Contacts of the helix formed by residues 418 - 428 (chain C) in PDB entry 5IWM
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 418 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379C HIS* 2.7 36.5 + - - -
412C GLN* 3.7 4.1 - - - +
416C LYS 4.4 0.2 + - - -
417C LEU* 1.3 77.2 - - - +
419C GLU* 1.3 64.7 + - - +
420C LYS* 3.6 4.7 + - - +
421C GLN* 3.2 19.6 + - - +
422C ALA* 3.2 19.9 + - - +
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Residues in contact with GLU 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408C MET* 3.5 24.8 - - + +
412C GLN* 3.9 20.2 + - - +
418C SER* 1.3 74.9 - - - +
420C LYS* 1.3 64.5 + - + +
422C ALA 3.4 0.9 + - - -
423C GLN* 3.1 36.5 + - + +
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Residues in contact with LYS 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376C ASP* 5.4 9.9 + - - -
379C HIS* 4.7 9.4 - - + +
380C ILE* 4.0 20.5 - - + +
418C SER* 3.3 7.5 + - - +
419C GLU* 1.3 77.3 - - + +
421C GLN* 1.3 64.3 + - - +
423C GLN* 3.4 6.8 + - - +
424C ALA* 3.2 23.0 + - - +
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Residues in contact with GLN 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379C HIS* 2.7 61.9 + - + +
380C ILE* 4.6 3.6 - - - +
382C GLU* 4.0 9.9 + - - +
383C GLY* 3.7 25.9 - - - +
386C ILE* 5.4 3.1 - - - +
416C LYS 4.6 1.9 - - - +
417C LEU* 3.6 18.1 - - + +
418C SER* 3.2 30.0 + - - +
420C LYS* 1.3 76.0 - - - +
422C ALA* 1.3 62.5 + - - +
424C ALA* 3.3 6.9 + - - +
425C ILE* 3.2 28.8 + - - +
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Residues in contact with ALA 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408C MET* 3.7 24.9 - - - +
411C LEU* 4.1 13.8 - - + +
412C GLN* 3.9 17.3 - - + -
417C LEU* 4.4 11.1 - - + +
418C SER 3.2 16.2 + - - +
419C GLU 3.8 2.5 - - - +
421C GLN* 1.3 78.0 - - - +
423C GLN* 1.3 61.7 + - - +
425C ILE* 3.4 5.5 + - - +
426C LEU* 3.2 26.5 + - - +
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Residues in contact with GLN 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A ARG* 2.8 32.6 + - - +
408C MET* 3.4 29.5 - - + +
419C GLU* 3.1 30.4 + - + +
420C LYS* 3.7 7.0 - - - +
422C ALA* 1.3 76.1 - - - +
424C ALA* 1.3 58.0 + - - +
426C LEU* 3.3 3.7 + - - +
427C ASP* 2.9 39.3 + - - +
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Residues in contact with ALA 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380C ILE* 3.8 31.0 - - + +
384C LEU* 3.9 12.4 - - + +
420C LYS 3.2 13.1 + - - +
421C GLN* 3.6 9.6 - - - +
422C ALA 3.3 0.2 - - - -
423C GLN* 1.3 78.0 - - - +
425C ILE* 1.3 61.8 + - - +
427C ASP* 3.4 7.6 + - - +
428C MET* 3.1 21.5 + - - +
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Residues in contact with ILE 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A LEU* 3.3 16.6 - - + +
383C GLY 3.5 24.2 - - - +
384C LEU* 4.2 12.1 - - + -
387C ALA* 3.8 22.9 - - + +
394C ILE* 3.9 31.6 - - + -
398C ILE* 4.9 1.3 - - + -
411C LEU* 4.8 10.1 - - + -
417C LEU* 3.7 28.5 - - + -
421C GLN 3.2 15.3 + - - +
422C ALA* 3.8 6.7 - - - +
423C GLN 3.3 0.2 - - - -
424C ALA* 1.3 74.8 - - - +
426C LEU* 1.3 59.8 + - - +
428C MET* 3.0 23.1 - - + +
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Residues in contact with LEU 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429A ARG* 3.5 4.3 - - - +
430A LEU* 3.3 10.2 + - - -
431A ARG* 3.2 70.6 + - + +
398C ILE* 3.9 30.7 - - + -
404C ASP* 4.3 9.6 - - + +
407C ALA* 4.3 7.0 - - + -
408C MET* 3.7 40.6 - - + +
411C LEU* 3.9 13.7 - - + -
422C ALA 3.2 8.1 + - - +
423C GLN 3.3 3.1 + - - +
425C ILE* 1.3 79.6 - - - +
427C ASP* 1.3 59.9 + - - +
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Residues in contact with ASP 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429A ARG* 2.7 47.9 + - - +
431A ARG* 2.7 29.2 + - - -
423C GLN* 2.9 25.1 + - - +
424C ALA* 3.9 7.6 + - - +
425C ILE 3.3 0.2 - - - -
426C LEU* 1.3 75.4 - - - +
428C MET* 1.3 64.3 + - - +
429C ARG* 3.4 0.7 + - - +
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Residues in contact with MET 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429A ARG* 3.4 0.4 - - - -
430A LEU* 3.0 54.5 + - + +
384C LEU* 4.2 24.0 - - + -
387C ALA* 4.4 13.0 - - + -
388C LEU* 4.8 11.9 - - + -
391C ILE* 4.8 9.9 - - + -
424C ALA 3.1 12.6 + - - +
425C ILE* 3.0 29.2 - - + +
426C LEU 3.2 0.4 - - - -
427C ASP* 1.3 76.1 - - - +
429C ARG* 1.3 67.6 + - - +
432C ARG* 3.6 36.8 - - + +
433C LEU* 4.9 7.6 - - + -
441C ILE* 4.9 5.4 - - - -
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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