Contacts of the helix formed by residues 4770 - 4784 (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 ASP4770 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4706F THR* 5.4 5.2 - - + -
4707F PRO* 5.6 6.5 - - + -
4768F SER 3.7 3.9 + - - +
4769F ILE* 1.3 75.4 - - - +
4771F VAL* 1.3 60.2 + - - +
4772F LYS* 4.3 3.6 - - + +
4773F TYR* 3.8 26.7 - - + +
4774F GLN* 2.9 31.6 + - - +
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Residues in contact with VAL4771 (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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4769F ILE 4.3 0.2 - - - -
4770F ASP* 1.3 72.4 - - - +
4772F LYS* 1.3 76.2 + - + +
4774F GLN* 4.2 4.3 - - - +
4775F ILE* 3.4 23.2 + - + +
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Residues in contact with LYS4772 (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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4702F LEU* 3.6 17.3 - - - +
4705F ASN* 3.5 57.2 + - - +
4706F THR* 4.2 11.3 + - + +
4707F PRO* 4.9 7.0 - - + +
4770F ASP* 3.2 3.5 - - + +
4771F VAL* 1.3 90.2 - - + +
4773F TYR* 1.3 59.7 + - - +
4775F ILE* 3.9 3.5 + - - +
4776F TRP* 3.7 15.2 + - - +
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Residues in contact with TYR4773 (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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4668F ILE* 5.5 3.7 - - + +
4703F VAL* 5.7 2.0 - - + -
4706F THR* 4.2 21.5 + - + +
4708F SER 5.5 0.9 - - - -
4710F PRO* 3.6 39.7 - - + +
4712F ASN* 4.8 5.9 + - - -
4770F ASP* 3.4 22.3 + - + +
4771F VAL 3.3 0.2 - - - -
4772F LYS* 1.3 79.0 - - - +
4774F GLN* 1.3 64.1 + - + +
4775F ILE 3.2 0.2 - - - -
4776F TRP* 4.8 9.9 - + - -
4777F LYS* 2.9 52.4 + - + +
4778F PHE* 6.4 1.8 - + - -
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Residues in contact with GLN4774 (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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4769F ILE* 6.3 2.5 - - + -
4770F ASP 2.9 18.8 + - - +
4771F VAL* 4.2 5.8 - - - +
4773F TYR* 1.3 81.6 - - + +
4775F ILE* 1.3 60.5 + - - +
4777F LYS* 4.8 1.6 - - - -
4778F PHE* 3.3 48.4 + - + +
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Residues in contact with ILE4775 (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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4699F TRP* 3.5 19.0 - - + -
4702F LEU* 5.2 7.4 - - + -
4771F VAL* 3.4 15.6 + - + +
4772F LYS* 4.3 4.5 - - - +
4773F TYR 3.2 0.8 - - - -
4774F GLN* 1.3 79.7 - - - +
4776F TRP* 1.3 57.9 + - - +
4778F PHE* 4.9 0.2 - - - +
4779F GLY* 3.1 19.9 + - - -
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Residues in contact with TRP4776 (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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4668F ILE* 4.7 19.1 - - + -
4671F ARG* 3.9 32.3 - - + +
4672F GLU* 5.1 14.1 - - + -
4675F LEU* 4.9 7.6 - - + -
4699F TRP* 3.3 38.3 + + - +
4700F ASP* 3.6 13.4 - - + +
4702F LEU* 3.9 13.9 - - + -
4703F VAL* 3.5 48.2 - - + +
4710F PRO* 4.3 21.8 - - + -
4772F LYS 3.7 10.0 + - - +
4773F TYR* 3.5 9.9 + + - +
4775F ILE* 1.3 78.5 - - - +
4777F LYS* 1.3 79.0 + - + +
4780F VAL* 3.3 27.2 + - + +
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Residues in contact with LYS4777 (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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4668F ILE* 4.4 9.4 - - + +
4773F TYR* 2.9 47.4 + - + +
4774F GLN* 4.6 1.6 - - - +
4776F TRP* 1.3 90.4 - - + +
4778F PHE* 1.3 73.4 + - + +
4779F GLY 3.3 0.9 + - - -
4780F VAL* 3.4 6.6 + - - +
4781F ILE* 3.2 21.9 - - - +
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Residues in contact with PHE4778 (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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4660F ASN* 6.3 1.6 - - - -
4773F TYR* 6.4 2.2 - + - -
4774F GLN* 3.3 36.9 + - + +
4775F ILE* 5.4 0.2 - - - -
4777F LYS* 1.3 83.8 - - + +
4779F GLY* 1.3 60.4 + - - +
4781F ILE* 3.9 10.5 - - + +
4782F PHE* 3.2 53.1 + + + -
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Residues in contact with GLY4779 (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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4699F TRP* 3.6 21.9 - - - -
4775F ILE 3.1 21.8 + - - -
4776F TRP 3.6 0.2 + - - -
4777F LYS 3.2 0.4 - - - -
4778F PHE* 1.3 78.8 - - - +
4780F VAL* 1.3 59.9 + - - +
4782F PHE* 3.6 4.9 + - - +
4783F THR* 2.8 32.3 + - - +
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Residues in contact with VAL4780 (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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4667F VAL* 5.6 6.7 - - + +
4668F ILE* 4.9 7.9 - - + -
4671F ARG* 3.4 49.1 - - + +
4699F TRP* 4.3 14.8 - - + -
4776F TRP* 3.3 24.7 - - + +
4777F LYS* 3.4 6.4 + - - +
4778F PHE 3.4 0.4 - - - -
4779F GLY* 1.3 74.8 - - - +
4781F ILE* 1.3 68.5 + - + +
4783F THR* 3.2 8.4 + - - +
4784F ASP* 2.9 31.0 + - + +
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Residues in contact with ILE4781 (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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4660F ASN* 6.2 1.1 - - - +
4664F VAL* 3.6 35.0 - - + -
4667F VAL* 4.2 13.2 - - + -
4668F ILE* 3.8 25.4 - - + -
4777F LYS 3.2 17.3 - - - +
4778F PHE* 3.5 12.9 + - + +
4779F GLY 3.3 0.4 - - - -
4780F VAL* 1.3 81.9 - - + +
4782F PHE* 1.3 64.7 + - + +
4784F ASP* 3.4 10.0 + - + +
4787F PHE* 3.2 60.8 - - + +
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Residues in contact with PHE4782 (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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4778F PHE* 3.2 40.9 + + + +
4779F GLY* 4.2 5.4 - - - +
4781F ILE* 1.3 79.8 - - + +
4783F THR* 1.3 62.8 + - + +
4784F ASP 4.5 3.0 - - - +
4787F PHE* 4.0 28.1 - + - -
4788F LEU* 4.8 8.8 - - - +
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Residues in contact with THR4783 (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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4699F TRP* 6.2 4.9 - - + -
4779F GLY 2.8 23.2 + - - +
4780F VAL* 3.2 12.5 + - - +
4781F ILE 3.2 0.2 - - - -
4782F PHE* 1.3 80.1 - - + +
4784F ASP* 1.3 64.0 + - - +
4785F ASN* 3.6 1.9 + - - -
4788F LEU* 5.6 0.7 - - - -
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Residues in contact with ASP4784 (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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4667F VAL* 5.8 8.5 - - + -
4780F VAL* 2.9 19.1 + - + +
4781F ILE* 3.4 15.5 + - + +
4782F PHE 4.5 0.2 - - - +
4783F THR* 1.3 78.4 - - - +
4785F ASN* 1.3 61.6 + - - +
4786F SER* 4.2 14.1 - - - +
4787F PHE* 4.1 6.0 - - + +
4788F LEU* 3.0 30.5 + - - +
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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