Contacts of the helix formed by residues 4221 - 4239 (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 GLY4221 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4219F GLU* 3.3 9.4 - - - +
4220F GLY* 1.3 76.0 - - - +
4222F GLU* 1.3 60.1 + - - -
4223F SER 3.4 1.6 - - - -
4224F GLU* 3.9 14.1 - - - +
4225F LYS* 3.1 27.5 + - - +
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Residues in contact with GLU4222 (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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4220F GLY 3.5 5.8 + - - +
4221F GLY* 1.3 70.7 - - - -
4223F SER* 1.3 65.3 + - - +
4225F LYS* 3.4 13.8 + - - +
4226F MET* 3.6 17.3 + - - +
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Residues in contact with SER4223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4221F GLY 3.4 0.2 - - - -
4222F GLU* 1.3 76.2 - - - +
4224F GLU* 1.3 65.0 + - - +
4226F MET* 3.3 24.0 + - - +
4227F GLU* 4.0 3.3 + - - +
4971H HIS* 6.5 0.4 - - - -
4973H PHE* 5.1 16.8 - - - -
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Residues in contact with GLU4224 (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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4221F GLY* 3.7 17.0 + - - +
4222F GLU 3.3 0.2 - - - -
4223F SER* 1.3 78.7 - - - +
4225F LYS* 1.3 61.2 + - - +
4226F MET 3.4 0.5 + - - -
4227F GLU* 3.4 15.7 + - - +
4228F LEU* 3.6 13.1 + - - +
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Residues in contact with LYS4225 (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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4212F PHE* 5.3 1.4 - - - -
4216F VAL* 4.4 25.3 - - + +
4219F GLU* 4.8 7.4 - - + +
4221F GLY 3.1 18.7 + - - +
4222F GLU* 3.6 8.5 - - - +
4223F SER 3.2 0.4 - - - -
4224F GLU* 1.3 76.0 - - - +
4226F MET* 1.3 64.9 + - + +
4228F LEU* 3.3 24.6 + - + +
4229F PHE* 3.6 7.1 + - - +
4957F PHE* 5.0 14.4 - - + -
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Residues in contact with MET4226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4222F GLU 3.6 15.7 - - - +
4223F SER* 3.5 13.2 - - - +
4224F GLU 3.2 0.6 - - - -
4225F LYS* 1.3 80.3 - - - +
4227F GLU* 1.3 61.4 + - - +
4229F PHE* 3.4 18.9 + - + +
4230F VAL* 3.9 9.5 - - - +
4957F PHE* 3.8 33.4 - - + +
4958F ILE* 5.3 4.0 - - - +
5017F TRP* 5.2 8.5 - - + +
5020F PHE* 3.7 48.3 - - + -
5022F ALA* 5.5 9.0 - - + -
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Residues in contact with GLU4227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4223F SER 4.0 3.6 + - - +
4224F GLU* 3.4 12.1 + - - +
4225F LYS 3.3 0.2 - - - -
4226F MET* 1.3 76.1 - - - +
4228F LEU* 1.3 64.0 + - - +
4230F VAL* 3.4 19.6 + - - +
4231F SER* 3.6 10.0 + - - -
5017F TRP* 5.1 21.7 - - + +
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Residues in contact with LEU4228 (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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4212F PHE* 3.7 22.2 - - + -
4215F ASP 5.5 6.7 - - - +
4216F VAL* 5.7 7.0 - - + -
4224F GLU 3.6 9.4 + - - +
4225F LYS* 3.3 17.8 + - + +
4226F MET 3.2 1.0 - - - -
4227F GLU* 1.3 75.4 - - - +
4229F PHE* 1.3 63.4 + - - +
4231F SER* 3.5 12.8 + - - +
4232F PHE* 3.2 15.2 + - - +
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Residues in contact with PHE4229 (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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4212F PHE* 3.5 33.1 - + + -
4225F LYS 3.6 6.4 + - - +
4226F MET* 3.4 14.0 + - + +
4227F GLU 3.2 0.4 - - - -
4228F LEU* 1.3 76.9 - - - +
4230F VAL* 1.3 63.8 + - - +
4232F PHE* 3.2 16.0 + + - +
4233F CYS* 3.2 46.0 + - - -
4957F PHE* 4.6 14.6 - + + -
4958F ILE* 5.2 11.7 - - + -
4983F LEU 5.2 8.3 - - - -
4986F TYR* 4.4 25.8 - + + -
4987F MET 5.8 0.4 - - - -
4990F LEU* 6.2 1.6 - - + -
5020F PHE* 3.5 34.3 - + + -
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Residues in contact with VAL4230 (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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4226F MET 3.9 14.8 - - - +
4227F GLU 3.8 7.9 - - - +
4228F LEU 3.3 0.6 - - - -
4229F PHE* 1.3 77.1 - - - +
4231F SER* 1.3 61.0 + - - +
4233F CYS* 3.5 7.8 + - - +
4234F GLU* 3.4 20.6 + - - +
4990F LEU* 4.5 10.2 - - + +
5012F TYR* 3.6 34.2 + - + +
5017F TRP* 3.5 33.9 - - + +
5019F PHE* 4.1 16.8 - - + -
5020F PHE* 4.4 5.8 - - + -
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Residues in contact with SER4231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4227F GLU 3.6 7.8 + - - -
4228F LEU* 3.5 18.5 + - - -
4229F PHE 3.3 0.6 - - - -
4230F VAL* 1.3 78.0 - - - +
4232F PHE* 1.3 62.1 + - - +
4234F GLU* 3.7 7.8 + - - +
4235F ASP* 3.5 19.6 + - - +
4669F PHE* 5.6 0.9 - - - -
4673F LYS* 5.3 9.0 - - - +
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Residues in contact with PHE4232 (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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4200F TRP* 5.9 7.6 - + - -
4205F VAL* 5.2 1.6 - - - -
4208F SER* 3.2 42.6 - - - -
4209F LYS* 3.7 20.0 - - + -
4212F PHE* 3.6 51.4 - + + -
4228F LEU 3.2 4.2 + - - +
4229F PHE* 3.2 15.4 + + - +
4230F VAL 3.2 0.8 - - - -
4231F SER* 1.3 76.5 - - - +
4233F CYS* 1.3 73.8 + - - +
4235F ASP* 3.3 14.0 + - + +
4236F THR* 3.3 31.4 + - + +
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Residues in contact with CYS4233 (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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4229F PHE* 3.2 45.3 + - - -
4230F VAL* 3.5 7.2 + - - +
4232F PHE* 1.3 82.2 - - - +
4234F GLU* 1.3 61.4 + - - +
4236F THR* 2.7 26.6 + - - -
4237F ILE* 3.2 14.7 - - + +
4986F TYR 5.3 0.2 - - - -
4987F MET* 4.3 27.4 - - + -
4990F LEU* 4.5 22.0 - - + -
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Residues in contact with GLU4234 (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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4230F VAL 3.4 15.5 + - - +
4231F SER* 4.0 8.3 - - - +
4232F PHE 3.3 0.6 - - - -
4233F CYS* 1.3 78.7 - - - +
4235F ASP* 1.3 61.2 + - - +
4238F PHE 3.5 8.3 + - - -
4669F PHE* 3.5 22.7 - - + -
4714F TRP* 3.5 42.4 - - + -
4990F LEU* 5.7 2.3 - - + +
5012F TYR* 5.3 4.3 - - - +
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Residues in contact with ASP4235 (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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4231F SER 3.5 10.1 + - - +
4232F PHE* 3.3 12.7 + - + +
4233F CYS 3.2 1.0 - - - -
4234F GLU* 1.3 76.8 - - - +
4236F THR* 1.3 65.8 + - + +
4238F PHE* 3.5 8.4 + - - +
4239F GLU* 3.3 19.6 + - - +
4666F LEU* 3.9 26.4 - - + +
4669F PHE* 4.1 13.8 - - + -
4670F LYS* 6.5 0.4 - - + -
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Residues in contact with THR4236 (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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4200F TRP* 6.1 5.2 - - + -
4205F VAL* 4.8 15.6 - - + +
4208F SER* 5.5 2.7 - - - +
4232F PHE* 3.3 39.3 - - + +
4233F CYS* 2.7 22.4 + - - -
4235F ASP* 1.3 77.2 - - + +
4237F ILE* 1.3 69.5 + - - +
4239F GLU* 3.0 41.8 + - - +
4987F MET* 4.4 8.1 - - + +
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Residues in contact with ILE4237 (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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4196F ASN* 4.8 4.0 - - - +
4233F CYS* 3.2 15.5 + - + +
4235F ASP 3.4 0.2 - - - -
4236F THR* 1.3 88.6 - - - +
4238F PHE* 1.3 62.6 + - - +
4239F GLU 3.4 6.1 + - - +
4714F TRP* 3.6 31.4 - - + +
4987F MET* 4.5 21.1 - - + +
4990F LEU* 6.2 2.9 - - + -
4991F MET* 3.7 39.7 - - + +
4994F ILE* 5.9 6.3 - - + -
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Residues in contact with PHE4238 (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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4234F GLU 3.5 10.6 + - - +
4235F ASP 3.5 10.7 + - - +
4236F THR 3.2 0.6 - - - -
4237F ILE* 1.3 80.9 - - - +
4239F GLU* 1.3 61.5 + - + +
4665F PRO* 3.2 42.2 - - + -
4666F LEU* 4.9 6.3 - - + -
4669F PHE* 4.1 21.1 - + + -
4711F SER 5.3 0.2 - - - -
4712F ASN* 3.2 56.5 - - + -
4714F TRP* 4.7 10.5 - + - +
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Residues in contact with GLU4239 (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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4204F GLN* 4.3 15.5 - - - +
4205F VAL* 3.3 29.8 - - - +
4235F ASP 3.3 14.6 - - - +
4236F THR* 3.0 27.7 - - - +
4237F ILE* 3.2 8.2 - - - +
4238F PHE* 1.3 82.9 - - + +
4662F LEU 5.7 4.9 - - - +
4666F LEU* 5.6 13.7 - - + -
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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
------------------------------------------------------------
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