Contacts of the helix formed by residues 408 - 421 (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 GLY 408 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A GLY 3.9 0.4 - - - -
407A VAL* 1.3 77.2 - - - +
409A ARG* 1.3 66.0 + - - +
410A THR 4.0 0.6 - - - +
411A ALA* 3.0 5.2 + - - +
412A GLN* 3.0 21.8 + - - +
445A VAL* 4.8 0.2 - - - -
446A GLN* 4.1 3.1 - - - -
450A GLN* 3.4 25.7 - - - +
502A PDV 2.9 24.2 + - - -
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Residues in contact with ARG 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU* 3.0 43.8 + - + +
286A ALA* 4.4 0.4 - - - +
287A SER 4.1 1.2 - - - +
290A GLU* 2.8 44.3 + - - -
354A PHE* 3.1 43.1 - - + -
356A ASP* 3.8 14.7 - - - +
359A ALA* 6.5 0.2 - - - -
403A CYS* 3.5 10.9 - - - +
404A ARG* 3.8 5.9 - - - +
408A GLY* 1.3 70.6 - - - -
410A THR* 1.3 61.5 + - - +
412A GLN* 3.3 10.9 + - - +
413A LEU* 3.0 19.6 + - - +
450A GLN* 3.5 4.5 - - - +
502A PDV 2.7 67.3 + - - +
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Residues in contact with THR 410 (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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258A ALA* 3.9 5.6 - - + -
285A LEU* 3.8 8.3 - - - +
401A ILE* 3.7 27.2 - - + +
402A HIS* 3.3 7.6 + - - -
403A CYS* 3.0 32.7 + - - +
406A GLY* 3.5 28.7 - - - +
408A GLY 3.1 0.4 - - - -
409A ARG* 1.3 78.5 - - - +
411A ALA* 1.3 56.4 + - - +
413A LEU* 3.4 3.6 + - - +
414A ILE* 3.0 43.0 + - + +
444A MET* 4.9 0.4 - - + -
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Residues in contact with ALA 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A VAL 3.3 10.2 - - - +
408A GLY 3.0 4.2 + - - +
410A THR* 1.3 77.2 - - - +
412A GLN* 1.3 61.4 + - - +
414A ILE* 4.4 0.2 - - - -
415A GLY* 2.9 25.8 + - - -
436A MET* 3.7 19.3 - - - +
444A MET* 3.9 18.8 - - + -
445A VAL* 3.2 40.9 - - + +
454A LEU* 4.5 0.7 - - - +
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Residues in contact with GLN 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A PHE* 5.9 2.3 - - - -
359A ALA* 4.4 6.8 - - - +
360A VAL* 3.1 30.5 + - - +
365A THR* 2.8 33.2 + - + -
408A GLY 3.0 12.1 + - - +
409A ARG* 3.3 11.5 + - - +
411A ALA* 1.3 76.4 - - - +
413A LEU* 1.3 61.2 + - - +
415A GLY 3.5 0.2 + - - -
416A ALA* 3.1 21.0 + - - +
445A VAL* 4.9 1.0 - - - +
450A GLN* 3.2 39.3 + - + +
453A VAL* 3.6 20.1 - - + +
454A LEU* 3.6 16.4 - - + +
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Residues in contact with LEU 413 (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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283A ALA* 4.2 12.6 - - + -
285A LEU* 4.0 23.6 - - + -
365A THR* 4.5 6.5 - - + +
368A LEU* 3.8 18.4 - - + +
369A ALA* 3.7 36.6 - - + +
372A VAL* 4.2 7.6 - - + -
401A ILE* 3.9 21.8 - - + -
409A ARG 3.0 16.2 + - - +
410A THR 3.7 4.3 - - - +
412A GLN* 1.3 74.3 - - - +
414A ILE* 1.3 61.0 + - - +
416A ALA* 3.1 4.1 + - + +
417A MET* 2.8 46.5 + - + +
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Residues in contact with ILE 414 (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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249A ILE* 4.7 3.8 - - + -
251A VAL* 4.2 18.8 - - + -
254A THR* 5.6 3.3 - - + +
256A THR* 3.8 26.7 - - + +
258A ALA* 3.8 29.4 - - + -
401A ILE* 4.0 24.2 - - + -
410A THR* 3.0 29.6 + - + +
411A ALA 3.4 4.2 + - - +
413A LEU* 1.3 73.7 - - - +
415A GLY* 1.3 62.6 + - - +
417A MET* 3.2 8.7 + - + +
418A CYS* 2.9 23.7 + - + +
436A MET* 3.9 15.7 - - + -
444A MET* 4.6 8.1 - - + -
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Residues in contact with GLY 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A VAL* 5.9 0.2 - - - -
411A ALA 2.9 16.5 + - - -
414A ILE* 1.3 76.8 - - - +
416A ALA* 1.3 60.7 + - - +
418A CYS* 3.2 15.9 - - - -
419A MET* 3.2 24.2 + - - +
432A MET* 4.4 6.7 - - - -
436A MET* 4.4 10.2 - - - +
454A LEU* 3.8 17.7 - - - -
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Residues in contact with ALA 416 (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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365A THR* 3.4 35.2 - - + +
366A LYS* 5.2 1.3 - - - +
369A ALA* 3.9 14.4 - - + -
412A GLN 3.1 7.3 + - - +
413A LEU 3.6 6.1 - - - +
415A GLY* 1.3 76.5 - - - +
417A MET* 1.3 62.7 + - - +
419A MET* 3.2 8.2 + - - +
420A ASN* 3.2 23.6 + - - +
454A LEU* 3.9 1.2 - - - +
457A LEU* 3.8 18.4 - - + -
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Residues in contact with MET 417 (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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254A THR* 4.5 11.9 + - + +
256A THR* 4.3 10.5 - - + -
369A ALA* 4.0 19.5 - - + +
372A VAL* 3.8 25.4 - - + -
373A ASP* 3.4 31.3 - - - +
399A PRO* 4.0 26.2 - - + -
401A ILE* 4.5 9.2 - - - -
413A LEU* 2.8 37.4 + - + +
414A ILE* 3.2 11.6 + - + +
416A ALA* 1.3 74.8 - - - +
418A CYS* 1.3 63.2 + - - +
420A ASN* 3.1 16.9 + - - +
421A ASP* 3.4 7.8 + - - +
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Residues in contact with CYS 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A VAL* 3.6 21.3 - - + -
254A THR* 3.6 20.1 - - + +
414A ILE 2.9 12.6 + - - +
415A GLY* 3.2 19.7 - - - -
417A MET* 1.3 77.7 - - - +
419A MET* 1.3 60.4 + - - +
421A ASP* 3.2 7.4 + - - +
424A ASN* 2.9 34.5 + - - +
427A LEU* 4.1 6.1 - - - -
432A MET* 3.4 37.2 - - - -
463A ARG* 5.9 0.4 - - - -
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Residues in contact with MET 419 (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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415A GLY 3.2 12.3 + - - +
416A ALA* 3.7 8.3 - - - +
417A MET 3.2 0.4 - - - -
418A CYS* 1.3 75.9 - - - +
420A ASN* 1.3 60.9 + - - +
421A ASP 3.3 2.3 + - - +
429A VAL* 5.0 0.7 - - + -
432A MET* 3.6 30.7 - - + -
454A LEU* 3.4 48.2 - - + +
457A LEU* 3.9 15.9 - - + -
458A ALA* 3.7 20.4 - - + -
461A GLN* 2.9 35.5 + - - +
463A ARG* 3.6 29.9 + - - +
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Residues in contact with ASN 420 (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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366A LYS* 4.5 9.9 + - - +
369A ALA* 3.4 35.8 - - - +
370A SER* 3.7 14.8 + - - +
373A ASP* 3.4 18.9 + - - +
416A ALA 3.2 8.6 + - - +
417A MET 3.1 12.0 + - - +
419A MET* 1.3 78.6 - - - +
421A ASP* 1.3 58.6 + - - +
422A SER* 3.5 3.3 + - - -
461A GLN* 5.3 2.6 + - - -
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Residues in contact with ASP 421 (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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254A THR* 2.7 25.2 + - + +
417A MET 3.4 4.9 + - - +
418A CYS 3.2 14.7 + - - +
419A MET 4.5 3.2 - - - +
420A ASN* 1.3 76.2 - - - +
422A SER* 1.3 61.6 + - - +
423A ARG* 2.8 60.4 + - - +
424A ASN* 3.1 27.2 + - - +
463A ARG* 5.1 1.4 + - - -
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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