Contacts of the helix formed by residues 430 - 441 (chain D) in PDB entry 4OMD
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D LEU 3.8 3.4 - - - -
133D ASN* 2.8 28.9 + - - +
400D THR* 3.7 16.7 + - - +
402D LYS* 3.0 30.2 + - + +
428D LEU 3.7 0.4 + - - -
429D LEU* 1.3 74.5 - - - +
431D ALA* 1.3 58.2 + - - +
433D ALA* 2.8 38.4 + - + +
434D MET* 2.8 33.9 + - - +
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Residues in contact with ALA 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D LEU 3.0 13.8 + - - +
133D ASN 3.3 12.3 - - - +
134D VAL* 3.7 20.9 - - + -
137D ALA* 4.0 10.1 - - + -
377D ILE* 3.9 28.7 - - + +
380D LEU* 4.6 5.8 - - + -
429D LEU 3.9 1.2 - - - -
430D ASP* 1.3 70.5 - - - +
432D GLY* 1.3 64.3 + - - +
434D MET* 3.2 2.0 + - - +
435D VAL* 3.0 28.4 + - - +
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Residues in contact with GLY 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ASN* 3.0 25.0 + - - -
136D ALA* 4.1 8.3 - - - -
137D ALA 4.1 4.0 - - - -
140D GLN* 3.2 23.9 + - - -
430D ASP* 3.2 4.9 + - - -
431D ALA* 1.3 75.2 - - - +
433D ALA* 1.3 61.6 + - - +
435D VAL* 3.3 0.8 - - - +
436D ALA* 3.1 20.3 + - - +
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Residues in contact with ALA 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ASN* 4.3 0.8 - - - +
400D THR* 3.7 14.7 - - + +
402D LYS* 3.7 12.3 - - - +
430D ASP* 2.8 37.4 + - + +
432D GLY* 1.3 71.3 - - - -
434D MET* 1.3 59.0 + - - +
436D ALA* 3.5 5.8 - - - +
437D LEU* 2.9 32.6 + - - +
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Residues in contact with MET 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377D ILE* 4.2 15.7 - - + -
378D ILE* 4.6 6.5 - - + -
381D THR* 3.4 28.4 - - + +
393D MET* 4.0 19.1 - - - -
396D LEU* 3.7 25.2 - - + +
397D VAL* 3.9 24.5 - - + -
400D THR* 3.3 24.9 - - - +
429D LEU* 5.3 5.4 - - + -
430D ASP 2.8 27.3 + - - +
431D ALA* 3.2 7.6 + - - +
433D ALA* 1.3 77.1 - - - +
435D VAL* 1.3 58.7 + - - +
437D LEU* 3.9 1.2 - - - +
438D ALA* 3.0 29.3 + - - +
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Residues in contact with VAL 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D ALA* 4.0 13.5 - - + -
140D GLN* 3.4 23.1 - - - +
142D TYR* 3.7 23.1 - - + -
377D ILE* 5.3 0.4 - - + +
380D LEU* 3.8 42.2 - - + +
381D THR* 4.0 3.8 - - - +
384D ALA* 3.8 4.0 - - + +
431D ALA 3.0 13.1 + - - +
432D GLY 3.3 11.9 - - - +
434D MET* 1.3 75.7 - - - +
436D ALA* 1.3 66.6 + - - +
438D ALA* 3.6 7.4 - - - +
439D GLN* 3.2 29.1 + - - +
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Residues in contact with ALA 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D GLN* 4.0 16.2 - - - +
432D GLY 3.1 20.1 + - - +
433D ALA* 3.5 7.6 - - - +
434D MET 3.2 0.2 - - - -
435D VAL* 1.3 81.2 - - - +
437D LEU* 1.3 63.6 + - - +
438D ALA 3.4 0.2 + - - -
439D GLN* 3.4 17.9 + - - +
440D ASN* 4.2 5.4 + - - +
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Residues in contact with LEU 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396D LEU* 3.4 25.8 - - + -
399D GLN* 3.7 29.8 - - + +
400D THR* 3.7 22.4 - - + -
433D ALA 2.9 17.2 + - - +
434D MET 4.1 0.9 - - - +
436D ALA* 1.3 76.4 - - - +
438D ALA* 1.3 62.8 + - - +
439D GLN 3.2 0.5 + - - -
440D ASN* 3.4 7.7 + - + +
441D TRP* 3.2 31.8 + - + +
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Residues in contact with ALA 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D THR* 3.6 33.2 - - + +
384D ALA* 4.1 4.0 - - + -
385D ASN* 2.9 28.4 + - + -
388D LEU* 4.1 4.7 - - + -
396D LEU* 4.0 12.7 - - + +
434D MET 3.0 19.5 + - - +
435D VAL* 3.6 8.3 - - - +
436D ALA 3.2 0.4 - - - -
437D LEU* 1.3 76.9 - - - +
439D GLN* 1.3 60.9 + - - +
441D TRP* 3.2 9.7 + - - +
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Residues in contact with GLN 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D GLN* 3.6 21.0 + - - +
142D TYR* 3.3 32.9 + - - +
384D ALA* 4.0 17.0 - - + +
385D ASN* 4.6 5.1 + - - +
435D VAL 3.2 19.7 + - - +
436D ALA* 3.7 9.9 - - - +
437D LEU 3.2 1.2 - - - -
438D ALA* 1.3 77.6 - - - +
440D ASN* 1.3 70.8 + - - +
441D TRP 3.3 1.3 + - - +
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Residues in contact with ASN 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436D ALA 4.2 4.0 + - - +
437D LEU* 3.4 10.5 + - + +
439D GLN* 1.3 87.8 + - - +
441D TRP* 1.3 64.1 + - - +
442D THR* 3.5 8.0 + - - -
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Residues in contact with TRP 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385D ASN* 3.9 11.4 + - - -
388D LEU* 3.7 23.1 - - + -
392D ASP* 2.8 27.4 + - - +
395D HIS* 3.5 29.4 - + + -
396D LEU* 3.4 25.1 - - + -
399D GLN* 3.3 38.6 - - - -
437D LEU* 3.2 21.2 + - + +
438D ALA* 3.2 20.9 + - - +
439D GLN 3.3 0.9 - - - +
440D ASN* 1.3 76.9 - - - +
442D THR* 1.3 76.5 + - - +
443D THR* 3.8 2.4 + - - -
444D VAL* 3.7 15.9 - - + -
483D ARG* 5.5 4.7 - - - -
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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