Contacts of the helix formed by residues 305 - 315 (chain B) in PDB entry 1Y5I
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 ASP 305 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B ASP* 3.2 33.1 + - + +
304B ASN* 1.3 76.6 - - - +
306B PRO* 1.3 73.0 - - - +
307B LYS* 2.9 30.5 + - - +
308B VAL* 2.8 25.4 + - + +
309B ILE* 2.9 12.0 + - - +
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Residues in contact with PRO 306 (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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304B ASN 3.4 9.8 - - - +
305B ASP* 1.3 86.5 - - - +
307B LYS* 1.3 60.8 + - - +
309B ILE* 3.7 14.8 - - + +
310B GLU* 2.9 38.3 + - + +
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Residues in contact with LYS 307 (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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305B ASP* 2.9 19.6 + - - +
306B PRO* 1.3 79.2 - - - +
308B VAL* 1.3 60.2 + - + +
310B GLU* 3.6 7.6 + - - +
311B GLN* 3.1 28.1 + - + +
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Residues in contact with VAL 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ILE* 3.6 16.7 - - + +
274B LEU* 4.2 16.2 - - + -
301B LEU* 3.8 35.7 - - + -
302B ASP* 3.3 33.7 - - + +
303B PRO* 4.5 1.6 - - + -
305B ASP* 2.8 17.1 + - + +
307B LYS* 1.3 78.9 - - + +
309B ILE* 1.3 61.0 + - - +
311B GLN* 3.3 1.2 + - - -
312B ALA* 2.8 29.6 + - - +
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Residues in contact with ILE 309 (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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274B LEU* 6.2 0.7 - - + -
303B PRO* 3.3 20.4 - - + +
304B ASN 4.0 12.3 - - - +
305B ASP 2.9 17.9 + - - +
306B PRO* 3.8 12.1 - - + +
308B VAL* 1.3 75.5 - - - +
310B GLU* 1.3 64.5 + - + +
312B ALA* 3.3 7.9 + - - +
313B ILE* 3.1 40.1 + - + +
322B ILE* 4.2 17.0 - - + -
326B GLN* 3.3 24.7 - - - +
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Residues in contact with GLU 310 (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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306B PRO* 2.9 29.7 + - + +
307B LYS* 4.0 6.1 - - - +
309B ILE* 1.3 79.6 - - + +
311B GLN* 1.3 62.6 + - - +
313B ILE* 3.5 8.9 + - + +
314B LYS* 3.0 22.4 + - - +
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Residues in contact with GLN 311 (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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1B MET* 3.6 33.8 + - + +
3B ILE* 3.4 22.9 - - + -
307B LYS* 3.1 19.4 + - + +
308B VAL* 3.7 4.0 - - - +
310B GLU* 1.3 74.9 - - - +
312B ALA* 1.3 55.8 + - - +
314B LYS* 2.9 46.3 + - - +
315B ASP* 2.8 57.9 + - - +
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Residues in contact with ALA 312 (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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3B ILE* 3.8 17.9 - - + +
274B LEU* 4.8 7.2 - - + -
308B VAL 2.8 18.5 + - - +
309B ILE* 3.3 7.8 + - - +
311B GLN* 1.3 76.5 - - - +
313B ILE* 1.3 62.2 + - - +
315B ASP 3.1 7.7 + - - +
316B GLY 3.1 0.5 + - - -
317B ILE* 2.9 42.2 + - + +
322B ILE* 3.7 21.1 - - + -
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Residues in contact with ILE 313 (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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309B ILE* 3.1 31.3 + - + +
310B GLU* 3.8 8.7 - - + +
312B ALA* 1.3 75.0 - - - +
314B LYS* 1.3 64.5 + - - +
316B GLY* 3.0 13.9 + - - -
317B ILE 4.2 7.1 - - - +
319B LEU* 3.9 25.1 - - + -
322B ILE* 3.6 14.8 - - + -
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Residues in contact with LYS 314 (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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310B GLU 3.0 14.3 + - - +
311B GLN* 2.9 48.8 + - - +
313B ILE* 1.3 79.1 - - - +
315B ASP* 1.3 62.0 + - - +
316B GLY 3.3 3.6 + - - -
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Residues in contact with ASP 315 (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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1B MET 4.8 0.7 - - - +
2B LYS* 3.5 8.1 - - - +
3B ILE* 2.8 45.0 + - + +
205B GLU* 5.3 4.7 - - - +
311B GLN* 2.8 47.6 + - - +
312B ALA 3.1 6.0 + - - +
314B LYS* 1.3 77.8 - - - +
316B GLY* 1.3 59.0 + - - +
317B ILE* 3.5 4.1 + - + +
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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