Contacts of the helix formed by residues 449 - 455 (chain A) in PDB entry 3PEI
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 ILE 449 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A GLY* 3.7 33.7 - - - +
276A GLY* 3.7 7.4 - - - +
357A LEU* 4.4 7.9 - - + -
358A ALA 2.8 23.4 + - - +
359A THR* 3.7 4.9 - - + -
373A SER* 3.9 7.4 - - - +
447A LEU* 3.8 20.9 - - + +
448A ASP* 1.3 74.7 - - - +
450A ALA* 1.3 65.4 + - - +
451A GLY 3.2 2.9 - - - -
452A SER* 3.3 18.2 - - - +
453A ALA* 2.9 36.3 + - + +
465A ARG 4.3 0.7 - - - +
466A PRO* 3.8 29.4 - - + -
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Residues in contact with ALA 450 (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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272A MSE 4.2 17.3 - - + -
359A THR* 3.7 22.9 - - - +
361A THR 3.2 26.9 - - - +
364A MSE 4.4 2.9 - - + -
365A ILE* 4.0 10.7 - - + +
448A ASP* 3.4 11.5 + - - +
449A ILE* 1.3 77.4 - - - +
451A GLY* 1.3 62.6 + - - +
454A MSE 3.6 24.6 - - - +
455A GLY 4.0 2.3 - - - +
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Residues in contact with GLY 451 (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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364A MSE 4.8 7.0 - - - +
365A ILE* 3.6 21.0 - - - +
369A GLY 3.7 13.9 - - - -
370A ASP* 3.6 10.0 - - - -
372A TYR 5.1 1.1 + - - -
449A ILE* 3.2 0.6 - - - +
450A ALA* 1.3 77.9 - - - +
452A SER* 1.3 64.6 + - - +
455A GLY* 3.1 29.7 + - - -
504A EDO 3.6 1.2 + - - -
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Residues in contact with SER 452 (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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370A ASP 3.3 11.2 + - - -
372A TYR 3.8 13.9 + - - -
373A SER* 2.6 30.3 + - - -
449A ILE* 3.3 20.8 - - - +
451A GLY* 1.3 74.8 - - - +
453A ALA* 1.3 49.7 + - - +
454A MSE 3.5 0.2 - - - -
463A SER* 2.6 24.8 + - - -
465A ARG* 3.6 31.5 + - - +
504A EDO 3.0 11.1 - - - -
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Residues in contact with ALA 453 (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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173A GLN* 3.1 28.1 + - - +
275A GLY* 4.7 1.8 - - - -
359A THR* 4.4 4.5 - - + -
449A ILE* 2.9 32.7 + - + +
452A SER* 1.3 79.1 + - - +
454A MSE 1.3 63.4 + - + +
455A GLY 3.7 0.2 - - - -
462A ALA* 3.6 0.5 - - - -
463A SER* 3.1 25.1 + - - -
465A ARG 3.9 17.7 - - - +
504A EDO 4.3 0.2 - - - -
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Residues in contact with MSE 454 (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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270A MSE 5.8 0.9 - - - +
271A LYS* 3.0 32.1 - - + +
272A MSE 4.3 14.4 - - - -
273A ASP* 3.8 41.7 - - + +
359A THR* 4.5 5.4 - - + -
365A ILE* 6.1 0.9 - - + -
450A ALA 3.6 19.9 + - - +
451A GLY 3.4 1.0 + - - -
453A ALA* 1.3 82.3 - - + +
455A GLY* 1.4 62.8 + - - +
460A CYS* 3.3 12.9 - - - -
461A LYS 2.8 37.0 + - - +
503A EDO 3.6 25.8 + - - +
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Residues in contact with GLY 455 (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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365A ILE* 4.5 4.2 - - - +
370A ASP* 3.9 5.2 - - - -
450A ALA 4.0 4.3 - - - +
451A GLY* 3.1 13.9 + - - +
454A MSE 1.4 89.5 - - - +
456A ASP* 1.3 61.7 + - - -
459A SER* 3.8 16.2 - - - -
460A CYS* 4.5 3.3 - - - -
504A EDO 2.9 21.4 + - - -
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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