Contacts of the helix formed by residues 298 - 305 (chain S) in PDB entry 1I84
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 SER 298 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296S GLY 3.4 5.0 + - - -
297S ALA* 1.3 71.7 - - - +
299S GLU* 1.3 54.5 + - - +
300S GLN* 3.3 8.8 + - - +
301S MET* 3.2 31.8 + - - +
302S ARG* 2.4 38.2 + - - +
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Residues in contact with GLU 299 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297S ALA 3.7 2.2 + - - -
298S SER* 1.3 69.7 + - - +
300S GLN* 1.3 62.7 + - - +
302S ARG* 2.6 41.2 + - - +
303S ASN* 3.2 14.0 + - - -
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Residues in contact with GLN 300 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298S SER* 3.2 7.0 + - - +
299S GLU* 1.3 78.1 - - - +
301S MET* 1.3 65.5 + - - +
302S ARG 2.6 14.6 + - - -
303S ASN* 2.7 30.5 - - - +
304S ASP* 3.3 23.0 + - - +
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Residues in contact with MET 301 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293S LEU* 3.2 34.8 - - + -
297S ALA* 3.7 5.8 - - + -
298S SER* 3.2 37.0 + - - +
300S GLN* 1.3 81.4 + - - +
302S ARG* 1.3 64.6 + - - +
303S ASN 3.3 0.2 - - - -
304S ASP* 3.2 27.2 + - + +
305S LEU* 3.4 32.6 + - + +
307S LEU* 3.2 22.1 - - + +
332S PHE* 4.6 10.8 - - - -
350S THR* 6.3 4.3 - - + -
353S LEU* 4.6 11.2 - - + -
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Residues in contact with ARG 302 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294S ILE 6.0 1.6 - - - +
297S ALA* 4.3 16.2 - - + +
298S SER 2.4 25.9 + - - +
299S GLU* 2.6 33.7 + - - +
300S GLN 2.6 4.0 + - - -
301S MET* 1.3 67.1 - - - +
303S ASN* 1.3 87.1 + - - +
306S LEU* 3.4 5.9 - - - +
307S LEU* 2.7 84.0 + - + +
308S GLU* 3.9 4.6 - - - +
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Residues in contact with ASN 303 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299S GLU* 3.2 22.2 + - - -
300S GLN* 2.7 27.1 + - - +
302S ARG* 1.3 96.6 - - - +
304S ASP* 1.3 71.6 + - - +
305S LEU 2.6 7.8 + - - -
306S LEU* 2.4 34.2 + - + +
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Residues in contact with ASP 304 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300S GLN* 3.3 25.8 + - - +
301S MET* 3.3 25.8 - - + +
303S ASN* 1.3 99.3 + - - +
305S LEU* 1.3 70.6 + - + +
306S LEU* 5.2 1.8 - - - +
354S ARG* 4.1 16.6 + - - +
390S LEU* 4.5 4.0 - - - +
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Residues in contact with LEU 305 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293S LEU* 4.2 0.4 - - + -
301S MET* 3.4 40.7 + - + +
303S ASN 2.6 1.8 + - - -
304S ASP* 1.3 92.0 - - + +
306S LEU* 1.3 77.9 + - - +
307S LEU* 3.5 12.3 - - + -
350S THR* 4.5 7.0 - - - +
353S LEU* 3.7 13.5 - - + +
354S ARG* 3.6 48.2 - - + +
357S SER* 3.1 29.5 - - - +
361S GLN* 5.1 0.2 - - - +
390S LEU* 4.0 13.1 - - - +
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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