Contacts of the helix formed by residues 6238 - 6253 (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 GLU6238 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6094B THR* 5.5 5.8 - - + -
6105B GLY* 4.8 11.9 - - - -
6218B GLY* 4.6 20.6 - - - -
6219B VAL 4.8 4.0 - - - +
6220B ILE* 4.2 22.1 - - + +
6231B ALA 5.3 1.7 - - - +
6232B GLU 4.2 2.3 - - - +
6233B THR* 3.0 40.0 + - - +
6234B MET* 3.9 4.0 + - - -
6237B THR* 1.3 100.9 + - + +
6239B SER* 1.3 62.1 + - - +
6240B HIS 3.1 3.0 + - - +
6241B ALA* 3.5 17.8 + - - +
6242B VAL* 4.2 5.9 + - - +
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Residues in contact with SER6239 (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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6236B GLN* 3.6 35.5 - - - +
6237B THR 3.0 2.4 + - - +
6238B GLU* 1.3 77.5 - - - +
6240B HIS* 1.3 69.8 + - - +
6242B VAL* 2.9 24.4 + - - +
6243B LYS* 2.9 14.2 + - - +
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Residues in contact with HIS6240 (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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6105B GLY 4.7 9.9 - - - +
6107B VAL* 4.0 17.3 - - + -
6147B ILE* 3.9 29.6 - - + +
6148B GLY 5.5 0.7 - - - -
6149B ALA* 4.1 16.7 - - + +
6237B THR 3.7 17.5 + - - +
6238B GLU 3.1 0.6 - - - -
6239B SER* 1.3 82.8 + - - +
6241B ALA* 1.3 62.8 + - - +
6243B LYS* 3.3 6.4 + - - +
6244B ILE* 2.9 29.9 + - - +
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Residues in contact with ALA6241 (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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6092B ILE* 4.2 16.6 - - + +
6107B VAL* 4.2 6.5 - - + +
6216B VAL* 4.4 4.6 - - + +
6217B ALA* 4.1 9.2 - - - +
6218B GLY* 4.0 26.7 - - - +
6238B GLU 3.5 12.6 + - - +
6239B SER 3.1 0.4 - - - -
6240B HIS* 1.3 77.7 - - - +
6242B VAL* 1.3 59.3 + - - +
6244B ILE* 3.1 16.9 - - - +
6245B VAL* 3.0 27.5 + - - +
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Residues in contact with VAL6242 (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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6034B ILE* 4.0 34.3 - - + -
6037B LEU* 3.4 28.9 - - + -
6092B ILE* 4.0 19.3 - - + -
6238B GLU 4.3 9.0 - - - +
6239B SER* 2.9 16.4 + - - +
6241B ALA* 1.3 73.5 - - - +
6243B LYS* 1.3 66.3 + - - +
6245B VAL* 2.8 27.5 - - + +
6246B VAL* 2.9 7.6 + - + +
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Residues in contact with LYS6243 (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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6037B LEU* 5.0 6.5 - - + +
6147B ILE* 3.3 38.6 - - + -
6239B SER* 2.9 11.9 + - - +
6240B HIS* 3.3 12.5 + - - +
6242B VAL* 1.3 77.6 - - - +
6244B ILE* 1.3 59.5 + - + +
6246B VAL* 3.3 12.2 + - - +
6247B GLU* 2.9 46.2 + - + +
6250B ARG* 6.0 1.6 - - - +
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Residues in contact with ILE6244 (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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6107B VAL* 3.9 22.2 - - + -
6109B VAL* 5.1 1.8 - - + -
6140B LEU* 4.3 11.4 - - + +
6143B ALA* 3.5 16.6 - - + +
6144B ALA* 4.1 26.0 - - + +
6147B ILE* 4.5 15.9 - - + -
6149B ALA* 4.9 5.4 - - + -
6216B VAL* 3.7 29.2 - - + -
6240B HIS 2.9 15.4 + - - +
6241B ALA* 3.1 12.3 - - - +
6243B LYS* 1.3 73.7 - - - +
6245B VAL* 1.3 61.6 + - - +
6247B GLU* 4.1 7.4 - - - -
6248B ALA* 2.7 35.5 + - - +
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Residues in contact with VAL6245 (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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6023B ILE* 4.1 22.0 - - + +
6034B ILE* 4.9 1.1 - - + -
6090B LEU* 3.8 27.7 - - + +
6091B ARG 4.3 1.3 - - - +
6092B ILE* 4.0 25.6 - - + -
6140B LEU* 4.2 3.8 - - + -
6216B VAL* 4.2 12.1 - - + -
6241B ALA 3.0 13.1 + - - +
6242B VAL* 2.8 31.6 + - + +
6244B ILE* 1.3 75.8 - - - +
6246B VAL* 1.3 68.3 + - + +
6248B ALA* 3.6 5.5 - - - +
6249B ALA* 3.0 26.3 + - - +
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Residues in contact with VAL6246 (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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6023B ILE* 4.4 6.7 - - + -
6034B ILE* 4.4 13.7 - - + +
6037B LEU* 4.4 20.6 - - + +
6038B MET* 4.1 10.3 - - + -
6057B LEU* 3.7 27.8 - - + +
6242B VAL* 2.9 28.9 + - + +
6243B LYS* 3.5 14.8 - - - +
6245B VAL* 1.3 79.5 - - + +
6247B GLU* 1.3 68.3 + - - +
6248B ALA 3.0 0.9 - - - -
6249B ALA* 2.8 18.6 + - - +
6250B ARG* 2.8 15.6 + - + +
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Residues in contact with GLU6247 (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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6143B ALA* 3.3 28.3 - - + +
6146B SER* 3.8 8.7 + - - +
6147B ILE* 5.3 2.0 - - + -
6243B LYS* 2.9 36.6 + - + +
6244B ILE* 3.8 4.9 - - - +
6246B VAL* 1.3 75.9 - - - +
6248B ALA* 1.3 61.3 + - - +
6250B ARG* 3.2 42.0 + - - +
6251B ARG* 3.4 28.8 + - - +
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Residues in contact with ALA6248 (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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6090B LEU* 4.3 5.6 - - + -
6139B ALA* 3.8 19.6 - - + +
6140B LEU* 3.5 27.6 - - + +
6143B ALA* 4.0 0.2 - - - -
6244B ILE 2.7 23.3 + - - +
6245B VAL 3.6 4.0 - - - +
6247B GLU* 1.3 72.1 - - - +
6249B ALA* 1.3 66.1 + - - +
6251B ARG* 2.9 26.1 + - - +
6252B LEU* 3.2 14.2 + - - +
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Residues in contact with ALA6249 (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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6021B LEU* 4.0 21.8 - - + -
6023B ILE* 4.3 8.7 - - + -
6057B LEU* 3.9 12.3 - - + -
6062B VAL* 5.2 2.2 - - + -
6090B LEU* 3.7 17.6 - - + +
6245B VAL 3.0 14.3 + - - +
6246B VAL* 2.8 11.5 + - - +
6248B ALA* 1.3 75.1 - - - +
6250B ARG* 1.3 65.1 + - - +
6252B LEU* 2.8 13.7 + - - +
6253B LEU* 3.2 18.4 + - - +
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Residues in contact with ARG6250 (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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6057B LEU* 3.2 37.6 - - + +
6058B ASP* 2.8 40.8 + - - +
6243B LYS* 6.0 1.8 - - - +
6246B VAL* 2.8 13.4 + - - +
6247B GLU* 3.2 30.5 + - - +
6249B ALA* 1.3 77.6 - - - +
6251B ARG* 1.3 60.1 + - + +
6253B LEU* 3.7 18.1 + - - +
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Residues in contact with ARG6251 (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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6139B ALA* 3.8 28.7 - - + +
6142B GLU* 3.6 39.6 + - - +
6143B ALA* 3.9 4.8 - - - +
6146B SER* 3.7 23.8 + - - -
6247B GLU* 3.4 37.0 + - - +
6248B ALA* 2.9 8.4 + - - +
6250B ARG* 1.3 78.4 - - + +
6252B LEU* 1.3 61.8 + - - +
6253B LEU 3.2 4.5 + - - -
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Residues in contact with LEU6252 (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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6021B LEU* 3.7 17.7 - - + +
6088B THR* 4.3 2.6 - - + -
6090B LEU* 3.6 40.2 - - + -
6135B ALA* 3.9 32.5 - - + +
6136B CYS* 3.9 17.7 - - - +
6139B ALA* 3.8 15.7 - - + -
6212B ARG* 3.5 34.2 + - - +
6248B ALA 3.2 4.7 + - - +
6249B ALA 2.8 4.2 + - - +
6251B ARG* 1.3 76.2 - - - +
6253B LEU* 1.3 64.3 + - - +
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Residues in contact with LEU6253 (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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6021B LEU* 3.9 22.0 - - + +
6057B LEU* 3.5 45.3 - - + +
6058B ASP* 5.0 3.6 - - + -
6060B LYS* 4.3 28.1 - - + +
6061B ALA 4.6 4.5 - - - +
6062B VAL* 3.5 26.2 - - + -
6249B ALA 3.2 16.4 - - - +
6250B ARG* 3.9 12.8 - - - +
6251B ARG 3.2 6.3 - - - -
6252B LEU* 1.3 82.0 - - - +
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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
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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