Contacts of the helix formed by residues 447 - 461 (chain A) in PDB entry 3F9B
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 LYS 447 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356A ASP 5.3 3.2 + - - -
357A GLN 4.1 22.6 + - - -
358A THR* 4.7 8.9 - - - +
359A ALA* 4.9 2.9 - - - +
445A VAL* 4.1 5.2 - - - +
446A GLN* 1.3 90.4 - - + +
448A ASP* 1.3 64.5 + - - +
449A GLU* 3.1 29.3 - - - +
450A GLN* 3.0 43.0 + - + +
451A LEU* 3.2 9.9 + - - +
502A PDV 3.7 28.2 + - - +
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Residues in contact with ASP 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A SER* 4.9 8.6 + - - -
446A GLN 4.4 0.7 + - - +
447A LYS* 1.3 72.5 - - - +
449A GLU* 1.3 64.2 + - - +
451A LEU* 3.3 14.3 + - - +
452A ASP* 2.9 39.4 + - - +
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Residues in contact with GLU 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A THR* 6.4 0.7 - - + -
359A ALA* 4.0 22.4 - - + +
447A LYS* 3.1 32.7 - - + +
448A ASP* 1.3 86.9 + - - +
450A GLN* 1.3 61.1 + - + +
452A ASP* 3.4 23.6 - - - +
453A VAL* 3.5 14.0 + - - +
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Residues in contact with GLN 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ALA* 4.8 6.2 - - + +
408A GLY* 3.4 20.7 - - - +
409A ARG* 3.5 2.0 - - - +
412A GLN* 3.2 32.4 - - + +
445A VAL* 3.8 10.3 - - + -
446A GLN* 3.1 13.0 + - - -
447A LYS* 3.0 43.5 + - + +
449A GLU* 1.3 75.3 - - - +
451A LEU* 1.3 65.1 + - - +
453A VAL* 3.1 13.3 + - - +
454A LEU* 3.3 16.0 + - - +
502A PDV 2.8 39.5 + - - -
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Residues in contact with LEU 451 (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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194A ARG 5.7 0.9 - - - +
197A LEU* 4.4 9.9 - - + -
198A SER* 5.0 13.9 - - - +
201A LEU* 4.0 21.8 - - + -
429A VAL* 4.0 25.6 - - + -
433A VAL* 4.1 17.5 - - + -
445A VAL* 3.6 17.5 - - + +
447A LYS 3.2 7.3 + - - +
448A ASP* 3.7 15.3 - - - +
450A GLN* 1.3 77.2 - - - +
452A ASP* 1.3 63.1 + - - +
454A LEU* 3.1 7.1 + - + +
455A ILE* 2.9 41.6 + - + +
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Residues in contact with ASP 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ARG* 3.0 29.2 + - - +
448A ASP* 2.9 24.5 + - - +
449A GLU* 3.4 17.9 - - - +
451A LEU* 1.3 77.0 - - - +
453A VAL* 1.3 57.8 + - + +
455A ILE* 3.3 6.7 + - - +
456A LYS* 3.0 27.7 + - - +
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Residues in contact with VAL 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ALA* 4.9 3.6 - - + -
360A VAL 3.5 20.6 - - - +
361A SER* 4.7 1.6 - - - -
362A SER* 3.8 23.3 - - - +
365A THR* 3.7 10.8 - - - +
412A GLN* 3.6 26.9 - - + +
449A GLU 3.5 14.3 + - - +
450A GLN 3.1 9.2 + - - +
452A ASP* 1.3 73.8 - - + +
454A LEU* 1.3 67.7 + - - +
456A LYS* 3.2 7.5 + - - +
457A LEU* 2.9 33.5 + - + +
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Residues in contact with LEU 454 (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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411A ALA 4.5 7.2 - - - +
412A GLN* 3.6 29.6 - - + +
415A GLY* 3.8 13.9 - - - -
416A ALA 3.9 2.7 - - - +
419A MET* 3.4 30.1 - - + +
429A VAL* 4.6 12.6 - - + -
432A MET* 5.4 2.5 - - - -
433A VAL* 4.3 14.8 - - + -
436A MET* 4.7 1.8 - - + -
445A VAL* 4.0 33.4 - - + -
450A GLN 3.3 9.1 + - - +
451A LEU* 3.1 9.0 + - + +
453A VAL* 1.3 76.4 - - - +
455A ILE* 1.3 57.7 + - - +
457A LEU* 3.3 7.7 + - + -
458A ALA* 2.9 27.4 + - - +
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Residues in contact with ILE 455 (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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189A TYR* 4.9 4.7 - - + -
194A ARG* 3.6 53.6 - - + +
197A LEU* 4.0 24.2 - - + -
429A VAL* 4.8 1.8 - - + -
451A LEU* 2.9 40.7 + - + +
452A ASP* 3.6 6.7 - - - +
454A LEU* 1.3 75.7 - - - +
456A LYS* 1.3 58.3 + - - +
458A ALA* 3.3 2.5 + - - +
459A GLU* 2.8 31.5 + - - +
465A LEU* 3.9 30.7 - - + +
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Residues in contact with LYS 456 (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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194A ARG* 6.1 0.9 - - - +
361A SER* 5.6 0.8 - - - -
362A SER* 2.8 32.8 + - - +
363A GLU* 3.0 24.3 + - - -
452A ASP 3.0 14.4 + - - +
453A VAL* 3.2 10.3 + - - +
455A ILE* 1.3 78.1 - - - +
457A LEU* 1.3 60.9 + - - +
459A GLU* 3.4 9.2 + - + +
460A GLY* 3.0 20.8 + - - -
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Residues in contact with LEU 457 (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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362A SER* 3.8 21.1 - - - +
365A THR* 4.2 4.9 - - + -
366A LYS* 3.5 36.8 - - + +
416A ALA* 3.8 33.4 - - + -
419A MET* 3.9 17.9 - - + -
453A VAL* 2.9 34.9 + - + +
454A LEU* 3.7 6.7 - - + +
456A LYS* 1.3 75.6 - - - +
458A ALA* 1.3 62.5 + - - +
460A GLY* 3.3 10.2 + - - -
461A GLN* 3.4 18.6 + - - +
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Residues in contact with ALA 458 (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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419A MET* 3.7 9.9 - - - -
429A VAL* 3.5 26.0 - - + -
454A LEU 2.9 17.4 + - - +
455A ILE 3.6 4.5 - - - +
457A LEU* 1.3 74.5 - - - +
459A GLU* 1.3 62.8 + - - +
461A GLN* 3.0 7.7 + - - -
463A ARG* 2.9 52.0 + - + +
465A LEU* 4.1 3.6 - - + -
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Residues in contact with GLU 459 (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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189A TYR* 3.6 56.7 + - + +
194A ARG* 5.0 8.5 + - - -
455A ILE* 2.8 18.9 + - - +
456A LYS* 3.7 10.2 - - + +
458A ALA* 1.3 76.4 - - - +
460A GLY* 1.3 61.6 + - - +
462A GLY* 3.1 12.8 + - - -
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Residues in contact with GLY 460 (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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456A LYS 3.0 14.5 + - - -
457A LEU* 3.3 4.9 + - - -
458A ALA 3.2 0.8 - - - -
459A GLU* 1.3 76.2 - - - +
461A GLN* 1.3 59.8 + - - +
462A GLY 3.5 0.4 + - - -
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Residues in contact with GLN 461 (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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419A MET* 2.9 36.7 + - - +
420A ASN* 5.1 2.4 + - - +
457A LEU* 3.4 11.2 + - - +
458A ALA 3.0 8.7 + - - +
460A GLY* 1.3 78.4 - - - +
462A GLY* 1.3 61.0 + - - +
463A ARG* 2.9 39.8 + - + +
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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