Contacts of the helix formed by residues 328 - 333 (chain Q) in PDB entry 5I2D
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 PHE 328 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601O ARG* 3.6 50.5 - - - -
611O GLN* 4.5 19.7 - - + -
317Q LEU 4.0 11.7 - - - +
318Q GLU* 4.0 24.0 - - + -
319Q THR 3.7 3.4 - - - +
320Q PRO* 4.7 5.4 - - + -
321Q ILE* 3.8 4.3 - - - -
325Q LYS* 4.2 17.0 - - + -
326Q ASP 6.5 0.2 - - - -
327Q SER* 1.3 85.7 - - - +
329Q TYR* 1.3 64.7 + - - +
330Q GLY* 3.3 2.0 - - - +
331Q ASP* 3.3 31.4 + - - +
332Q PHE* 3.1 20.3 - - - -
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Residues in contact with TYR 329 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530O VAL* 3.8 25.3 - - + +
536O ALA* 4.6 2.5 - - + -
315Q VAL* 4.5 13.2 - - + -
316Q SER 4.2 13.5 - - - -
317Q LEU* 3.6 8.9 + - + +
319Q THR* 2.9 27.8 + - + +
321Q ILE* 3.7 19.9 - - + +
328Q PHE* 1.3 67.9 - - - +
330Q GLY* 1.3 58.2 + - - +
331Q ASP 3.0 4.5 - - - -
332Q PHE* 2.9 31.5 + + + +
333Q ILE* 3.7 29.6 - - + +
7U T 4.3 27.4 - + + +
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Residues in contact with GLY 330 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014N SER* 4.1 6.4 + - - -
1015N LEU* 4.5 6.1 + - - +
317Q LEU* 3.1 40.8 + - - -
328Q PHE* 3.3 1.9 - - - +
329Q TYR* 1.3 77.0 - - - +
331Q ASP* 1.3 62.2 + - - +
332Q PHE 3.1 1.0 + - - -
333Q ILE* 3.3 22.4 + - - +
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Residues in contact with ASP 331 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014N SER* 4.3 10.4 + - - -
1021N LEU* 3.3 27.9 - - - +
1022N GLY 4.6 3.6 + - - -
326Q ASP 5.2 0.9 - - - +
327Q SER* 4.3 5.0 - - - -
328Q PHE* 3.3 44.0 + - - +
329Q TYR 3.0 0.8 - - - -
330Q GLY* 1.3 79.0 - - - +
332Q PHE* 1.3 65.5 + - + +
333Q ILE 3.4 0.4 - - - -
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Residues in contact with PHE 332 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021N LEU* 4.1 8.9 - - - +
1022N GLY* 4.5 9.4 - - - -
1023N GLY* 5.8 0.7 - - - -
1026N GLN* 3.6 43.8 - - + +
321Q ILE* 3.9 26.5 - - + -
327Q SER* 4.3 16.2 - - - -
328Q PHE 3.1 28.5 - - - -
329Q TYR* 2.9 20.7 + + + +
331Q ASP* 1.3 84.9 - - + +
333Q ILE* 1.3 59.8 + - + +
334Q PRO* 3.5 9.2 - - - +
4U G 5.5 5.4 - - - -
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Residues in contact with ILE 333 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015N LEU* 3.7 33.1 + - + +
1021N LEU* 4.0 7.9 - - - +
528O VAL* 4.7 6.3 - - + -
529O GLN 5.8 0.9 - - - +
530O VAL* 3.7 35.4 - - + -
536O ALA* 4.4 1.6 - - + -
317Q LEU* 3.7 29.8 - - + -
329Q TYR* 3.7 30.5 - - + +
330Q GLY* 3.3 14.6 + - - +
331Q ASP 3.4 0.8 - - - -
332Q PHE* 1.3 80.8 - - - +
334Q PRO* 1.3 78.3 - - + +
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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