Contacts of the helix formed by residues 430 - 439 (chain F) in PDB entry 1P8J
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 ASP 430 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132F LEU 4.0 2.2 - - - -
133F ASN* 2.6 37.8 + - - +
377F ILE* 4.9 0.2 - - - -
400F THR* 3.8 20.6 + - - +
401F SER* 4.9 1.0 - - - +
402F LYS* 3.0 33.9 + - + +
428F LEU 3.6 0.8 + - - -
429F LEU* 1.3 75.1 - - - +
431F ALA* 1.3 58.7 + - - +
432F GLY 3.2 3.3 + - - -
433F ALA* 3.1 13.8 + - + +
434F MET* 2.8 36.8 + - - +
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Residues in contact with ALA 431 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F LEU 3.0 15.4 + - - +
133F ASN 3.2 14.4 - - - +
134F VAL* 3.6 22.4 - - + -
137F ALA* 4.2 9.4 - - + -
377F ILE* 3.9 25.1 - - + +
380F LEU* 4.5 5.8 - - + -
429F LEU 3.9 1.2 - - - -
430F ASP* 1.3 71.3 + - - +
432F GLY* 1.3 64.4 + - - +
434F MET* 3.5 1.7 - - - +
435F VAL* 2.9 28.4 + - - +
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Residues in contact with GLY 432 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F ASN* 3.1 18.2 + - - -
136F GLU* 3.4 37.0 - - - +
137F ALA* 4.4 7.4 - - - +
140F GLN* 4.2 1.8 + - - -
430F ASP* 3.2 2.6 + - - -
431F ALA* 1.3 73.7 - - - +
433F ALA* 1.3 57.8 + - - +
435F VAL* 3.5 2.5 + - - +
436F ALA* 2.9 28.6 + - - +
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Residues in contact with ALA 433 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F ASN* 4.3 0.6 - - - +
136F GLU* 4.9 0.2 + - - -
400F THR* 3.7 16.9 - - + +
402F LYS* 3.7 15.0 - - - +
430F ASP* 3.1 28.2 + - - +
432F GLY* 1.3 72.1 - - - +
434F MET* 1.3 60.7 + - - +
436F ALA* 3.2 6.6 + - - +
437F LEU* 2.9 34.1 + - - +
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Residues in contact with MET 434 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377F ILE* 4.2 11.9 - - + -
378F ILE* 4.5 10.3 - - + -
381F THR* 3.4 33.2 - - + +
393F MET* 4.0 18.6 - - - -
396F LEU* 3.7 25.2 - - + +
397F VAL* 3.7 26.2 - - + -
400F THR* 3.3 24.9 - - - +
429F LEU* 5.1 5.8 - - + -
430F ASP 2.8 30.8 + - - +
431F ALA* 3.5 6.7 - - - +
433F ALA* 1.3 73.0 - - - +
435F VAL* 1.3 62.6 + - - +
437F LEU* 3.8 1.4 - - - +
438F ALA* 2.9 25.5 + - - +
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Residues in contact with VAL 435 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F ALA* 4.1 15.5 - - + -
140F GLN* 3.9 13.9 - - - +
142F PHE* 3.2 41.1 - - + -
380F LEU* 3.7 34.3 - - + +
381F THR* 4.1 2.5 - - - +
384F ALA* 4.0 3.3 - - + +
431F ALA 2.9 17.5 + - - +
432F GLY 3.8 1.8 - - - +
434F MET* 1.3 77.0 - - - +
436F ALA* 1.3 64.9 + - - +
438F ALA* 3.3 6.4 + - - +
439F GLN* 3.0 34.2 + - - +
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Residues in contact with ALA 436 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F GLU* 5.1 2.7 - - - +
140F GLN* 4.9 7.0 - - - +
432F GLY 2.9 18.3 + - - +
433F ALA* 3.2 8.0 + - - +
435F VAL* 1.3 83.0 - - - +
437F LEU* 1.3 61.5 + - - +
438F ALA 3.3 0.3 + - - -
439F GLN* 3.5 21.3 + - - +
440F ASN* 4.2 2.6 + - - +
951F NAG 5.5 1.2 - - - +
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Residues in contact with LEU 437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396F LEU* 3.5 24.5 - - + -
399F GLN* 3.9 26.9 - - + +
400F THR* 3.4 25.1 - - + -
433F ALA 2.9 19.5 + - - +
434F MET 4.0 2.2 - - - +
436F ALA* 1.3 73.7 - - - +
438F ALA* 1.3 62.4 + - - +
439F GLN 3.6 0.2 + - - -
440F ASN 3.6 12.9 - - - +
441F TRP* 3.4 26.0 - - + +
951F NAG 5.5 9.0 - - + +
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Residues in contact with ALA 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381F THR* 3.6 32.5 - - + +
384F ALA* 4.3 2.9 - - + -
385F ASN* 2.8 30.0 + - + +
388F LEU* 4.0 6.1 - - + -
396F LEU* 3.8 13.2 - - + +
434F MET 2.9 18.3 + - - +
435F VAL 3.6 5.2 - - - +
436F ALA 3.2 0.2 - - - -
437F LEU* 1.3 77.1 - - - +
439F GLN* 1.3 64.8 + - - +
440F ASN 3.0 1.4 + - - -
441F TRP* 3.3 9.3 + - - +
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Residues in contact with GLN 439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F GLN* 3.1 26.3 + - - -
142F PHE* 3.5 27.8 - - - -
384F ALA* 4.0 23.0 - - + +
385F ASN* 4.7 3.3 + - - -
435F VAL* 3.0 18.8 + - - +
436F ALA* 3.7 12.3 + - - +
437F LEU 3.4 0.2 - - - -
438F ALA* 1.3 76.1 - - - +
440F ASN* 1.3 62.4 + - + +
441F TRP 3.8 0.4 + - - -
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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