Contacts of the helix formed by residues 4233 - 4251 (chain F) in PDB entry 1Y1S
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 THR4233 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4104F VAL* 6.2 4.9 - - + -
4220F ILE* 5.2 8.7 - - + +
4229F PRO* 5.1 5.6 - - + -
4230F ASN 3.2 36.6 + - - +
4231F ALA 4.4 0.3 - - - -
4232F GLU* 1.3 90.3 + - - +
4234F MET* 1.3 83.3 + - + +
4235F LYS 2.9 12.2 + - - -
4236F GLN* 3.1 12.8 + - - +
4237F THR* 3.4 17.1 + - - -
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Residues in contact with MET4234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007A PHE* 4.8 13.0 - - + -
1048A ARG* 6.0 3.6 - - - +
4030F ARG* 6.1 2.7 - - - +
4094F THR* 4.4 14.1 - - + +
4220F ILE* 3.8 41.7 - - + +
4229F PRO* 5.3 1.1 - - + -
4233F THR* 1.3 96.1 - - + +
4235F LYS* 1.3 63.3 + - - +
4236F GLN 2.7 8.0 + - - -
4237F THR* 4.1 3.1 - - - -
4238F GLU* 2.8 57.9 + - + +
4239F SER 3.5 0.9 + - - -
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Residues in contact with LYS4235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4232F GLU* 3.1 44.5 + - + +
4233F THR* 2.9 1.0 + - - +
4234F MET* 1.3 77.6 - - - +
4236F GLN* 1.3 89.3 + - - +
4238F GLU* 5.6 1.3 - - - -
4239F SER* 3.7 15.6 + - - -
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Residues in contact with GLN4236 (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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4232F GLU* 4.3 22.3 - - + +
4233F THR 3.1 4.6 + - - +
4234F MET 2.7 3.6 + - - -
4235F LYS* 1.3 118.0 + - + +
4237F THR* 1.3 56.6 + - - +
4238F GLU 3.2 1.6 - - - -
4239F SER* 3.0 7.3 + - - -
4240F HIS* 2.7 36.5 + - - +
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Residues in contact with THR4237 (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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4094F THR* 6.3 0.4 - - + -
4104F VAL* 4.8 4.9 - - - +
4105F GLY* 3.8 25.7 + - - +
4107F VAL* 5.9 0.2 - - - +
4218F GLY* 3.8 23.6 - - - +
4219F VAL 3.5 23.1 + - - +
4220F ILE* 4.4 8.1 - - + +
4233F THR* 3.4 17.5 + - - -
4234F MET* 4.1 5.6 - - - -
4236F GLN* 1.3 76.0 - - - +
4238F GLU* 1.3 64.0 + - - +
4240F HIS* 3.2 8.7 - - - +
4241F ALA* 3.1 23.6 + - - +
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Residues in contact with GLU4238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4030F ARG* 2.9 45.8 + - + +
4033F LYS* 3.4 23.2 + - - +
4092F ILE* 6.3 1.3 - - + -
4094F THR* 5.6 10.1 - - + +
4234F MET* 2.8 42.2 + - + +
4235F LYS* 5.6 1.0 - - - -
4237F THR* 1.3 77.5 - - - +
4239F SER* 1.3 64.5 + - - +
4241F ALA* 3.5 5.2 + - - +
4242F VAL* 2.9 40.1 + - + +
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Residues in contact with SER4239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4037F LEU* 5.2 0.3 - - - +
4234F MET 3.5 2.4 + - - -
4235F LYS 3.7 16.6 + - - -
4236F GLN* 3.0 11.1 + - - -
4238F GLU* 1.3 79.8 + - - +
4240F HIS* 1.3 57.6 + - - +
4242F VAL* 3.3 7.8 + - - +
4243F LYS* 2.8 48.1 + - - +
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Residues in contact with HIS4240 (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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4105F GLY 4.0 18.2 + - - +
4107F VAL* 4.0 7.9 - - + +
4147F ILE* 3.9 19.2 + - + +
4148F GLY 2.9 20.8 + - - -
4149F ALA* 3.2 29.2 - - + +
4150F THR 5.1 0.4 - - - -
4236F GLN 2.7 16.8 + - - +
4237F THR* 3.2 14.1 - - + +
4239F SER* 1.3 71.8 - - - +
4241F ALA* 1.3 56.4 + - - +
4243F LYS* 2.7 34.7 + - + +
4244F ILE* 3.0 13.2 + - + +
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Residues in contact with ALA4241 (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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4092F ILE* 3.1 31.8 - - + +
4093F GLY 4.9 1.1 - - - +
4107F VAL* 4.7 4.9 - - + +
4216F VAL* 4.8 5.9 - - + +
4217F ALA 4.6 2.2 - - - -
4218F GLY* 4.1 22.2 - - - +
4237F THR 3.1 11.9 + - - +
4238F GLU* 4.0 4.0 - - - +
4240F HIS* 1.3 78.6 - - - +
4242F VAL* 1.3 57.4 + - - +
4244F ILE* 3.2 13.4 + - - +
4245F VAL* 2.9 25.5 + - - +
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Residues in contact with VAL4242 (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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4030F ARG* 5.9 2.0 - - + -
4033F LYS* 4.8 4.5 - - + +
4034F ILE* 3.9 36.1 - - + +
4037F LEU* 3.5 22.4 - - + -
4092F ILE* 4.3 12.8 - - + -
4238F GLU* 2.9 40.5 + - + +
4239F SER* 3.4 7.6 - - - +
4241F ALA* 1.3 76.1 - - - +
4243F LYS* 1.3 62.8 + - - +
4245F VAL* 3.0 7.9 - - + +
4246F VAL* 2.9 36.0 + - + +
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Residues in contact with LYS4243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4037F LEU* 4.2 22.4 - - + -
4147F ILE* 3.8 30.1 - - + +
4239F SER* 2.8 31.1 + - - +
4240F HIS* 2.7 21.9 + - + +
4242F VAL* 1.3 72.7 - - - +
4244F ILE* 1.3 57.4 + - - +
4246F VAL* 3.6 2.7 + - - +
4247F GLU* 3.1 24.1 + - - +
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Residues in contact with ILE4244 (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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4107F VAL* 3.5 39.5 - - + -
4140F LEU* 3.7 26.7 - - + +
4143F ALA* 3.2 11.2 - - + +
4144F ALA* 3.8 18.6 - - + +
4147F ILE* 3.7 26.0 - - + -
4149F ALA* 4.1 10.8 - - + -
4216F VAL* 4.6 13.7 - - + -
4240F HIS* 3.0 12.8 + - + +
4241F ALA* 3.5 7.2 - - - +
4242F VAL 3.1 0.2 - - - -
4243F LYS* 1.3 74.7 - - - +
4245F VAL* 1.3 62.1 + - - +
4247F GLU 3.2 1.0 + - - -
4248F ALA* 2.8 24.9 + - - +
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Residues in contact with VAL4245 (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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4023F ILE* 3.9 22.5 - - + +
4034F ILE* 5.2 0.9 - - + -
4090F LEU* 3.8 31.5 - - + +
4092F ILE* 4.1 15.7 - - + -
4140F LEU* 4.5 4.5 - - + -
4216F VAL* 4.1 20.1 - - + +
4241F ALA 2.9 15.4 + - - +
4242F VAL* 3.0 27.8 - - + +
4244F ILE* 1.3 77.8 - - - +
4246F VAL* 1.3 62.4 + - + +
4248F ALA* 3.3 6.9 + - - +
4249F ALA* 3.0 26.5 + - - +
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Residues in contact with VAL4246 (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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4023F ILE* 4.6 5.2 - - + -
4034F ILE* 4.3 12.8 - - + +
4037F LEU* 3.7 33.2 - - + +
4038F MET* 4.0 28.0 - - + -
4057F LEU* 3.7 12.0 - - + +
4242F VAL* 2.9 34.3 + - + +
4243F LYS 3.8 4.7 - - - +
4245F VAL* 1.3 79.9 - - + +
4247F GLU* 1.3 62.1 + - - +
4249F ALA* 3.2 8.4 + - - +
4250F ARG* 3.2 20.0 + - + +
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Residues in contact with GLU4247 (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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4143F ALA* 3.6 22.0 - - + +
4146F SER* 4.4 14.9 + - - -
4147F ILE* 4.2 11.4 - - + +
4243F LYS 3.1 16.9 + - - +
4244F ILE 3.6 4.0 - - - +
4246F VAL* 1.3 76.9 - - - +
4248F ALA* 1.3 64.9 + - - +
4249F ALA 3.2 0.2 - - - -
4250F ARG* 3.2 39.6 + - - +
4251F ARG* 3.5 36.2 + - - +
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Residues in contact with ALA4248 (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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4090F LEU* 4.0 6.5 - - + -
4139F ALA* 3.7 6.9 - - + +
4140F LEU* 3.5 44.9 - - + +
4143F ALA* 3.6 5.8 - - + +
4244F ILE 2.8 17.5 + - - +
4245F VAL 3.6 5.6 - - - +
4247F GLU* 1.3 76.3 - - - +
4249F ALA* 1.3 63.7 + - - +
4251F ARG* 3.3 12.4 + - - +
4252F LEU* 3.2 19.5 + - + +
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Residues in contact with ALA4249 (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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4021F LEU* 3.8 22.1 - - + +
4023F ILE* 4.3 10.3 - - + -
4057F LEU* 4.0 12.3 - - + -
4062F VAL* 5.4 1.8 - - + -
4090F LEU* 3.7 15.4 - - + +
4245F VAL 3.0 13.1 + - - +
4246F VAL 3.3 10.1 - - - +
4247F GLU 3.2 0.2 - - - -
4248F ALA* 1.3 74.3 - - - +
4250F ARG* 1.3 64.7 + - - +
4251F ARG 3.1 1.6 - - - -
4252F LEU* 3.0 11.6 + - - -
4253F LEU* 3.2 19.7 + - - +
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Residues in contact with ARG4250 (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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4057F LEU* 3.5 35.0 - - + +
4058F ASP* 2.7 46.1 + - - +
4246F VAL* 3.2 10.2 + - - +
4247F GLU* 3.2 40.8 + - - +
4249F ALA* 1.3 80.2 - - - +
4251F ARG* 1.3 61.1 + - + +
4252F LEU 3.5 0.5 + - - -
4253F LEU* 3.7 18.1 + - - +
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Residues in contact with ARG4251 (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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4139F ALA* 3.8 32.2 - - + +
4142F GLU* 3.6 30.5 + - - +
4143F ALA* 4.0 9.2 - - - +
4146F SER* 3.5 20.2 + - - -
4247F GLU* 3.5 30.6 + - - +
4248F ALA* 3.3 8.5 + - - +
4249F ALA 3.1 0.8 - - - -
4250F ARG* 1.3 78.8 - - + +
4252F LEU* 1.3 59.7 + - - +
4253F LEU 3.5 3.0 + - - +
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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
------------------------------------------------------------
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