Contacts of the helix formed by residues 509 - 526 (chain C) in PDB entry 6E7P
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 VAL 509 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428C PHE* 4.0 14.0 - - + -
432C VAL* 3.8 36.8 - - + -
435C ILE* 6.3 2.2 - - + -
504C LEU* 3.5 12.8 + - + +
505C PHE* 3.5 39.0 - - + +
508C MET* 1.3 82.6 - - + +
510C LEU* 1.3 67.8 + - - +
511C SER 3.2 1.3 - - - -
512C LEU* 3.2 16.6 + - - +
513C PHE* 3.7 14.2 + - + -
418D LEU* 6.1 2.2 - - + -
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Residues in contact with LEU 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B ILE* 4.4 12.6 - - + +
507B TYR* 3.7 35.2 - - + -
510B LEU* 6.4 1.8 - - + -
468C ILE 5.9 1.3 - - - +
505C PHE 2.8 16.5 + - - +
506C ILE* 3.4 34.1 + - + +
509C VAL* 1.3 73.7 - - - +
511C SER* 1.3 60.9 + - - +
513C PHE* 3.3 17.0 + - + +
514C ILE* 3.4 26.0 + - + +
510D LEU* 6.5 0.4 - - + -
514D ILE* 6.4 0.9 - - + -
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Residues in contact with SER 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506C ILE 4.0 7.0 + - - -
507C TYR 3.6 13.6 + - - -
508C MET 4.7 3.8 - - - -
509C VAL 3.2 1.6 - - - +
510C LEU* 1.3 75.5 - - - +
512C LEU* 1.3 59.8 + - - +
513C PHE 3.4 0.2 - - - -
514C ILE* 3.5 12.0 + - - +
515C ALA* 3.0 27.4 + - - +
513D PHE* 3.1 30.4 + - - +
514D ILE* 3.9 14.0 - - - +
517D ILE* 3.8 20.5 - - - +
518D THR* 5.1 1.2 + - - -
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Residues in contact with LEU 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C PHE* 3.7 29.4 - - + -
508C MET 3.3 26.0 - - - +
509C VAL 3.2 10.6 + - - +
511C SER* 1.3 78.7 - - - +
513C PHE* 1.3 56.5 + - - +
515C ALA* 2.8 7.8 + - + -
516C LEU* 2.7 47.2 + - + +
414D LEU* 4.5 20.4 - - + +
417D THR* 4.6 15.7 - - + -
418D LEU* 3.7 19.7 - - + -
517D ILE* 3.7 22.4 - - + -
521D TYR* 4.9 3.6 - - + -
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Residues in contact with PHE 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B TYR* 3.6 60.1 - + + +
511B SER* 3.0 16.3 + - - +
425C VAL* 3.9 38.4 - - + -
428C PHE* 3.4 32.5 - + + -
429C CYS* 4.8 15.7 - - + -
432C VAL* 5.1 4.7 - - + -
509C VAL* 3.7 18.1 + - + -
510C LEU* 3.3 12.0 + - + +
512C LEU* 1.3 76.8 - - - +
514C ILE* 1.3 57.0 + - + +
516C LEU* 4.3 5.8 - - + +
517C ILE* 3.3 22.0 + - - +
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Residues in contact with ILE 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B LEU* 6.3 1.6 - - + -
511B SER* 3.9 16.3 - - - +
514B ILE* 3.8 48.7 - - + -
510C LEU* 3.4 29.0 + - + +
511C SER 3.9 6.5 - - - +
512C LEU 3.1 0.6 - - - -
513C PHE* 1.3 79.5 - - + +
515C ALA* 1.3 60.7 + - - +
517C ILE* 3.7 1.9 + - - +
518C THR* 3.0 32.4 + - - +
514D ILE* 3.9 40.2 - - + -
518D THR* 5.2 1.6 - - - +
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Residues in contact with ALA 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511C SER 3.0 17.2 + - - +
512C LEU* 2.8 11.5 + - + +
514C ILE* 1.3 76.3 - - - +
516C LEU* 1.3 61.4 + - - +
518C THR* 3.8 3.9 - - - -
519C GLY* 2.8 25.8 + - - -
517D ILE* 4.6 5.6 - - + -
518D THR* 3.8 35.0 + - + +
521D TYR* 4.3 17.5 - - + -
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Residues in contact with LEU 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C ALA* 5.0 2.0 - - + +
424C SER* 3.7 39.5 - - - +
425C VAL* 4.5 14.4 - - + +
428C PHE* 4.6 9.9 - - + -
512C LEU* 2.7 31.2 + - + +
513C PHE* 4.8 8.3 - - + +
515C ALA* 1.3 72.4 - - - +
517C ILE* 1.3 62.5 - - + +
519C GLY* 3.3 1.9 + - - -
520C ALA* 2.8 29.6 + - - +
414D LEU* 3.9 21.3 - - + -
521D TYR* 3.5 39.2 - - + +
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Residues in contact with ILE 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B TYR 4.6 4.0 - - - +
508B MET* 4.8 12.8 - - + +
511B SER* 3.7 27.1 - - - +
512B LEU* 3.7 35.0 - - + -
515B ALA* 4.6 2.5 - - + -
417C THR* 4.7 6.2 - - + +
418C LEU* 5.3 4.3 - - + -
421C ALA* 3.7 25.4 - - + -
425C VAL* 4.3 17.9 - - + -
513C PHE 3.3 18.6 - - - +
514C ILE 3.7 2.1 + - - +
515C ALA 3.3 0.2 - - - -
516C LEU* 1.3 74.9 - - + +
518C THR* 1.3 61.4 + - - +
520C ALA* 3.2 3.6 + - - +
521C TYR* 2.8 28.8 + - - +
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Residues in contact with THR 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B SER 5.0 0.2 + - - -
514B ILE* 5.1 1.7 - - - +
515B ALA* 3.7 27.1 + - + +
518B THR* 4.9 18.6 + - + -
514C ILE* 3.0 24.0 + - - +
515C ALA* 3.9 5.4 - - - -
517C ILE* 1.3 78.5 - - - +
519C GLY* 1.3 61.7 + - - +
521C TYR* 3.2 12.5 + - + +
522C ASP* 3.3 24.5 + - - +
518D THR* 4.9 16.6 - - + -
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Residues in contact with GLY 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C ALA 2.8 18.9 + - - -
516C LEU 3.5 2.9 - - - -
518C THR* 1.3 76.5 - - - +
520C ALA* 1.3 58.0 + - - +
522C ASP* 4.2 7.6 + - - +
523C THR* 3.5 21.3 + - - +
521D TYR* 4.5 17.4 - - - -
522D ASP* 6.0 1.6 - - - -
525D LYS* 5.4 6.0 + - - -
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Residues in contact with ALA 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417C THR* 4.5 6.8 - - + +
420C VAL* 4.3 15.0 - - + +
421C ALA* 3.9 26.0 - - + -
516C LEU 2.8 16.8 + - - +
517C ILE* 3.8 4.3 - - - +
518C THR 3.2 0.2 - - - -
519C GLY* 1.3 74.4 - - - +
521C TYR* 1.3 62.8 + - - +
522C ASP 3.2 1.8 - - - -
523C THR* 2.6 26.3 + - - -
524C ILE* 3.4 9.4 + - - +
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Residues in contact with TYR 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B SER* 5.6 1.4 + - - -
512B LEU* 4.9 5.6 - - + -
515B ALA* 4.3 23.6 - - + -
516B LEU* 3.5 33.0 + - + +
519B GLY* 4.5 15.2 - - - -
413C ILE* 4.8 12.8 - - + +
414C LEU* 4.5 9.7 - - + +
417C THR* 4.0 27.8 - - + +
517C ILE* 2.8 16.8 + - + +
518C THR* 3.2 8.2 + - - +
520C ALA* 1.3 74.3 - - - +
522C ASP* 1.3 70.2 + - - +
524C ILE* 3.4 17.6 - - + +
525C LYS* 3.5 40.1 - - + +
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Residues in contact with ASP 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519B GLY* 5.9 2.4 - - - -
518C THR* 3.3 22.8 + - - +
519C GLY* 4.4 7.8 - - - +
520C ALA 3.2 0.6 - - - -
521C TYR* 1.3 85.6 - - - +
523C THR* 1.3 63.3 + - + +
525C LYS* 4.6 6.2 - - - +
526C HIS* 3.3 33.6 + - + +
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Residues in contact with THR 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420C VAL* 4.7 6.8 - - - +
519C GLY 3.5 17.7 - - - +
520C ALA* 2.6 25.2 + - - +
522C ASP* 1.3 79.0 - - + +
524C ILE* 1.3 63.5 + - - +
525C LYS 3.5 0.2 + - - -
526C HIS 3.6 17.0 + - - +
525D LYS* 5.2 10.8 - - - +
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Residues in contact with ILE 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413C ILE* 3.3 44.6 - - + +
416C ALA* 3.5 19.7 - - + +
417C THR* 3.4 31.6 - - - +
420C VAL* 5.1 8.5 - - + -
520C ALA 3.4 10.3 + - - +
521C TYR* 3.4 21.8 - - + +
523C THR* 1.3 81.6 + - - +
525C LYS* 1.3 63.5 + - + +
526C HIS 5.2 0.3 - - - +
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Residues in contact with LYS 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B GLY* 5.4 4.8 + - - -
523B THR* 5.2 12.5 - - - +
413C ILE* 5.3 8.7 - - + -
521C TYR* 3.5 49.8 - - + +
522C ASP* 4.6 3.1 - - - +
523C THR 3.3 0.2 - - - -
524C ILE* 1.3 83.1 - - + +
526C HIS* 1.3 106.7 + - + +
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Residues in contact with HIS 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C ASP* 3.3 23.3 + - + +
523C THR* 3.7 15.1 - - - +
524C ILE 3.5 0.9 - - - +
525C LYS* 1.3 128.4 + - + +
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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