Contacts of the helix formed by residues 430 - 451 (chain B) in PDB entry 3FZ7
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 GLU 430 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU 4.4 2.8 - - - +
15A ASP* 3.5 28.9 - - - +
16A SER* 2.7 49.2 + - - -
17A ARG* 3.5 22.8 - - - +
345B ALA* 4.6 2.6 - - - +
349B VAL* 3.9 7.7 - - - +
428B GLY* 3.0 30.0 + - - +
429B PHE* 1.3 78.1 + - - +
431B MET* 1.3 69.3 + - + +
432B ASP* 3.2 5.6 - - + +
433B PHE* 2.8 26.2 + - + -
434B ALA* 2.9 10.7 + - - +
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Residues in contact with MET 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU 5.0 12.6 - - - +
14A LEU 5.7 6.3 - - - +
22A SER* 5.0 12.3 - - - +
24A SER* 5.8 4.3 - - - +
348B GLN* 3.6 40.8 - - + +
349B VAL* 3.5 18.1 - - + +
352B TYR* 3.7 38.4 - - + -
430B GLU* 1.3 73.7 + - + +
432B ASP* 1.3 59.5 + - - +
434B ALA* 3.3 5.9 + - - +
435B GLU* 3.0 31.7 + - + +
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Residues in contact with ASP 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE 4.1 4.3 - - - +
24A SER* 2.5 33.3 + - - -
25A THR* 2.7 40.5 + - - +
26A ILE* 3.3 30.5 + - + +
45A ILE* 5.5 1.2 - - - +
49A GLU* 4.6 3.9 - - - +
430B GLU* 3.1 4.9 + - + +
431B MET* 1.3 76.4 - - - +
433B PHE* 1.3 67.6 + - + +
435B GLU* 3.5 2.1 + - - +
436B LEU* 3.1 22.3 + - - +
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Residues in contact with PHE 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 4.2 15.9 - - - -
45A ILE 5.4 0.7 - - - -
48A ASP* 3.8 31.9 - - + -
49A GLU* 4.0 15.0 - - + -
52A LEU* 3.9 41.3 - - + -
57B ARG* 5.9 1.6 - - + -
404B TRP* 3.7 8.6 - + + -
428B GLY 3.6 16.2 - - - -
429B PHE* 3.8 22.0 - + + -
430B GLU* 2.8 33.4 + - + +
432B ASP* 1.3 77.9 - - + +
434B ALA* 1.4 60.7 + - - +
436B LEU* 3.1 7.5 + - + +
437B LEU* 2.9 28.8 + - - +
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Residues in contact with ALA 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B VAL* 3.9 24.5 - - + -
352B TYR* 4.5 10.8 - - + -
353B LEU* 3.8 19.9 - - + +
429B PHE* 3.9 12.8 - - + -
430B GLU 2.9 10.3 + - - +
431B MET* 3.4 11.7 - - - +
433B PHE* 1.4 75.8 - - - +
435B GLU* 1.3 57.8 + - - +
437B LEU* 3.3 3.7 + - - +
438B LEU* 2.9 32.7 + - - +
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Residues in contact with GLU 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 4.1 28.0 - - + +
352B TYR* 2.1 41.9 + - + +
431B MET* 3.0 18.8 + - + +
432B ASP* 3.6 10.3 - - - +
433B PHE 3.2 0.2 - - - -
434B ALA* 1.3 73.9 - - - +
436B LEU* 1.3 64.5 + - - +
438B LEU* 3.2 15.7 + - - +
439B GLU* 3.0 33.6 + - - +
442B LYS* 5.4 4.9 + - - -
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Residues in contact with LEU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 4.8 6.9 - - + +
52A LEU* 3.2 31.6 - - + -
404B TRP* 4.1 11.4 - - + -
432B ASP 3.1 13.7 + - - +
433B PHE* 3.1 11.2 + - + +
435B GLU* 1.3 77.4 - - - +
437B LEU* 1.3 61.7 + - - +
439B GLU* 3.0 24.1 + - - +
440B ASP* 3.0 36.4 + - - +
92F GLN* 3.6 17.9 - - - +
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Residues in contact with LEU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 3.8 25.6 - - + -
353B LEU* 4.2 28.5 - - + -
357B ILE* 5.3 0.9 - - + -
399B LEU* 3.7 28.0 - - + -
404B TRP* 3.6 30.9 - - + +
406B VAL* 4.2 11.4 - - + -
423B ILE* 4.3 15.0 - - + -
429B PHE* 4.4 1.3 - - + -
433B PHE 2.9 15.6 + - - +
434B ALA* 3.5 8.5 - - - +
436B LEU* 1.3 70.3 - - - +
438B LEU* 1.3 53.9 + - + +
440B ASP 3.1 1.9 + - - -
441B TYR* 2.7 44.0 + - + +
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Residues in contact with LEU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B TYR* 3.6 10.3 - - + -
353B LEU* 3.9 10.5 - - + -
356B GLU* 3.4 42.8 - - + +
357B ILE* 4.1 21.8 - - + -
360B LEU* 4.3 16.6 - - + -
434B ALA 2.9 14.8 + - - +
435B GLU* 3.3 33.0 - - - +
437B LEU* 1.3 76.5 - - + +
439B GLU* 1.3 61.6 + - - +
441B TYR* 3.3 7.4 + - + +
442B LYS* 3.0 40.5 + - - +
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Residues in contact with GLU 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 5.4 10.0 - - - +
402B ARG* 5.2 0.4 - - - -
435B GLU* 3.0 23.6 + - - +
436B LEU* 3.0 26.5 + - + +
438B LEU* 1.3 77.6 - - - +
440B ASP* 1.3 59.5 + - - +
442B LYS* 3.4 15.3 + - + +
443B ALA* 3.0 28.3 + - - +
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Residues in contact with ASP 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B LEU* 4.2 4.0 - - + -
402B ARG* 2.9 48.1 + - + +
404B TRP* 2.8 38.5 + - + +
436B LEU* 3.0 30.0 + - - +
437B LEU 3.7 3.8 - - - +
439B GLU* 1.3 73.8 - - - +
441B TYR* 1.3 56.7 + - - +
443B ALA* 3.7 1.2 - - - +
444B SER* 2.6 39.9 + - - -
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Residues in contact with TYR 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ILE* 4.1 30.1 - - + -
360B LEU* 3.9 20.4 - - + -
363B TYR* 2.8 29.5 + - - -
380B PHE* 3.5 15.6 - + - -
395B LEU* 3.1 28.4 - - + +
399B LEU* 4.1 25.5 - - + +
421B MET* 4.6 3.1 - - - -
423B ILE* 5.5 1.6 - - + -
437B LEU* 2.7 28.3 + - + +
438B LEU* 3.4 11.9 - - + +
440B ASP* 1.3 69.8 - - - +
442B LYS* 1.3 66.1 + - - +
444B SER* 3.0 6.3 + - - -
445B LEU* 3.0 53.5 + - + +
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Residues in contact with LYS 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B GLU* 5.2 8.4 + - - -
360B LEU* 4.0 34.5 - - + -
435B GLU* 5.4 4.8 + - - -
438B LEU* 3.0 34.4 + - - +
439B GLU* 3.6 14.8 - - + +
441B TYR* 1.3 73.9 - - - +
443B ALA* 1.3 62.9 + - - +
445B LEU* 2.9 13.2 + - - +
446B LYS* 2.9 22.0 + - - +
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Residues in contact with ALA 443 (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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402B ARG* 3.5 40.9 + - - +
439B GLU 3.0 15.2 + - - +
440B ASP 3.9 2.0 - - - +
441B TYR 3.4 0.2 - - - -
442B LYS* 1.3 75.6 - - - +
444B SER* 1.3 59.1 + - - +
446B LYS* 3.4 11.3 + - - +
447B TYR* 3.2 22.2 + - - +
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Residues in contact with SER 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B LEU* 4.0 13.9 - - - -
398B ARG* 3.6 36.1 + - - +
399B LEU* 4.1 6.8 - - - +
402B ARG* 4.8 5.4 + - - +
440B ASP 2.6 25.4 + - - -
441B TYR* 3.0 6.3 + - - -
443B ALA* 1.3 73.2 - - - +
445B LEU* 1.3 65.9 + - - +
447B TYR* 3.5 6.1 + - - +
448B LEU* 3.2 29.1 + - - +
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Residues in contact with LEU 445 (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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360B LEU* 3.5 35.9 - - + +
363B TYR* 4.3 2.9 - - - +
390B TYR* 3.4 41.6 - - + +
395B LEU* 4.1 16.8 - - + -
441B TYR* 3.0 38.5 + - + +
442B LYS* 2.9 9.5 + - - +
444B SER* 1.3 75.9 - - - +
446B LYS* 1.3 66.1 + - - +
448B LEU* 3.3 4.7 + - + +
449B SER* 3.0 23.4 + - - -
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Residues in contact with LYS 446 (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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442B LYS 2.9 12.2 + - - +
443B ALA* 3.7 13.0 - - - +
444B SER 3.2 0.2 - - - -
445B LEU* 1.3 76.1 - - - +
447B TYR* 1.3 56.1 + - - +
449B SER* 3.2 8.3 + - - -
450B ASP* 2.9 52.9 + - - +
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Residues in contact with TYR 447 (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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397A GLU* 4.5 5.9 + - - -
457A ILE* 4.5 4.2 + - + +
458A ALA* 4.3 19.4 - - - +
459A GLN* 4.8 3.1 + - - +
460A GLN* 6.2 1.0 - - + +
398B ARG* 3.7 28.5 - - + +
443B ALA 3.2 12.7 + - - +
444B SER* 3.7 9.6 - - - +
445B LEU 3.3 0.2 - - - -
446B LYS* 1.3 74.8 - - - +
448B LEU* 1.3 60.8 + - + +
450B ASP* 3.2 3.3 + - - -
451B HIS* 2.9 71.8 + + - +
454B LEU* 3.9 19.7 - - + -
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Residues in contact with LEU 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B GLY 4.6 9.3 - - - +
390B TYR* 3.9 38.4 - - + -
394B ASP* 4.0 21.1 - - + +
395B LEU* 4.3 17.3 - - + -
398B ARG* 3.9 25.8 - - + -
444B SER 3.2 22.9 + - - +
445B LEU* 3.3 7.1 + - - +
447B TYR* 1.3 77.0 - - - +
449B SER* 1.3 62.8 + - - +
451B HIS* 3.4 18.0 + - - +
452B PRO* 3.6 6.9 - - - +
454B LEU* 4.1 24.7 - - + -
455B GLN 5.5 0.2 - - - +
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Residues in contact with SER 449 (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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445B LEU 3.0 13.8 + - - -
446B LYS* 3.3 11.2 - - - -
448B LEU* 1.3 80.8 - - - +
450B ASP* 1.3 65.7 + - - +
451B HIS 3.3 1.2 + - - -
452B PRO* 3.6 15.4 - - - +
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Residues in contact with ASP 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B LYS* 2.9 43.7 + - - +
447B TYR* 3.2 2.1 + - + +
449B SER* 1.3 83.3 + - - +
451B HIS* 1.3 85.0 + - + +
452B PRO* 3.6 5.4 - - - +
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Residues in contact with HIS 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A ILE* 3.9 29.7 + - + -
459A GLN* 3.6 29.0 + - - +
447B TYR* 2.9 68.4 + + + +
448B LEU 3.5 5.0 - - - +
449B SER 3.2 0.8 - - - -
450B ASP* 1.3 99.1 + - + +
452B PRO* 1.3 67.8 - - - +
453B LYS* 2.9 5.8 + - - +
454B LEU* 2.9 21.4 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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