Contacts of the helix formed by residues 510 - 526 (chain B) in PDB entry 6BFN
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 PRO 510 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403B VAL* 6.3 2.7 - - + -
407B THR* 5.2 0.9 - - - +
508B ARG 4.4 1.6 - - - +
509B PRO* 1.3 89.3 - - + +
511B MET* 1.3 60.9 + - - +
512B THR* 3.1 13.9 - - - +
513B GLN* 3.0 52.7 + - + +
514B VAL* 3.2 8.9 + - - +
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Residues in contact with MET 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B ALA* 4.0 21.8 - - - +
326B ILE* 3.6 17.3 - - + -
327B GLN* 3.7 17.2 - - + +
330B HIS* 3.5 39.5 + - + +
407B THR* 3.7 29.8 + - - +
410B PHE* 3.9 20.0 - - + -
509B PRO 3.8 0.6 + - - -
510B PRO* 1.3 72.1 - - - +
512B THR* 1.3 57.3 + - - +
514B VAL* 3.3 34.5 + - + +
515B TYR* 2.9 29.1 + - - +
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Residues in contact with THR 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ASN* 4.7 4.9 + - - +
327B GLN* 3.6 28.9 - - + +
330B HIS* 6.1 2.0 - - + -
331B GLN* 3.8 25.8 - - + +
510B PRO* 3.8 16.1 - - - +
511B MET* 1.3 77.6 - - - +
513B GLN* 1.3 62.3 + - - +
515B TYR* 3.3 5.0 + - - +
516B GLU* 2.9 41.2 + - - +
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Residues in contact with GLN 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509B PRO* 4.1 7.3 - - + +
510B PRO* 3.0 36.5 + - + +
512B THR* 1.3 82.0 + - - +
514B VAL* 1.3 57.8 + - - +
516B GLU* 3.2 15.5 + - - +
517B ARG* 2.9 61.8 + - + +
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Residues in contact with VAL 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B PHE* 3.6 32.1 - - + -
496B LEU* 3.7 30.0 - - + +
500B CYS* 4.1 6.3 - - - -
509B PRO* 3.9 24.0 - - + +
510B PRO 3.2 13.4 + - - +
511B MET* 3.5 30.3 - - + +
512B THR 3.3 0.2 - - - -
513B GLN* 1.3 76.3 - - - +
515B TYR* 1.3 63.5 + - - +
517B ARG* 3.3 4.2 + - - +
518B LEU* 3.0 27.1 + - + +
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Residues in contact with TYR 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ASN* 3.4 39.1 + - + -
320B LEU* 3.5 36.6 - - + +
323B ALA* 4.2 10.5 - - + -
324B ARG* 2.9 58.7 + - + -
327B GLN* 4.1 13.2 - - + -
511B MET 2.9 16.5 + - - +
512B THR* 3.6 5.2 - - - +
514B VAL* 1.3 77.1 - - - +
516B GLU* 1.3 60.1 + - + +
518B LEU* 3.2 4.6 + - - +
519B GLU* 2.9 57.4 + - - +
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Residues in contact with GLU 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ASN* 4.9 11.4 + - - +
512B THR* 2.9 25.4 + - - +
513B GLN* 3.5 19.9 + - - +
515B TYR* 1.3 85.5 - - + +
517B ARG* 1.3 57.1 + - + +
519B GLU* 3.3 11.0 + - - +
520B LYS* 2.9 50.3 + - - +
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Residues in contact with ARG 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495B GLN* 5.5 0.4 - - - +
496B LEU* 3.8 34.9 - - + +
499B CYS* 3.9 25.9 - - - +
509B PRO* 4.0 15.9 - - - +
513B GLN* 2.9 45.8 + - + +
514B VAL* 3.6 4.9 - - - +
516B GLU* 1.3 75.0 - - + +
518B LEU* 1.3 58.7 + - - +
520B LYS* 3.3 14.8 + - + +
521B LEU* 2.9 36.1 + - + +
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Residues in contact with LEU 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B LEU* 4.0 15.5 - - + +
319B LEU* 3.6 34.5 - - + +
320B LEU* 3.6 14.0 - - + +
323B ALA* 3.6 19.3 - - + -
410B PHE* 3.8 13.5 - - + -
414B VAL* 6.0 0.4 - - + -
493B LEU* 3.7 30.1 - - + -
496B LEU* 3.7 15.5 - - + -
514B VAL* 3.0 21.9 + - + +
515B TYR 3.6 3.8 - - - +
517B ARG* 1.3 76.0 - - - +
519B GLU* 1.3 57.5 + - - +
521B LEU* 3.3 9.6 + - + +
522B GLN* 2.9 27.4 + - - +
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Residues in contact with GLU 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ASN* 4.7 3.1 - - - +
320B LEU* 3.4 14.8 - - + +
515B TYR* 2.9 46.2 + - + +
516B GLU* 3.5 10.7 - - - +
518B LEU* 1.3 74.0 - - - +
520B LYS* 1.3 65.0 + - + +
522B GLN* 3.1 16.1 + - - +
523B ALA* 2.9 21.9 + - - +
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Residues in contact with LYS 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516B GLU* 2.9 41.0 + - - +
517B ARG* 3.5 14.3 - - + +
519B GLU* 1.3 76.5 - - + +
521B LEU* 1.3 57.2 + - - +
523B ALA* 3.1 10.6 + - - +
524B VAL* 2.9 33.5 + - + +
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Residues in contact with LEU 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B LEU* 4.1 10.5 - - + -
488B GLU* 3.6 28.5 - - + +
489B LEU* 4.7 5.2 - - + +
492B GLY* 4.0 29.2 - - - +
493B LEU* 4.2 18.6 - - + +
496B LEU* 5.6 2.5 - - + -
517B ARG* 2.9 20.6 + - + +
518B LEU* 3.4 16.4 - - + +
520B LYS* 1.3 75.1 - - + +
522B GLN* 1.3 58.1 + - - +
524B VAL* 3.2 12.7 + - + +
525B VAL* 2.9 35.2 + - + +
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Residues in contact with GLN 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B LEU* 3.6 21.2 - - + +
317B ASP* 2.8 30.0 + - - +
320B LEU* 3.7 25.9 - - + +
518B LEU 2.9 12.9 + - - +
519B GLU* 3.1 17.5 + - - +
521B LEU* 1.3 75.8 - - - +
523B ALA* 1.3 62.3 + - - +
525B VAL* 3.5 2.6 + - + +
526B ALA* 3.1 22.7 + - - +
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Residues in contact with ALA 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519B GLU* 2.9 12.5 + - + +
520B LYS* 3.1 12.5 + - - +
522B GLN* 1.3 78.0 + - - +
524B VAL* 1.3 64.0 + - + +
526B ALA* 3.4 21.7 + - - +
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Residues in contact with VAL 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488B GLU* 3.9 32.3 - - + +
520B LYS* 2.9 21.5 + - + +
521B LEU* 3.2 15.2 + - + +
523B ALA* 1.3 76.1 - - + +
525B VAL* 1.3 67.4 + - + +
526B ALA 3.2 5.4 + - - -
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Residues in contact with VAL 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B PRO* 4.6 19.3 - - + -
316B LEU* 3.7 15.7 - - + -
486B PRO* 5.4 9.6 - - + -
488B GLU* 5.7 2.5 - - + -
489B LEU* 3.6 42.8 - - + +
521B LEU* 2.9 22.2 + - + +
522B GLN* 3.8 4.5 - - + +
523B ALA 3.4 0.2 - - - -
524B VAL* 1.3 79.4 - - + +
526B ALA* 1.3 62.6 - - - +
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Residues in contact with ALA 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522B GLN 3.1 13.4 + - - +
523B ALA* 3.4 18.1 - - - +
524B VAL 3.1 6.7 - - - +
525B VAL* 1.3 82.6 - - - +
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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