Contacts of the helix formed by residues 430 - 439 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132G LEU 3.4 2.7 - - - -
133G ASN* 3.5 19.9 - - - +
136G GLU* 4.0 1.7 - - - +
377G ILE* 4.9 0.2 - - - -
400G THR* 4.0 15.6 + - - +
401G SER* 5.1 0.4 - - - +
402G LYS* 3.6 30.8 + - + +
428G LEU 3.6 0.8 + - - +
429G LEU* 1.3 75.6 - - - +
431G ALA* 1.3 53.2 + - - +
432G GLY* 3.1 6.9 + - - -
433G ALA* 3.1 32.0 + - + +
434G MET* 2.8 41.2 + - - +
4029G SO4 3.9 10.6 + - - -
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Residues in contact with ALA 431 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132G LEU 2.7 18.4 + - - +
133G ASN 3.6 8.7 - - - +
134G VAL* 3.6 23.6 - - + -
137G ALA* 4.2 10.1 - - + -
377G ILE* 4.0 28.6 - - + +
380G LEU* 4.4 5.6 - - + -
429G LEU 4.0 1.0 - - - -
430G ASP* 1.3 69.5 - - - +
432G GLY* 1.3 63.2 + - - +
434G MET* 3.3 1.4 + - - +
435G VAL* 3.0 29.0 + - - +
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Residues in contact with GLY 432 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G ASN 3.4 6.3 + - - -
136G GLU* 2.9 35.2 - - - -
137G ALA* 4.5 6.1 - - - -
140G GLN* 4.9 4.6 + - - -
430G ASP* 3.1 4.4 + - - -
431G ALA* 1.3 80.2 - - - +
433G ALA* 1.3 56.7 + - - +
435G VAL* 3.8 3.2 - - - +
436G ALA* 3.0 29.3 + - - +
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Residues in contact with ALA 433 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G GLU* 3.9 1.6 + - - -
400G THR* 3.7 24.4 - - + +
430G ASP* 3.1 28.4 + - + +
432G GLY* 1.3 72.2 - - - +
434G MET* 1.3 59.1 + - - +
436G ALA* 3.2 5.7 + - - +
437G LEU* 2.8 34.1 + - - +
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Residues in contact with MET 434 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377G ILE* 4.2 12.6 - - + -
378G ILE* 4.5 10.5 - - + -
381G THR* 3.4 33.8 - - + +
393G MET* 4.1 18.8 - - - -
396G LEU* 3.7 24.8 - - + +
397G VAL* 3.7 25.6 - - + -
400G THR* 3.3 23.3 - - - +
429G LEU* 5.1 4.9 - - + -
430G ASP 2.8 33.8 + - - +
431G ALA* 3.5 6.7 - - - +
433G ALA* 1.3 73.0 - - - +
435G VAL* 1.3 61.9 + - - +
437G LEU* 3.4 1.4 + - - +
438G ALA* 3.0 25.5 + - - +
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Residues in contact with VAL 435 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G ALA* 4.0 17.0 - - + -
140G GLN* 3.9 16.2 - - - +
142G PHE* 3.3 38.6 - - + -
380G LEU* 3.8 34.5 - - + +
381G THR* 4.1 4.0 - - - +
384G ALA* 4.0 2.7 - - + +
431G ALA 3.0 18.0 + - - +
432G GLY 3.8 3.8 - - - +
434G MET* 1.3 76.8 - - - +
436G ALA* 1.3 65.7 + - - +
438G ALA* 3.3 13.3 + - - +
439G GLN* 3.4 16.4 + - - +
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Residues in contact with ALA 436 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G GLN* 5.2 7.6 - - - +
432G GLY 3.0 18.3 + - - +
433G ALA* 3.5 8.1 - - - +
435G VAL* 1.3 82.5 - - + +
437G LEU* 1.3 62.3 + - - +
438G ALA 3.4 0.2 + - - -
439G GLN* 3.5 19.5 + - - +
440G ASN 4.6 1.4 + - - -
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Residues in contact with LEU 437 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396G LEU* 3.4 25.6 - - + -
399G GLN* 3.5 29.6 - - + +
400G THR* 3.8 22.4 - - + -
433G ALA 2.8 19.7 + - - +
434G MET 4.1 2.7 - - - +
436G ALA* 1.3 72.4 - - - +
438G ALA* 1.3 65.1 + - - +
439G GLN 3.5 0.2 + - - -
440G ASN 4.0 1.6 + - - -
441G TRP* 3.5 28.7 + - + +
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Residues in contact with ALA 438 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381G THR* 3.6 32.5 - - + +
384G ALA* 4.3 2.7 - - + -
385G ASN* 2.8 29.9 + - + +
388G LEU* 4.1 5.6 - - + -
396G LEU* 3.9 12.5 - - + +
434G MET 3.0 18.7 + - - +
435G VAL 3.6 6.7 - - - +
436G ALA 3.2 0.2 - - - -
437G LEU* 1.3 79.1 - - - +
439G GLN* 1.3 61.7 + - - +
441G TRP* 3.2 8.8 + - - +
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Residues in contact with GLN 439 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G GLN* 4.2 6.7 + - - +
142G PHE* 3.3 32.9 - - - -
384G ALA* 3.6 22.9 - - + +
385G ASN* 4.6 5.1 + - - -
435G VAL* 3.4 18.0 + - - +
436G ALA* 3.9 13.5 - - - +
437G LEU 3.3 1.8 - - - -
438G ALA* 1.3 77.7 - - - +
440G ASN* 1.3 61.1 + - + +
441G TRP 3.5 0.4 + - - -
4O FUC 5.8 1.0 - - - -
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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