Contacts of the helix formed by residues 6070 - 6085 (chain B) 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 GLY6070 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6069B ILE* 1.3 78.7 - - - +
6071B GLY* 1.3 61.6 + - - -
6072B PRO* 3.4 3.1 - - - -
6073B SER* 3.4 1.9 + - - -
6074B THR* 2.7 30.3 + - - -
6197B MET* 3.2 14.6 + - - -
6198B GLU* 2.8 14.1 + - - +
3072D PRO* 3.7 21.5 - - - -
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Residues in contact with GLY6071 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6070B GLY* 1.3 68.6 - - - -
6072B PRO* 1.3 62.9 - - - +
6074B THR* 3.8 4.7 - - - -
6075B SER* 2.6 38.3 + - - -
6119B ALA* 4.2 5.2 - - - -
6160B ASP* 4.5 3.0 + - - -
6197B MET 3.7 6.7 + - - -
6198B GLU* 5.0 0.2 - - - -
6201B THR* 3.1 36.1 + - - +
3072D PRO* 4.5 1.8 - - - +
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Residues in contact with PRO6072 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6069B ILE 5.1 0.4 - - - +
6070B GLY* 3.4 4.7 - - - -
6071B GLY* 1.3 86.7 - - - +
6073B SER* 1.3 62.0 + - - +
6075B SER* 2.6 21.4 + - - +
6076B ILE* 3.2 9.9 + - - +
6119B ALA* 4.8 2.5 - - + -
6160B ASP* 4.8 3.4 - - - +
3069D ILE* 4.2 3.4 - - - +
3070D GLY* 3.6 23.3 - - - +
3072D PRO* 3.7 26.5 - - + -
3160D ASP* 3.2 49.4 - - - +
3197D MET* 4.1 9.4 - - + +
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Residues in contact with SER6073 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6049B GLU* 3.2 25.4 + - - -
6050B PHE* 3.1 25.8 - - - -
6067B THR 2.6 22.5 + - - -
6068B GLY 3.5 4.0 - - - -
6069B ILE 3.3 20.1 + - - -
6070B GLY 3.4 2.1 + - - -
6072B PRO* 1.3 78.6 - - - +
6074B THR* 1.3 58.2 + - - +
6076B ILE* 3.3 1.9 + - - -
6077B ALA 3.0 22.3 + - - -
3069D ILE* 3.9 13.7 + - - +
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Residues in contact with THR6074 (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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6024B VAL* 6.3 0.2 - - + -
6067B THR* 3.4 28.9 + - + +
6068B GLY 4.0 0.2 + - - -
6070B GLY 2.7 23.4 + - - -
6071B GLY* 3.1 10.2 + - - -
6073B SER* 1.3 76.2 + - - +
6075B SER* 1.3 61.1 + - - +
6077B ALA* 3.2 1.6 + - - +
6078B VAL* 2.9 43.9 + - + +
6091B ARG* 6.1 1.3 - - - -
6198B GLU* 3.4 23.0 - - + +
6201B THR* 4.9 1.6 - - - +
6202B LEU* 4.5 23.1 - - + -
6205B MET* 5.2 0.4 - - - -
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Residues in contact with SER6075 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6071B GLY 2.6 18.5 + - - -
6072B PRO* 2.6 23.6 + - - +
6074B THR* 1.3 72.2 - - - +
6076B ILE* 1.3 61.9 + - - +
6079B GLU* 3.1 27.0 + - - +
6119B ALA* 4.9 0.2 - - - -
6123B PHE* 4.1 25.0 - - - -
6201B THR* 4.5 2.9 + - - -
6205B MET* 3.6 18.1 - - - +
3161D THR* 3.9 22.6 - - - +
3162D PHE 4.6 1.2 + - - -
3163D TYR* 5.2 2.4 - - - -
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Residues in contact with ILE6076 (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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6008B HIS* 3.7 39.9 - - + +
6009B LEU* 4.7 1.3 - - + -
6050B PHE* 3.6 16.2 - - + -
6072B PRO 3.2 6.8 + - - +
6073B SER 3.4 6.7 - - - +
6074B THR 3.1 0.2 - - - -
6075B SER* 1.3 81.9 + - - +
6077B ALA* 1.3 71.2 + - - +
6079B GLU* 3.6 3.3 - - - +
6080B GLU* 3.1 28.4 + - - +
3069D ILE* 3.5 42.4 - - + -
3162D PHE* 3.9 27.1 - - + +
3163D TYR* 4.7 6.1 - - + -
3197D MET* 4.5 4.0 - - + -
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Residues in contact with ALA6077 (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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6009B LEU* 3.8 18.3 - - + +
6024B VAL* 6.0 0.2 - - + -
6050B PHE* 4.0 12.3 - - + -
6065B CYS* 5.0 0.4 - - - +
6066B SER 4.0 14.4 - - - +
6067B THR* 4.2 14.8 - - + -
6073B SER 3.0 10.5 + - - +
6074B THR 3.5 7.2 - - - +
6076B ILE* 1.3 81.4 - - - +
6078B VAL* 1.3 65.5 + - + +
6081B LEU* 2.9 36.8 + - + +
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Residues in contact with VAL6078 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6024B VAL* 5.8 2.2 - - + -
6067B THR* 5.6 3.1 - - + -
6074B THR* 2.9 30.4 + - + +
6077B ALA* 1.3 72.9 - - + +
6079B GLU* 1.3 53.5 + - - +
6081B LEU* 3.3 0.6 + - - +
6082B ALA* 2.7 37.1 + - - +
6089B PHE* 3.4 38.1 - - + -
6202B LEU* 3.8 25.4 - - + -
6205B MET* 3.5 28.9 - - + -
6206B CYS* 4.3 11.0 - - - -
6211B LEU* 4.4 7.9 - - + -
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Residues in contact with GLU6079 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6075B SER 3.1 19.1 + - - +
6076B ILE 3.6 2.5 - - - +
6078B VAL* 1.3 78.5 - - - +
6080B GLU* 1.3 52.5 + - - +
6082B ALA* 2.9 8.4 + - - +
6083B GLN* 2.7 55.7 + - - +
6123B PHE* 5.4 4.0 - - + -
6205B MET* 4.1 6.1 - - + +
6209B GLN* 4.3 15.9 + - - +
6211B LEU* 6.3 0.2 - - - -
3163D TYR* 3.8 26.5 - - + +
3164D PRO* 6.0 0.5 - - - +
3171D THR* 3.1 15.0 - - - +
3172D TYR* 2.7 36.8 + - - +
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Residues in contact with GLU6080 (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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6006B VAL* 3.2 25.6 - - + +
6007B PHE 3.8 2.1 + - - +
6008B HIS* 2.7 55.5 + - - +
6009B LEU* 3.2 22.4 + - + +
6076B ILE* 3.1 17.8 + - - +
6079B GLU* 1.3 78.4 - - - +
6081B LEU* 1.3 57.4 + - - +
6083B GLN* 3.2 11.4 + - - +
6084B LEU* 2.9 33.2 + - - +
3163D TYR* 2.7 30.6 + - + +
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Residues in contact with LEU6081 (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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6009B LEU* 3.2 23.3 - - + -
6011B LEU* 4.3 10.1 - - + -
6016B LEU* 5.3 2.0 - - + -
6022B ALA* 4.3 11.4 - - + -
6024B VAL* 4.4 7.6 - - + -
6063B ILE* 4.9 7.0 - - + -
6065B CYS* 3.9 28.9 - - + -
6077B ALA* 2.9 23.4 + - + +
6078B VAL 3.5 4.0 - - - +
6080B GLU* 1.3 76.8 - - - +
6082B ALA* 1.3 57.6 + - - +
6084B LEU* 3.1 19.4 + - + +
6085B GLY 3.1 19.8 + - - -
6086B ILE* 3.1 25.2 + - + +
6089B PHE* 3.9 22.4 - - + -
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Residues in contact with ALA6082 (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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6078B VAL 2.7 18.8 + - - +
6079B GLU* 3.3 7.4 - - - +
6081B LEU* 1.3 73.8 - - - +
6083B GLN* 1.3 64.3 + - - +
6084B LEU 3.0 1.3 - - - -
6085B GLY 3.0 9.4 + - - -
6086B ILE 3.4 20.2 - - - +
6087B ARG* 3.1 19.6 + - - +
6089B PHE* 4.1 2.4 - - + -
6211B LEU* 4.0 23.6 - - + -
3172D TYR* 3.6 18.0 - - + -
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Residues in contact with GLN6083 (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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6005B ASP 4.9 4.5 - - - +
6006B VAL* 4.4 14.6 - - + +
6013B LYS* 3.8 16.6 + - - -
6079B GLU* 2.7 45.0 + - - +
6080B GLU* 3.4 15.6 - - - +
6082B ALA* 1.3 77.3 - - - +
6084B LEU* 1.3 61.2 + - - +
6085B GLY* 3.4 0.9 + - - -
6087B ARG* 5.2 1.6 + - - -
3163D TYR* 4.0 14.0 + - - -
3170D ASP 4.0 6.8 + - - -
3171D THR* 3.7 13.6 - - - +
3172D TYR* 3.9 16.8 - - - +
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Residues in contact with LEU6084 (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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6005B ASP* 3.9 18.6 - - + -
6006B VAL* 3.7 14.4 - - + -
6009B LEU* 4.7 0.4 - - + -
6011B LEU* 3.5 36.1 - - + -
6012B THR* 3.6 5.6 - - - +
6013B LYS* 3.4 57.3 - - + +
6016B LEU* 3.5 23.8 - - + +
6080B GLU 2.9 18.5 + - - +
6081B LEU* 3.2 21.1 - - + +
6082B ALA 3.0 0.2 - - - -
6083B GLN* 1.3 79.5 - - - +
6085B GLY* 1.3 55.5 + - - +
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Residues in contact with GLY6085 (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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6016B LEU* 4.8 0.7 - - - -
6019B ALA 3.8 3.7 - - - +
6020B GLN* 3.7 17.5 - - - +
6081B LEU 3.1 0.2 + - - -
6082B ALA 3.0 10.4 + - - -
6083B GLN 3.2 0.8 - - - -
6084B LEU* 1.3 80.8 - - - +
6086B ILE* 1.3 70.1 + - - +
6087B ARG* 3.4 21.7 + - - +
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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