Contacts of the helix formed by residues 437 - 443 (chain D) in PDB entry 1S77
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 ASN 437 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397D SER* 5.7 3.6 + - - -
398D LEU* 6.0 5.5 - - - +
401D MET* 5.7 3.6 - - - +
436D GLY* 1.3 74.2 - - - +
438D ASP* 1.3 59.7 + - - +
439D MET* 3.4 11.4 + - - +
440D THR* 2.6 43.0 + - - -
441D LYS* 2.8 32.2 + - - +
2R A 5.2 0.4 - - - -
3R G 4.1 14.3 - - - +
4R C 4.4 26.8 + - - +
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Residues in contact with ASP 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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437D ASN* 1.3 77.3 - - - +
439D MET* 1.3 57.6 + - - +
441D LYS* 3.3 11.4 + - - +
442D GLY* 2.8 27.0 + - - -
506D ASP 5.2 1.1 - - - +
507D SER* 3.2 35.1 - - - -
508D PRO* 3.0 16.9 - - + +
509D PHE* 2.8 29.0 + - - +
510D CYS* 3.3 18.9 + - - -
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Residues in contact with MET 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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338D ALA* 4.5 4.0 - - + -
342D THR* 4.3 17.7 - - - -
352D ILE* 4.9 7.4 - - + -
398D LEU* 3.9 39.3 - - + +
401D MET* 4.0 16.8 - - + -
402D LEU* 3.9 16.6 - - + -
437D ASN* 3.3 11.0 + - - +
438D ASP* 1.3 80.3 + - - +
440D THR* 1.3 64.6 + - - +
442D GLY* 3.2 1.6 + - - -
443D LEU* 3.0 55.3 + - + +
509D PHE* 3.6 36.1 - - + +
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Residues in contact with THR 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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401D MET* 3.2 22.6 - - + +
432D PHE* 3.7 26.7 - - + -
433D ASN 3.3 28.9 - - - +
436D GLY* 3.9 5.2 - - - -
437D ASN* 2.6 37.7 + - - -
439D MET* 1.3 77.5 - - - +
441D LYS* 1.3 63.4 + - - +
443D LEU* 3.0 21.3 + - - +
444D LEU* 3.2 12.9 + - + +
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Residues in contact with LYS 441 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328D TRP* 5.9 0.3 - - - -
434D PRO* 4.0 15.9 - - - +
436D GLY 3.5 15.1 + - - +
437D ASN* 2.8 27.1 + - - +
438D ASP* 4.2 4.9 + - - +
440D THR* 1.3 74.3 - - - +
442D GLY* 1.3 58.1 + - - +
444D LEU* 2.8 28.8 + - - +
510D CYS* 3.4 24.4 - - - -
533D PRO* 5.3 3.6 - - - +
810D ILE* 3.6 22.7 - - + -
2R A 3.4 28.8 + - - -
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Residues in contact with GLY 442 (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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331D ASN* 3.6 6.9 + - - +
334D VAL* 3.1 33.2 - - - +
438D ASP 2.8 17.1 + - - -
439D MET 3.7 1.8 - - - -
440D THR 3.1 0.2 - - - -
441D LYS* 1.3 75.6 - - - +
443D LEU* 1.3 60.8 + - - +
444D LEU 3.2 2.0 - - - +
509D PHE* 4.1 16.2 - - - -
510D CYS* 3.7 10.7 - - - -
513D ALA* 4.5 4.0 - - - +
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Residues in contact with LEU 443 (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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330D ILE* 3.3 9.9 - - - +
331D ASN* 2.7 29.9 + - - -
334D VAL* 3.8 11.9 - - + +
335D LEU* 3.5 37.7 - - + +
338D ALA* 4.0 6.7 - - + -
401D MET 5.1 2.0 - - - +
402D LEU* 4.0 9.0 - - + -
405D ALA* 3.8 25.8 - - + -
432D PHE* 4.5 7.9 - - + -
439D MET* 3.0 54.1 + - + +
440D THR* 3.0 10.4 + - - +
442D GLY* 1.3 78.8 - - - +
444D LEU* 1.3 56.5 + - - +
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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