Contacts of the helix formed by residues 4544 - 4556 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4543B GLU* 1.3 78.1 - - + +
4545B GLN* 1.3 63.2 + - - +
4546B ARG 3.2 0.4 - - - -
4547B VAL* 3.3 14.1 - - + +
4548B LYS* 3.3 22.3 + - - +
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Residues in contact with GLN4545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4543B GLU 3.2 7.0 - - - +
4544B VAL* 1.3 77.0 - - - +
4546B ARG* 1.3 59.0 + - - +
4548B LYS* 3.8 6.3 - - - +
4549B PHE* 3.0 28.8 + - - +
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Residues in contact with ARG4546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4543B GLU* 3.4 15.7 + - - +
4544B VAL 3.2 1.0 - - - -
4545B GLN* 1.3 77.6 - - - +
4547B VAL* 1.3 66.4 + - + +
4549B PHE* 3.4 10.0 + - - +
4550B LEU* 3.3 25.3 + - - +
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Residues in contact with VAL4547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4543B GLU 4.3 8.5 - - - +
4544B VAL* 3.3 21.5 - - + +
4546B ARG* 1.3 79.6 - - + +
4548B LYS* 1.3 57.4 + - + +
4550B LEU* 3.8 10.6 + - + +
4551B ASN* 2.6 36.8 + - - +
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Residues in contact with LYS4548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4544B VAL 3.3 15.3 + - - +
4545B GLN* 4.0 6.3 - - - +
4546B ARG 3.2 0.4 - - - -
4547B VAL* 1.3 82.1 - - + +
4549B PHE* 1.3 63.9 + - - +
4550B LEU 3.2 0.7 - - - -
4551B ASN* 3.5 6.1 + - - +
4552B TYR* 3.1 23.6 + - - +
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Residues in contact with PHE4549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4545B GLN 3.0 18.4 + - - +
4546B ARG* 3.4 6.7 + - - +
4548B LYS* 1.3 75.3 - - - +
4550B LEU* 1.3 76.6 + - + +
4552B TYR* 3.9 19.0 - + - +
4553B LEU* 3.2 32.8 + - + +
4654B LEU* 5.4 13.0 - - + -
4657B ILE* 5.0 14.1 - - + -
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Residues in contact with LEU4550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4546B ARG 3.3 18.8 + - - +
4547B VAL* 4.1 11.4 - - + +
4548B LYS 3.2 0.6 - - - -
4549B PHE* 1.3 91.0 - - + +
4551B ASN* 1.3 61.7 + - - +
4553B LEU* 3.6 3.3 + - - +
4554B SER* 2.9 26.5 + - - -
4657B ILE* 5.5 12.5 - - + +
4658B GLY* 5.4 1.0 - - - -
4661B CYS* 4.2 29.6 - - - -
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Residues in contact with ASN4551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4547B VAL* 2.6 29.3 + - - +
4548B LYS* 3.5 6.9 + - - +
4549B PHE 3.4 0.2 - - - -
4550B LEU* 1.3 77.0 - - - +
4552B TYR* 1.3 63.2 + - - +
4554B SER* 3.0 17.2 + - - -
4555B ARG* 3.2 16.1 + - - +
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Residues in contact with TYR4552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4548B LYS 3.1 17.6 + - - +
4549B PHE* 3.9 22.2 - + - +
4550B LEU 3.3 0.2 - - - -
4551B ASN* 1.3 78.5 - - - +
4553B LEU* 1.3 65.1 + - + +
4555B ARG* 3.6 3.1 + - + +
4556B ASN* 3.3 53.2 + - + +
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Residues in contact with LEU4553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4549B PHE* 3.2 32.7 + - + +
4550B LEU* 4.2 3.6 - - - +
4552B TYR* 1.3 80.2 - - + +
4554B SER* 1.3 60.2 + - - +
4556B ASN* 3.5 4.1 - - - +
4557B PHE* 3.0 29.1 + - - +
4560B LEU* 5.7 4.0 - - + +
4654B LEU* 4.5 10.8 - - + +
4657B ILE* 5.1 2.2 - - + -
4658B GLY* 4.1 22.7 - - - +
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Residues in contact with SER4554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4550B LEU 2.9 20.0 + - - -
4551B ASN* 3.0 18.2 + - - -
4553B LEU* 1.3 74.5 - - - +
4555B ARG* 1.3 61.2 + - - +
4557B PHE* 3.5 18.7 + - - +
4558B TYR* 4.9 1.2 + - - -
4658B GLY* 4.2 16.3 - - - -
4661B CYS* 4.4 19.7 - - - +
4662B LEU* 4.1 11.5 - - - +
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Residues in contact with ARG4555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4551B ASN 3.2 16.2 + - - +
4552B TYR* 4.0 3.4 - - + +
4554B SER* 1.3 80.6 + - - +
4556B ASN* 1.3 68.1 + - - +
4557B PHE 3.3 2.5 + - - -
4558B TYR* 4.6 7.3 + - - +
4559B THR* 4.8 1.7 + - - +
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Residues in contact with ASN4556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4552B TYR* 3.3 51.3 + - + +
4553B LEU* 3.5 6.1 - - - +
4555B ARG* 1.3 84.1 - - - +
4557B PHE* 1.3 58.4 + - - +
4558B TYR 3.4 0.7 - - - -
4559B THR* 3.0 25.9 + - - +
4560B LEU* 3.0 21.6 + - + +
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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