Contacts of the helix formed by residues 437 - 449 (chain L) in PDB entry 5XTE
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 437 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385L GLU* 2.8 24.3 - - - +
388L VAL* 4.3 4.3 - - - -
435L GLU 3.5 4.9 + - - +
436L VAL* 1.3 75.7 - - - +
438L ALA* 1.3 79.5 + - - +
439L SER* 3.2 12.7 + - - +
440L VAL* 2.9 20.4 + - + +
441L VAL* 2.9 30.7 + - - +
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Residues in contact with ALA 438 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383L ALA* 3.4 26.9 - - - +
385L GLU* 3.3 23.1 + - + +
388L VAL* 3.7 25.5 - - + +
437L ASP* 1.3 85.8 + - - +
439L SER* 1.3 56.6 + - - +
441L VAL* 3.5 2.8 - - - +
442L ARG* 2.9 35.7 + - - +
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Residues in contact with SER 439 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437L ASP* 3.2 11.8 + - - -
438L ALA* 1.3 74.9 - - - +
440L VAL* 1.3 63.7 + - - +
442L ARG* 3.1 19.9 - - - +
443L GLU* 2.9 30.4 + - - +
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Residues in contact with VAL 440 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303L ALA* 4.4 8.7 - - + -
435L GLU* 4.8 6.1 - - + +
436L VAL* 5.0 5.4 - - + -
437L ASP* 2.9 30.7 + - + +
439L SER* 1.3 76.0 - - - +
441L VAL* 1.3 60.5 + - - +
443L GLU* 3.2 5.0 + - - +
444L ILE* 2.9 51.8 + - + +
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Residues in contact with VAL 441 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303L ALA* 4.8 12.3 - - + +
306L VAL* 4.7 7.4 - - + -
307L ALA* 4.6 11.9 - - + -
310L ILE* 4.9 4.5 - - + -
379L LEU* 4.7 12.8 - - + +
383L ALA* 5.0 4.0 - - + -
388L VAL* 4.0 23.1 - - + -
436L VAL* 3.7 22.2 - - + -
437L ASP 2.9 17.5 + - - +
438L ALA* 3.5 8.3 - - - +
440L VAL* 1.3 77.5 - - - +
442L ARG* 1.3 58.5 + - - +
444L ILE* 4.2 0.4 - - - +
445L CYS* 2.9 50.5 + - - -
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Residues in contact with ARG 442 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G GLU* 6.1 0.6 - - - +
16G ASN* 2.8 45.3 + - - +
379L LEU 3.3 21.9 - - - +
380L CYS 4.2 5.7 - - - +
381L THR* 3.0 28.3 + - - +
383L ALA* 3.1 29.7 + - + +
438L ALA* 2.9 21.2 + - - +
439L SER* 3.1 25.4 - - - +
441L VAL* 1.3 76.3 - - - +
443L GLU* 1.3 64.0 + - + +
445L CYS* 4.2 0.2 - - - +
446L SER* 2.9 31.0 + - - -
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Residues in contact with GLU 443 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ARG* 5.2 0.2 + - - -
439L SER* 2.9 20.3 + - - +
440L VAL* 3.5 7.6 - - - +
441L VAL 3.2 0.2 - - - -
442L ARG* 1.3 82.1 - - - +
444L ILE* 1.3 63.2 + - + +
446L SER* 3.5 5.8 + - - -
447L LYS* 2.9 28.7 + - + +
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Residues in contact with ILE 444 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300L ASP* 3.6 31.4 - - + +
303L ALA* 3.5 27.6 - - + -
304L LEU* 3.6 28.5 - - + -
440L VAL* 2.9 29.9 + - + +
441L VAL 4.2 1.1 - - - +
443L GLU* 1.3 77.9 - - + +
445L CYS* 1.3 61.2 + - - +
447L LYS* 2.9 24.4 + - + +
448L TYR* 2.9 32.7 + - + +
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Residues in contact with CYS 445 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303L ALA 5.5 0.7 - - - -
304L LEU* 4.4 13.5 - - - -
307L ALA* 3.6 31.0 - - - -
379L LEU* 4.0 23.6 - - + +
380L CYS* 3.8 4.2 - - - -
441L VAL* 2.9 34.7 + - - +
444L ILE* 1.3 77.5 - - - +
446L SER* 1.3 57.7 + - - +
448L TYR 4.5 0.4 - - - +
449L ILE* 2.8 54.0 + - + +
450L TYR 3.4 0.5 + - - -
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Residues in contact with SER 446 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ARG* 2.4 49.0 + - - -
380L CYS* 4.2 15.6 + - - -
442L ARG 2.9 22.0 + - - -
443L GLU* 3.7 7.2 - - - -
445L CYS* 1.3 76.8 - - - +
447L LYS* 1.3 60.9 + - - +
448L TYR 3.4 0.3 + - - -
450L TYR* 3.5 33.2 + - - +
480L PHE* 5.9 2.6 - - - -
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Residues in contact with LYS 447 (chain L).
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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104C ARG* 4.8 5.9 - - - +
16D ARG* 3.7 7.4 + - - +
300L ASP* 4.1 7.5 + - - +
443L GLU* 2.9 17.8 + - + +
444L ILE* 2.9 17.6 + - + +
446L SER* 1.3 78.8 - - - +
448L TYR* 1.3 97.1 + - + +
452L GLN* 4.6 11.7 + - - -
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Residues in contact with TYR 448 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C ARG* 3.5 30.5 + - - -
291L VAL* 3.9 12.5 - - - +
292L GLU* 3.9 18.2 - - + +
294L PRO* 3.4 34.6 - - + +
300L ASP* 2.8 29.1 + - - -
304L LEU* 4.6 2.9 - - + -
354L LEU* 4.0 19.5 - - + -
444L ILE* 2.9 40.8 + - + +
447L LYS* 1.3 111.2 + - + +
449L ILE* 1.3 61.9 + - + +
452L GLN* 3.2 23.5 + - - +
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Residues in contact with ILE 449 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291L VAL* 4.4 17.9 - - + -
304L LEU* 5.5 0.9 - - + -
307L ALA* 5.8 2.9 - - + -
354L LEU* 4.7 13.5 - - + -
376L TRP* 3.7 59.2 - - + +
377L MET* 5.7 2.5 - - - -
379L LEU* 6.0 2.0 - - + -
380L CYS* 3.8 9.9 - - - -
445L CYS* 2.8 43.1 + - + +
448L TYR* 1.3 75.9 - - + +
450L TYR* 1.3 66.5 + - - +
451L ASP 3.3 2.6 + - - -
452L GLN* 3.4 6.5 + - - +
475L MET* 3.4 20.0 - - + +
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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