Contacts of the helix formed by residues 406 - 416 (chain C) in PDB entry 1P4V
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 GLY 406 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A VAL* 5.6 1.6 - - - -
106A GLY* 6.0 4.3 - - - -
380C ALA 3.0 12.9 + - - -
381C CYS* 3.1 24.0 + - - +
382C MET* 4.6 2.6 - - - -
383C GLU 5.8 0.7 - - - -
405C VAL* 1.3 71.2 - - - +
407C ASP* 1.3 68.4 + - - -
409C ALA* 2.9 15.7 + - - +
410C LEU* 3.1 11.9 + - - +
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Residues in contact with ASP 407 (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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62A ARG* 4.7 11.5 + - - +
107A ASP* 4.2 21.3 - - - +
178A HIS* 4.3 15.5 + - + +
362C ARG* 5.8 1.4 + - - -
383C GLU* 5.1 6.2 - - - +
405C VAL 3.6 0.2 + - - -
406C GLY* 1.3 72.1 - - - -
408C GLY* 1.3 56.4 + - - +
410C LEU* 3.2 12.9 + - - +
411C GLU* 2.8 31.0 + - - +
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Residues in contact with GLY 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A MET* 5.6 1.0 - - - +
178A HIS* 3.2 45.2 - - - +
404C LEU* 4.4 3.6 - - - +
405C VAL 3.4 6.1 + - - -
406C GLY 3.1 1.0 - - - -
407C ASP* 1.3 80.0 - - - +
409C ALA* 1.3 60.8 + - - +
411C GLU* 3.5 6.4 + - - +
412C PHE* 3.0 23.6 + - - +
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Residues in contact with ALA 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C VAL* 4.4 7.0 - - + -
382C MET* 3.8 26.0 - - + +
391C VAL* 4.3 2.9 - - - +
404C LEU* 3.7 37.8 - - + +
405C VAL* 3.4 8.4 + - - -
406C GLY 2.9 10.1 + - - +
408C GLY* 1.3 75.3 - - - +
410C LEU* 1.3 59.1 + - - +
412C PHE* 3.2 4.7 + - - +
413C ALA* 2.9 28.2 + - - +
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Residues in contact with LEU 410 (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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382C MET* 4.1 6.6 - - + -
383C GLU* 3.4 25.8 - - + +
384C HIS* 3.8 27.8 - - + +
385C ILE* 3.6 24.0 - - + -
406C GLY 3.1 9.2 + - - +
407C ASP* 3.5 13.5 - - - +
409C ALA* 1.3 76.4 - - - +
411C GLU* 1.3 67.4 + - - +
413C ALA* 3.0 6.1 + - - +
414C LEU* 2.9 45.4 + - + +
420C LYS* 4.2 14.1 - - + +
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Residues in contact with GLU 411 (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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59A ARG* 5.0 9.2 + - - -
60A ASP* 4.0 17.8 - - - +
178A HIS* 4.6 10.1 + - - +
407C ASP 2.8 20.5 + - - +
408C GLY* 3.9 5.6 - - - +
410C LEU* 1.3 73.9 - - - +
412C PHE* 1.3 63.4 + - - +
414C LEU* 3.4 11.7 + - - +
415C SER* 3.0 23.2 + - - -
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Residues in contact with PHE 412 (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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177A MET* 3.7 20.4 - - + -
391C VAL* 4.0 9.6 - - + -
394C ALA* 3.5 22.9 - - + -
395C VAL* 3.5 30.3 - - + -
398C LYS* 4.2 4.0 - - + -
399C THR* 3.4 26.0 - - + -
404C LEU* 3.7 21.3 - - + -
408C GLY 3.0 17.7 + - - +
409C ALA 3.5 2.7 - - - +
411C GLU* 1.3 76.2 - - - +
413C ALA* 1.3 66.3 + - - +
415C SER* 2.5 28.8 + - - -
416C GLN* 3.0 37.8 + - + +
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Residues in contact with ALA 413 (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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382C MET* 4.2 0.4 - - - -
385C ILE* 3.8 30.1 - - + -
391C VAL* 3.8 24.0 - - + -
409C ALA 2.9 13.4 + - - +
410C LEU* 3.3 8.3 - - - +
412C PHE* 1.3 78.3 - - - +
414C LEU* 1.3 57.1 + - - +
416C GLN* 3.0 15.7 + - - -
418C PHE* 3.1 31.4 + - + -
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Residues in contact with LEU 414 (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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385C ILE* 4.2 3.4 - - + -
410C LEU* 2.9 44.8 + - + +
411C GLU* 3.8 8.3 - - - +
413C ALA* 1.3 75.0 - - - +
415C SER* 1.3 62.6 + - - +
417C GLY* 3.2 13.9 + - - -
418C PHE 3.5 20.3 - - - +
420C LYS* 4.0 35.9 - - + +
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Residues in contact with SER 415 (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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411C GLU* 3.0 14.9 + - - -
412C PHE* 2.5 34.4 + - - -
414C LEU* 1.3 76.5 - - - +
416C GLN* 1.3 68.2 + - - +
417C GLY 3.3 1.4 + - - -
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Residues in contact with GLN 416 (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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394C ALA* 4.3 5.3 - - + +
398C LYS* 3.6 30.8 - - - +
412C PHE* 3.0 49.8 + - + +
413C ALA 3.0 9.8 + - - +
415C SER* 1.3 87.7 + - - +
417C GLY* 1.3 58.9 + - - +
418C PHE* 3.4 21.2 + - + -
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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