Contacts of the helix formed by residues 535 - 548 (chain A) in PDB entry 4L0D
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 THR 535 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445A GLN* 5.4 5.4 - - - +
503A LEU* 3.8 9.6 - - - +
507A HIS* 3.5 47.3 - - + +
508A PHE* 4.0 13.7 - - + -
533A VAL* 5.2 2.7 - - + -
534A VAL* 1.3 91.5 - - - +
536A ALA* 1.3 66.2 + - - +
537A ILE* 3.3 22.2 + - + +
538A ASP* 3.3 25.8 + - - +
539A LEU 3.5 3.3 + - - -
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Residues in contact with ALA 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503A LEU* 3.5 26.2 - - + +
507A HIS* 4.6 2.6 + - + -
535A THR* 1.3 76.9 - - - +
537A ILE* 1.3 61.1 + - + +
539A LEU* 3.3 5.6 + - - +
540A LEU* 2.9 29.1 + - - +
189B VAL* 3.7 41.1 - - + -
210B LEU* 5.2 4.5 - - + -
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Residues in contact with ILE 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507A HIS* 5.3 4.5 - - + +
535A THR* 3.2 14.3 - - + +
536A ALA* 1.3 78.3 - - - +
538A ASP* 1.3 61.6 + - - +
540A LEU* 3.3 6.8 + - + +
541A ASN* 2.9 38.7 + - - +
200B PRO 5.4 1.8 - - - +
206B VAL* 4.4 31.0 - - + -
209B ARG* 3.3 54.5 - - + +
210B LEU* 4.5 12.8 - - + -
213B GLU* 4.7 13.2 - - + -
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Residues in contact with ASP 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A LEU* 4.8 4.8 - - + +
419A LEU* 5.4 2.9 - - + +
445A GLN* 5.2 4.7 + - - -
533A VAL 3.3 23.2 - - - +
534A VAL* 3.7 11.0 - - + +
535A THR* 3.3 25.7 + - - +
536A ALA 3.2 0.6 - - - -
537A ILE* 1.3 78.6 - - - +
539A LEU* 1.3 64.1 + - - +
541A ASN* 3.1 14.4 + - - +
542A PHE* 2.9 23.3 + - - +
209B ARG* 5.7 1.2 + - - -
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Residues in contact with LEU 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A TRP* 4.7 10.5 - - + +
417A LEU* 4.5 9.9 - - + -
496A LEU* 4.0 30.7 - - + +
499A LEU* 3.9 30.3 - - + -
500A SER* 3.8 22.2 - - - +
503A LEU* 4.3 12.8 - - + -
534A VAL* 4.7 1.0 - - - +
535A THR 3.5 7.7 + - - +
536A ALA* 3.4 9.0 - - - +
538A ASP* 1.3 78.4 - - - +
540A LEU* 1.3 58.4 + - - +
542A PHE* 3.3 6.5 + - + +
543A VAL* 2.9 45.8 + - + +
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Residues in contact with LEU 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A TRP* 6.6 0.2 - - + -
536A ALA 2.9 17.3 + - - +
537A ILE* 3.5 7.0 - - - +
539A LEU* 1.3 76.9 - - - +
541A ASN* 1.3 65.0 + - - +
543A VAL* 3.3 9.8 + - + +
544A ALA* 2.9 29.3 + - + +
164B ARG* 5.5 5.8 - - - +
210B LEU* 3.6 27.8 - - + -
213B GLU* 3.7 24.7 - - + +
214B ILE* 3.6 31.9 - - + -
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Residues in contact with ASN 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537A ILE* 2.9 28.7 + - - +
538A ASP* 3.1 14.7 + - - +
540A LEU* 1.3 74.9 - - - +
542A PHE* 1.3 58.5 + - - +
544A ALA* 3.8 4.4 - - - +
545A ALA* 2.9 31.6 + - - +
548A ARG* 5.5 0.9 + - - -
209B ARG* 5.9 2.2 - - - +
213B GLU* 3.0 34.6 + - - +
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Residues in contact with PHE 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A TRP* 4.4 11.2 - + - -
409A TRP* 5.1 0.7 - - + -
412A LEU* 4.6 6.5 - - + -
416A GLU* 3.4 43.3 - - + -
417A LEU* 3.4 36.8 - - + -
496A LEU* 4.1 20.0 - - + -
538A ASP 2.9 8.1 + - - +
539A LEU* 3.3 7.9 - - + +
541A ASN* 1.3 76.8 - - - +
543A VAL* 1.3 77.0 + - + +
545A ALA* 3.0 9.8 + - + +
546A GLN* 2.9 56.4 + - + +
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Residues in contact with VAL 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A TRP* 3.9 6.1 - - + -
409A TRP* 3.4 53.2 - - + -
539A LEU* 2.9 25.5 + - + +
540A LEU* 3.9 10.5 - - + +
542A PHE* 1.3 87.5 - - + +
544A ALA* 1.3 57.9 + - - +
546A GLN* 2.9 22.2 + - - +
547A GLU* 2.9 35.7 + - + +
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Residues in contact with ALA 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540A LEU* 2.9 24.2 + - + +
541A ASN* 3.8 5.4 - - - +
543A VAL* 1.3 76.2 - - - +
545A ALA* 1.3 58.5 + - - +
547A GLU* 2.9 32.5 + - - +
548A ARG* 3.2 28.8 + - - +
213B GLU* 4.3 22.2 - - - +
215B PRO* 6.3 0.9 - - + -
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Residues in contact with ALA 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541A ASN 2.9 19.7 + - - +
542A PHE* 3.2 8.5 - - + +
544A ALA* 1.3 76.7 - - - +
546A GLN* 1.3 65.9 + - + +
548A ARG* 3.6 19.2 + - - +
549A ASP* 3.4 19.6 + - - +
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Residues in contact with GLN 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A TRP* 3.5 34.0 - - + -
416A GLU* 5.8 1.2 + - - +
542A PHE* 2.9 46.3 + - + +
543A VAL 2.9 10.5 + - - +
545A ALA* 1.3 81.1 - - - +
547A GLU* 1.3 63.2 + - - +
549A ASP* 3.3 27.1 + - - +
550A GLN* 3.9 8.5 + - - +
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Residues in contact with GLU 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A TRP* 3.7 16.6 + - - -
409A TRP* 5.0 1.6 - - - -
543A VAL* 2.9 37.7 + - + +
544A ALA* 2.9 16.5 + - - +
546A GLN* 1.3 78.8 - - - +
548A ARG* 1.3 60.2 + - + +
550A GLN* 3.0 41.2 + - - +
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Residues in contact with ARG 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541A ASN 5.5 0.6 + - - -
544A ALA* 3.2 20.3 + - - +
545A ALA* 3.9 23.0 - - - +
546A GLN 3.2 0.2 - - - -
547A GLU* 1.3 74.5 - - + +
549A ASP* 1.3 59.4 + - - +
550A GLN 3.2 13.6 + - - +
213B GLU* 4.7 23.2 + - - +
215B PRO* 6.1 2.6 - - - +
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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