Contacts of the helix formed by residues 418 - 428 (chain A) in PDB entry 5M4G
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 418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A ALA* 3.6 23.3 - - + +
254A LEU* 4.6 3.6 - - + -
362A VAL 5.1 2.8 + - - +
365A PRO* 4.0 22.9 - - + -
416A TYR* 3.7 27.8 + - + +
417A PHE* 1.3 74.8 - - - +
419A ASP* 1.3 66.5 + - - +
420A HIS* 4.1 5.8 - - + +
421A LEU* 3.1 24.9 + - + +
422A LEU* 2.9 26.6 + - - +
105B ALA 3.8 22.0 - - - +
106B THR* 3.7 19.7 - - - +
109B GLY* 6.2 0.7 - - - -
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Residues in contact with ASP 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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417A PHE 3.9 4.9 + - - +
418A ILE* 1.3 71.6 - - - +
420A HIS* 1.3 56.7 + - - +
422A LEU* 3.3 1.8 + - - +
423A ASP* 2.9 42.6 + - - +
444A ARG* 3.0 41.8 + - - +
445A GLY 5.1 3.2 + - - -
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Residues in contact with HIS 420 (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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418A ILE* 3.2 3.4 + - + +
419A ASP* 1.3 77.6 - - - +
421A LEU* 1.3 65.6 + - + +
423A ASP* 4.0 4.6 - - - +
424A GLU* 3.1 46.4 + - + +
102B ALA* 3.7 26.0 + - + +
103B SER* 3.6 20.6 - - - -
105B ALA* 3.8 28.7 - - + +
106B THR* 3.5 23.3 - - - -
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Residues in contact with LEU 421 (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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361A ALA 4.0 6.3 - - - +
362A VAL* 3.5 35.2 - - + +
365A PRO* 3.8 33.0 - - + -
418A ILE* 3.1 24.9 + - + +
420A HIS* 1.3 79.8 - - + +
422A LEU* 1.3 64.3 + - - +
424A GLU* 3.4 21.2 + - - +
425A ALA* 3.0 23.6 + - - +
431A ARG* 5.0 0.7 + - - -
106B THR* 3.8 27.8 - - + +
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Residues in contact with LEU 422 (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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362A VAL* 3.8 22.0 - - + +
363A PHE* 4.0 24.2 - - + -
416A TYR 5.5 0.2 - - - +
417A PHE* 4.0 15.9 - - + -
418A ILE 2.9 36.5 + - - +
419A ASP* 3.9 4.0 - - - +
421A LEU* 1.3 77.3 - - + +
423A ASP* 1.3 58.2 + - - +
425A ALA* 3.3 3.8 + - - +
426A LEU* 2.9 34.4 + - - +
435A LEU* 4.9 3.5 - - + +
440A LEU* 4.0 23.1 - - + -
444A ARG* 3.8 37.5 - - - +
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Residues in contact with ASP 423 (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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419A ASP* 2.9 26.6 + - - +
420A HIS* 4.0 4.7 - - - +
422A LEU* 1.3 75.9 - - - +
424A GLU* 1.3 62.5 + - - +
426A LEU* 3.3 9.3 + - - +
427A ALA* 3.1 23.2 + - - +
444A ARG* 2.9 30.5 + - - -
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Residues in contact with GLU 424 (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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420A HIS* 3.1 35.1 + - + +
421A LEU* 3.6 25.1 - - - +
423A ASP* 1.3 78.0 - - - +
425A ALA* 1.3 62.3 + - - +
427A ALA* 3.2 16.1 + - - +
428A ASP* 3.3 13.3 + - - +
431A ARG* 3.9 18.5 + - - +
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Residues in contact with ALA 425 (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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359A LEU* 4.7 0.2 - - + -
362A VAL* 3.9 24.5 - - + -
421A LEU 3.0 16.8 + - - +
422A LEU* 3.6 4.9 - - - +
424A GLU* 1.3 76.0 - - - +
426A LEU* 1.3 62.2 + - - +
428A ASP* 3.1 23.2 + - - +
431A ARG* 3.7 21.3 - - + +
432A ALA 3.4 8.5 + - - -
435A LEU* 3.8 20.0 - - + -
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Residues in contact with LEU 426 (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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422A LEU 2.9 21.2 + - - +
423A ASP* 3.8 9.6 - - - +
424A GLU 3.3 0.2 - - - -
425A ALA* 1.3 75.3 - - - +
427A ALA* 1.3 59.4 + - - +
432A ALA* 3.5 13.5 - - - +
435A LEU* 3.9 28.5 - - + -
437A ARG* 3.2 68.4 + - + +
440A LEU* 4.1 12.6 - - + -
444A ARG* 4.0 23.3 - - - +
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Residues in contact with ALA 427 (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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423A ASP 3.1 13.2 + - - +
424A GLU* 3.6 10.8 - - - +
425A ALA 3.2 0.4 - - - -
426A LEU* 1.3 76.6 - - - +
428A ASP* 1.3 58.2 + - - +
429A PRO* 3.4 12.1 - - - +
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Residues in contact with ASP 428 (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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424A GLU 3.3 4.3 + - - +
425A ALA 3.1 8.4 + - - +
426A LEU 3.3 0.2 - - - -
427A ALA* 1.3 76.6 - - - +
429A PRO* 1.3 66.2 - - - +
430A ALA* 3.0 23.5 + - - +
431A ARG* 2.9 45.0 + - - +
432A ALA* 2.8 29.6 + - - +
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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