Contacts of the helix formed by residues 430 - 441 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132E LEU 3.8 2.5 - - - -
133E ASN* 2.7 35.3 + - - +
400E THR* 3.7 10.2 + - - +
401E SER* 5.0 0.2 - - - +
402E LYS* 2.8 41.4 + - + +
428E LEU 3.7 0.6 + - - -
429E LEU* 1.3 73.7 - - - +
431E ALA* 1.3 57.2 + - - +
433E ALA* 3.0 20.6 + - + +
434E MET* 2.8 34.5 + - - +
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Residues in contact with ALA 431 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E LEU 3.0 14.6 + - - +
133E ASN 3.4 12.6 - - - +
134E VAL* 3.7 20.9 - - + -
137E ALA* 4.0 11.9 - - + -
377E ILE* 3.8 27.6 - - + +
380E LEU* 4.7 4.7 - - + -
429E LEU 4.0 0.8 - - - -
430E ASP* 1.3 70.7 - - - +
432E GLY* 1.3 63.8 + - - +
434E MET* 3.1 2.6 + - - +
435E VAL* 3.0 28.0 + - + +
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Residues in contact with GLY 432 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E ASN* 3.1 28.4 + - - -
136E ALA* 4.1 7.0 - - - -
137E ALA 4.1 2.5 - - - -
140E GLN* 3.3 17.0 + - - -
430E ASP* 3.3 1.4 + - - -
431E ALA* 1.3 73.4 - - - +
433E ALA* 1.3 61.2 + - - +
435E VAL* 3.1 7.7 - - - +
436E ALA* 3.1 24.5 + - - +
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Residues in contact with ALA 433 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E ASN* 4.2 0.6 - - - +
400E THR* 3.7 15.6 - - + +
402E LYS* 3.5 16.2 - - - +
430E ASP* 3.0 30.4 + - + -
432E GLY* 1.3 74.8 - - - +
434E MET* 1.3 57.7 + - - +
436E ALA* 3.5 6.3 - - - +
437E LEU* 2.9 33.1 + - - +
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Residues in contact with MET 434 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377E ILE* 4.1 16.2 - - + -
378E ILE* 4.6 6.5 - - + -
381E THR* 3.4 33.1 - - + +
393E MET* 4.0 18.4 - - - -
396E LEU* 3.8 23.3 - - + +
397E VAL* 3.6 26.5 - - + -
400E THR* 3.3 24.9 - - - +
429E LEU* 5.3 5.8 - - + -
430E ASP 2.8 24.2 + - - +
431E ALA* 3.3 10.1 - - - +
433E ALA* 1.3 78.1 - - - +
435E VAL* 1.3 59.3 + - - +
437E LEU* 3.4 1.2 + - - +
438E ALA* 2.9 30.2 + - - +
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Residues in contact with VAL 435 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ALA* 3.9 15.5 - - + -
140E GLN* 3.4 22.7 - - - +
142E TYR* 3.7 20.6 - - + -
377E ILE 5.3 0.2 - - - +
380E LEU* 3.8 42.2 - - + +
381E THR* 4.1 3.8 - - - +
384E ALA* 3.8 3.4 - - + +
431E ALA* 3.0 11.2 + - - +
432E GLY 3.1 12.8 - - - +
434E MET* 1.3 78.7 - - - +
436E ALA* 1.3 68.1 + - - +
438E ALA* 3.6 7.8 - - - +
439E GLN* 3.3 26.8 + - - +
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Residues in contact with ALA 436 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E GLN* 3.8 16.4 - - - +
432E GLY 3.1 19.8 + - - +
433E ALA* 3.5 8.3 - - - +
434E MET 3.2 0.2 - - - -
435E VAL* 1.3 80.3 - - - +
437E LEU* 1.3 63.5 + - - +
439E GLN* 3.4 16.9 + - - +
440E ASN* 4.2 4.7 + - - +
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Residues in contact with LEU 437 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396E LEU* 3.7 21.5 - - + -
399E GLN* 3.6 31.0 - - + +
400E THR* 3.6 24.7 - - + -
433E ALA 2.9 17.2 + - - +
434E MET 4.1 2.0 - - - +
436E ALA* 1.3 76.5 - - - +
438E ALA* 1.3 63.7 + - - +
439E GLN 3.3 0.3 + - - -
440E ASN* 3.4 6.5 + - + +
441E TRP* 3.3 30.7 + - + +
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Residues in contact with ALA 438 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381E THR* 3.6 33.0 - - + +
384E ALA* 4.1 4.0 - - + -
385E ASN* 3.0 26.6 + - + -
388E LEU* 4.2 4.5 - - + -
396E LEU* 4.1 10.0 - - + +
434E MET 2.9 19.3 + - - +
435E VAL* 3.6 8.3 - - - +
436E ALA 3.2 0.2 - - - -
437E LEU* 1.3 77.5 - - - +
439E GLN* 1.3 61.4 + - - +
441E TRP* 3.2 13.7 + - - +
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Residues in contact with GLN 439 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E GLN* 3.7 14.8 + - - +
142E TYR* 3.2 38.7 + - - +
384E ALA* 3.9 16.2 - - + +
385E ASN* 4.7 4.5 + - - -
435E VAL 3.3 18.1 + - - +
436E ALA* 3.4 9.1 + - - +
437E LEU 3.2 0.8 - - - -
438E ALA* 1.3 77.7 - - - +
440E ASN* 1.3 71.2 + - - +
441E TRP 3.3 1.1 + - - +
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Residues in contact with ASN 440 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436E ALA 4.2 4.1 + - - +
437E LEU* 3.4 10.8 + - + +
439E GLN* 1.3 90.2 + - - +
441E TRP* 1.3 63.4 + - - +
442E THR* 3.5 8.0 + - - -
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Residues in contact with TRP 441 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385E ASN* 3.9 11.3 + - - -
388E LEU* 3.7 21.1 - - + -
392E ASP* 2.7 30.0 + - + +
395E HIS* 3.5 31.2 - + + -
396E LEU* 3.5 24.5 - - + -
399E GLN* 3.3 37.9 - - - -
437E LEU* 3.3 21.7 + - + +
438E ALA* 3.2 20.9 + - - +
439E GLN 3.3 1.3 - - - +
440E ASN* 1.3 77.7 - - - +
442E THR* 1.3 76.2 + - - +
443E THR* 3.8 2.9 + - - -
444E VAL* 3.8 16.4 - - + -
483E ARG* 5.7 3.1 - - - -
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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