Contacts of the helix formed by residues 537 - 548 (chain A) in PDB entry 2VKT
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 SER 537 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324A SER* 4.3 0.6 + - - -
476A GLU* 4.8 1.6 + - - -
527A PRO* 3.0 45.0 + - - +
530A SER* 5.1 2.7 - - - -
531A SER* 2.9 27.7 + - - +
535A LYS 3.5 2.2 + - - -
536A PRO* 1.3 68.2 - - - +
538A PRO* 1.3 68.0 - - - +
539A PRO* 3.4 5.5 - - - +
540A TYR* 3.0 20.2 + - - +
541A LEU 2.9 22.0 + - - -
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Residues in contact with PRO 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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464A LEU* 4.6 0.4 - - + -
467A LEU* 3.7 43.4 - - + +
468A TYR* 3.6 34.5 - - + -
476A GLU* 5.1 1.8 - - - +
530A SER* 6.0 0.9 - - - +
535A LYS* 6.1 7.2 - - + -
536A PRO 3.0 10.1 - - - +
537A SER* 1.3 82.9 - - - +
539A PRO* 1.4 66.1 - - + +
541A LEU* 3.1 9.7 + - + +
542A GLY 2.8 27.9 + - - -
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Residues in contact with PRO 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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396A LEU* 3.9 26.5 - - + +
464A LEU* 3.9 17.0 - - + -
468A TYR* 3.4 33.4 - - + +
519A TYR* 2.5 27.7 + - - +
523A VAL* 4.8 5.4 - - + -
527A PRO* 3.8 21.5 - - + -
537A SER* 3.4 11.7 - - - +
538A PRO* 1.4 91.7 - - + +
540A TYR* 1.3 54.1 + - - +
543A LEU* 3.3 12.8 + - - +
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Residues in contact with TYR 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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317A VAL* 3.9 15.9 - - + +
320A ALA* 4.0 15.0 - - + +
321A LEU* 3.6 35.0 - - + -
324A SER* 3.5 11.9 - - - +
368A LEU* 4.2 14.3 - - + +
370A PRO* 5.5 0.9 - - - +
396A LEU* 4.1 20.4 - - + -
398A VAL* 4.0 9.1 - - + +
527A PRO* 3.7 16.8 - - + -
528A GLU* 3.1 48.2 + - + +
537A SER* 3.0 28.3 + - - +
539A PRO* 1.3 76.0 - - - +
541A LEU* 1.3 65.5 + - - +
543A LEU* 3.4 5.3 + - + +
544A LEU* 3.2 29.5 + - - +
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Residues in contact with LEU 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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324A SER* 3.4 34.3 + - - +
327A ALA* 4.2 13.9 - - + -
328A ILE* 4.2 13.0 - - + -
467A LEU* 5.1 4.9 - - + +
536A PRO* 4.2 21.8 - - + +
537A SER 2.9 12.6 + - - +
538A PRO* 3.6 11.2 - - + +
540A TYR* 1.3 73.6 - - - +
542A GLY* 1.3 61.9 + - - +
544A LEU* 3.4 1.4 + - + -
545A LEU* 2.9 43.4 + - + +
554A TYR* 3.8 31.6 - - + +
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Residues in contact with GLY 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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467A LEU* 3.6 19.8 - - - +
519A TYR* 3.4 24.6 - - - -
538A PRO 2.8 10.7 + - - -
541A LEU* 1.3 74.9 - - - +
543A LEU* 1.3 64.4 + - - +
545A LEU* 3.3 5.9 + - - +
546A ALA* 2.9 26.7 + - - +
551A LEU* 4.6 2.9 - - - +
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Residues in contact with LEU 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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301A ILE* 4.3 16.2 - - + -
321A LEU* 4.3 23.1 - - + -
366A GLY* 4.4 1.3 - - - -
367A ILE 3.8 19.7 - - - +
368A LEU* 4.3 12.3 - - + -
394A PRO* 3.7 35.7 - - + +
395A PHE 3.9 9.2 - - - +
396A LEU* 4.3 16.4 - - + -
519A TYR* 3.2 15.6 - - + -
539A PRO 3.3 11.5 + - - +
540A TYR* 3.5 9.6 - - + +
541A LEU 3.3 0.2 - - - -
542A GLY* 1.3 74.1 - - - +
544A LEU* 1.3 58.7 + - + +
546A ALA* 3.4 2.3 + - - +
547A ALA* 2.9 29.5 + - - +
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Residues in contact with LEU 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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299A CYS* 4.3 19.5 - - + -
301A ILE* 4.5 11.4 - - + -
321A LEU* 3.7 31.0 - - + +
324A SER* 3.6 20.9 - - - +
325A ALA* 3.6 34.1 - - + -
328A ILE* 4.0 12.6 - - + -
330A HIS* 5.6 0.2 - - + -
332A LEU* 4.5 10.3 - - + -
540A TYR 3.2 22.4 + - - +
541A LEU* 4.0 3.4 - - + +
543A LEU* 1.3 77.9 - - + +
545A LEU* 1.3 65.7 + - - +
547A ALA* 3.2 4.0 + - - +
548A THR* 3.1 29.6 + - - +
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Residues in contact with LEU 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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328A ILE* 3.7 28.0 - - + +
467A LEU* 4.3 3.4 - - + -
541A LEU* 2.9 40.5 + - + +
542A GLY 3.7 2.9 - - - +
544A LEU* 1.3 70.9 - - - +
546A ALA* 1.3 60.9 + - - +
548A THR* 3.1 11.8 + - - -
550A ASN* 2.9 51.8 + - + +
551A LEU* 4.0 23.3 - - + -
554A TYR* 3.6 41.5 - - + -
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Residues in contact with ALA 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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394A PRO* 3.7 15.8 - - + +
518A PRO* 4.9 6.2 - - + +
519A TYR* 3.5 30.7 - - + -
542A GLY 2.9 16.8 + - - +
543A LEU 3.7 2.7 - - - +
545A LEU* 1.3 77.1 - - - +
547A ALA* 1.3 63.1 + - - +
548A THR 3.1 1.2 + - - -
549A GLY* 3.2 11.8 + - - +
551A LEU* 4.2 18.3 - - + +
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Residues in contact with ALA 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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299A CYS* 3.6 23.3 - - - -
301A ILE* 4.1 7.6 - - + -
365A ASP* 3.4 45.7 - - - +
366A GLY* 4.0 4.9 - - - +
394A PRO* 3.9 2.2 - - + -
543A LEU 2.9 18.2 + - - +
544A LEU* 3.2 3.7 + - - +
546A ALA* 1.3 76.8 - - - +
548A THR* 1.3 58.5 + - - +
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Residues in contact with THR 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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298A ILE 5.8 0.2 - - - +
299A CYS* 3.7 17.5 - - + -
328A ILE* 3.5 12.4 - - + +
330A HIS* 3.5 33.0 - - + +
544A LEU 3.1 13.2 + - - +
545A LEU 3.1 9.4 + - - -
547A ALA* 1.3 81.9 - - - +
549A GLY* 1.3 57.8 + - - +
550A ASN* 2.8 31.3 + - - -
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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