Contacts of the helix formed by residues 430 - 439 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H LEU 3.8 2.9 - - - -
133H ASN* 2.5 36.6 + - - +
377H ILE* 4.9 0.2 - - - -
400H THR* 3.7 21.4 + - - +
401H SER* 4.9 0.4 - - - +
402H LYS* 2.6 32.7 + - + +
428H LEU 3.6 0.6 + - - -
429H LEU* 1.3 75.0 - - - +
431H ALA* 1.3 59.4 + - - +
433H ALA* 3.1 15.5 + - + +
434H MET* 2.8 36.8 + - - +
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Residues in contact with ALA 431 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H LEU 3.1 11.8 + - - +
133H ASN 3.3 13.9 - - - +
134H VAL* 3.6 25.4 - - + -
137H ALA* 4.1 10.1 - - + -
377H ILE* 4.0 25.6 - - + +
380H LEU* 4.5 5.2 - - + -
429H LEU 4.0 1.0 - - - -
430H ASP* 1.3 71.8 - - - +
432H GLY* 1.3 64.9 + - - +
434H MET* 3.4 1.5 - - - +
435H VAL* 2.9 28.5 + - - +
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Residues in contact with GLY 432 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H ASN* 3.1 23.6 + - - -
136H GLU* 3.7 21.1 - - - -
137H ALA* 4.4 8.0 - - - +
140H GLN* 4.2 6.1 + - - -
430H ASP* 3.2 2.0 + - - -
431H ALA* 1.3 79.1 - - - +
433H ALA* 1.3 57.2 + - - +
435H VAL* 3.4 2.1 + - - +
436H ALA* 2.9 30.1 + - - +
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Residues in contact with ALA 433 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H ASN* 4.3 0.6 - - - +
136H GLU* 4.6 0.4 + - - -
400H THR* 3.8 22.0 - - + -
402H LYS* 4.0 8.3 - - - +
430H ASP* 3.1 29.3 + - + +
432H GLY* 1.3 72.4 - - - +
434H MET* 1.3 65.8 + - - +
436H ALA* 3.2 6.3 + - - +
437H LEU* 2.8 27.7 + - - +
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Residues in contact with MET 434 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377H ILE* 4.2 12.3 - - + -
378H ILE* 4.5 10.3 - - + -
381H THR* 3.3 34.5 - - + +
393H MET* 4.0 19.5 - - - -
396H LEU* 3.7 24.1 - - + +
397H VAL* 3.8 24.9 - - + -
400H THR* 3.2 26.4 - - - +
429H LEU* 5.1 5.6 - - + -
430H ASP 2.8 26.9 + - - +
431H ALA* 3.4 7.0 - - - +
433H ALA* 1.3 76.9 - - - +
435H VAL* 1.3 58.7 + - - +
437H LEU* 3.8 1.6 - - - +
438H ALA* 2.9 31.2 + - - +
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Residues in contact with VAL 435 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H ALA* 4.1 16.8 - - + -
140H GLN* 3.9 17.0 - - - +
142H PHE* 3.2 39.5 - - + -
380H LEU* 3.8 35.0 - - + +
381H THR* 4.1 2.7 + - - +
384H ALA* 4.0 3.6 - - + +
431H ALA 2.9 17.3 + - - +
432H GLY 3.8 1.6 - - - +
434H MET* 1.3 77.0 - - - +
436H ALA* 1.3 64.2 + - - +
438H ALA* 3.5 7.6 + - - +
439H GLN* 3.2 26.2 + - - +
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Residues in contact with ALA 436 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140H GLN* 4.8 8.3 - - - +
432H GLY 2.9 18.6 + - - +
433H ALA* 3.5 7.6 - - - +
435H VAL* 1.3 82.4 - - - +
437H LEU* 1.3 61.5 + - - +
439H GLN* 3.4 20.2 + - - +
440H ASN* 3.8 6.4 + - - +
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Residues in contact with LEU 437 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396H LEU* 3.4 24.2 - - + -
399H GLN* 3.7 28.9 - - + +
400H THR* 3.7 23.8 - - + -
433H ALA 2.8 19.1 + - - +
434H MET 4.0 2.2 - - - +
436H ALA* 1.3 70.4 - - - +
438H ALA* 1.3 66.4 + - - +
439H GLN 3.4 0.2 + - - -
440H ASN* 3.4 16.1 + - + +
441H TRP* 3.4 25.9 + - + +
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Residues in contact with ALA 438 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381H THR* 3.6 33.7 - - + +
384H ALA* 4.4 1.8 - - + -
385H ASN* 2.8 30.3 + - + -
388H LEU* 4.1 6.1 - - + -
396H LEU* 3.8 13.9 - - + +
434H MET 2.9 18.4 + - - +
435H VAL* 3.7 7.2 - - - +
436H ALA 3.2 0.2 - - - -
437H LEU* 1.3 78.5 - - - +
439H GLN* 1.3 61.1 + - - +
441H TRP* 3.4 9.0 + - - +
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Residues in contact with GLN 439 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140H GLN* 3.5 16.8 + - - -
142H PHE* 3.4 35.0 - - - -
384H ALA* 4.0 20.8 - - + +
385H ASN* 4.5 4.3 + - - +
435H VAL* 3.2 17.6 + - - +
436H ALA* 3.4 8.7 + - - +
437H LEU 3.2 0.6 - - - -
438H ALA* 1.3 78.7 - - - +
440H ASN* 1.3 58.7 + - + +
441H TRP 3.3 4.9 + - - +
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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