with ASN4551 (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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4547F VAL* 2.6 29.7 + - - +
4548F LYS* 3.5 7.6 + - - +
4549F PHE 3.4 0.2 - - - -
4550F LEU* 1.3 77.8 - - - +
4552F TYR* 1.3 64.1 + - - +
4554F SER* 3.0 17.7 + - - -
4555F ARG* 3.2 15.8 + - - +
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Residues in contact with TYR4552 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4548F LYS 3.1 18.0 + - - +
4549F PHE* 3.9 22.2 - + - +
4550F LEU 3.3 0.4 - - - -
4551F ASN* 1.3 79.0 - - - +
4553F LEU* 1.3 65.6 + - + +
4555F ARG* 3.6 3.1 + - + +
4556F ASN* 3.3 54.3 + - + +
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Residues in contact with LEU4553 (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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4549F PHE* 3.2 31.8 + - + +
4550F LEU* 4.2 3.6 - - - +
4552F TYR* 1.3 79.2 - - + +
4554F SER* 1.3 61.7 + - - +
4556F ASN* 3.5 4.3 - - - +
4557F PHE* 3.0 28.8 + - - +
4560F LEU* 5.7 4.7 - - + +
4654F LEU* 4.5 11.0 - - + +
4657F ILE* 5.1 2.0 - - + -
4658F GLY* 4.1 21.7 - - - +
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Residues in contact with SER4554 (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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4550F LEU 2.9 20.3 + - - -
4551F ASN* 3.0 18.4 + - - -
4553F LEU* 1.3 75.1 - - - +
4555F ARG* 1.3 61.6 + - - +
4557F PHE* 3.5 18.1 + - - +
4558F TYR* 4.9 1.0 + - - -
4658F GLY* 4.2 15.9 - - - -
4661F CYS* 4.4 19.9 - - - +
4662F LEU* 4.1 11.6 - - - +
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Residues in contact with ARG4555 (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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4551F ASN 3.2 16.4 + - - +
4552F TYR* 4.0 4.0 - - + +
4553F LEU 3.3 0.2 - - - -
4554F SER* 1.3 82.2 + - - +
4556F ASN* 1.3 66.1 + - - +
4557F PHE 3.3 2.9 + - - -
4558F TYR* 4.6 7.3 + - - +
4559F THR* 4.7 1.7 + - - +
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Residues in contact with ASN4556 (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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4552F TYR* 3.3 51.5 + - + +
4553F LEU* 3.5 5.4 - - - +
4554F SER 3.4 0.2 - - - -
4555F ARG* 1.3 84.9 - - - +
4557F PHE* 1.3 58.4 + - - +
4558F TYR 3.4 0.9 - - - -
4559F THR* 3.0 26.4 + - - +
4560F LEU* 3.0 21.2 + - + +
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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