Contacts of the helix formed by residues 415 - 419 (chain A) in PDB entry 2P20
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 GLN 415 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A VAL* 4.4 0.4 - - - -
413A TRP* 4.0 9.3 - - + -
414A TRP* 1.3 99.6 - - - +
416A THR* 1.3 67.4 + - - +
417A GLU* 3.4 13.6 - - - +
418A THR* 2.9 24.5 + - + +
419A GLY 3.5 0.2 + - - -
496A TYR* 2.7 37.5 + - - -
498A SER* 2.8 35.4 + - - -
500A ASP* 3.8 0.2 + - - -
515A ARG* 3.4 7.5 - - - +
526A ARG* 4.5 1.8 - - - +
999A PRX 2.8 42.0 + - - +
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Residues in contact with THR 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A LEU* 4.1 16.9 - - + +
264A THR* 3.3 30.1 + - - +
274A VAL* 3.9 16.4 - - + -
276A HIS* 2.8 33.6 + - + +
310A VAL* 3.7 33.1 + - + +
415A GLN* 1.3 71.4 - - - +
417A GLU* 1.3 60.5 + - - +
418A THR 3.2 1.0 + - - -
419A GLY* 3.4 3.8 + - - -
999A PRX 2.7 30.3 + - - -
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Residues in contact with GLU 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A THR* 4.3 2.3 - - - +
274A VAL* 4.0 13.6 - - + +
415A GLN* 3.1 7.5 - - - +
416A THR* 1.3 82.4 + - - +
418A THR* 1.3 57.6 + - - +
419A GLY 3.5 0.2 - - - -
470A TRP* 4.3 0.7 - - - -
473A GLN* 3.8 7.1 - - - +
474A ALA* 2.8 36.6 + - + +
484A PHE* 5.9 2.0 - - + -
488A TYR* 2.7 42.1 + - + +
496A TYR* 3.0 25.5 - - + +
526A ARG* 2.5 48.1 + - - -
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Residues in contact with THR 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A TRP* 5.2 2.7 - - + -
414A TRP* 3.3 2.9 - - - +
415A GLN* 2.9 50.5 + - + +
417A GLU* 1.3 78.1 - - - +
419A GLY* 1.3 57.4 + - - +
420A GLY 2.8 23.4 + - - +
422A MET* 3.5 27.6 - - + -
470A TRP* 2.9 40.5 + - + -
472A GLY 3.0 12.4 - - - +
496A TYR* 4.3 7.2 - - + -
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Residues in contact with GLY 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A HIS* 3.3 16.7 - - - -
281A TYR* 3.6 13.7 - - - -
284A TYR* 4.7 2.9 - - - -
285A ALA* 5.1 3.0 - - - +
310A VAL* 5.0 1.6 - - - -
314A SER* 2.7 29.2 + - - -
414A TRP* 3.7 7.4 - - - -
415A GLN 3.5 2.2 + - - -
416A THR 3.4 8.3 + - - -
418A THR* 1.3 74.9 + - - +
420A GLY* 1.3 54.0 + - - +
472A GLY* 3.3 13.2 - - - -
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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