Contacts of the helix formed by residues 440 - 457 (chain B) in PDB entry 3F3U
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 THR 440 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B VAL* 3.6 18.1 - - - +
432B GLU* 4.4 3.9 + - + +
438B ARG* 4.2 14.8 + - + +
439B PHE* 1.3 79.4 - - - +
441B ILE* 1.3 67.1 + - - +
442B LYS* 2.9 20.8 + - - +
443B SER* 2.8 28.0 + - - -
444B ASP 3.1 5.9 + - - -
503B PRO* 5.1 3.6 - - + +
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Residues in contact with ILE 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B MET* 4.0 6.3 - - + +
377B VAL 4.6 0.4 - - - -
378B GLU* 3.4 57.0 - - + +
381B ASN* 6.5 0.7 - - - -
382B TYR 4.0 17.3 - - - +
383B VAL* 3.9 8.0 - - + +
440B THR* 1.3 76.2 - - - +
442B LYS* 1.3 70.3 + - + +
444B ASP* 3.2 18.0 - - - +
445B VAL* 3.2 23.2 + - - +
509B PHE* 3.6 17.3 - - + -
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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
----------------------------------------------------------
378B GLU* 5.3 1.8 + - - +
440B THR* 2.9 11.1 + - - +
441B ILE* 1.3 87.0 - - + +
443B SER* 1.3 62.9 + - - +
445B VAL* 3.4 7.1 + - + +
446B TRP 3.4 6.4 + - - -
503B PRO* 3.7 36.6 - - + +
504B GLU* 4.6 14.1 + - - +
506B ARG* 2.9 57.5 + - + +
507B PRO 3.5 20.9 + - - +
508B THR* 3.6 19.0 - - - +
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Residues in contact with SER 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B VAL* 5.0 0.3 - - - +
385B ARG* 6.1 0.3 - - - -
430B ALA* 3.8 14.7 + - - +
432B GLU* 3.4 20.0 - - - -
433B ALA* 4.2 9.7 - - - +
438B ARG 4.1 5.4 - - - -
439B PHE* 3.4 11.6 - - - +
440B THR* 2.8 37.7 + - - -
442B LYS* 1.3 71.5 - - - +
444B ASP* 1.3 66.3 + - - +
445B VAL 3.0 1.3 - - - -
446B TRP* 3.0 13.9 + - - +
447B SER* 3.1 15.9 + - - -
506B ARG* 3.8 3.8 - - - +
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Residues in contact with ASP 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B MET* 3.6 20.2 - - + +
383B VAL* 3.5 9.3 - - - +
384B HIS* 2.6 35.8 + - - +
385B ARG* 2.8 28.3 + - - -
386B ASP 4.3 0.5 + - - -
387B LEU* 3.3 17.8 - - + +
440B THR 3.1 10.1 + - - +
441B ILE* 3.2 19.2 - - - +
442B LYS 3.3 0.2 - - - -
443B SER* 1.3 79.1 + - - +
445B VAL* 1.3 54.2 + - - +
447B SER* 3.4 5.3 + - - -
448B PHE 3.0 22.3 + - - -
509B PHE* 3.8 3.4 - - + -
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Residues in contact with VAL 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B GLU* 4.8 2.0 - - - +
441B ILE 3.2 10.7 + - - +
442B LYS* 3.4 15.0 + - + +
443B SER 3.0 1.0 - - - -
444B ASP* 1.3 72.3 - - - +
446B TRP* 1.3 66.0 + - - +
448B PHE* 3.2 3.7 + - - +
449B GLY 3.0 16.8 + - - -
498B CYS* 3.6 26.1 - - - +
506B ARG* 4.0 8.7 - - + -
507B PRO* 3.3 37.9 - - + +
509B PHE* 3.4 37.2 - - + +
512B LEU* 3.8 6.1 - - + -
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Residues in contact with TRP 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LYS 5.2 1.2 + - - -
428B TRP 3.8 9.5 - - - -
429B THR 3.9 7.8 + - - -
430B ALA* 3.3 29.4 - - + -
431B PRO* 3.6 31.9 - - + -
442B LYS 3.4 3.8 + - - -
443B SER 3.0 10.6 + - - +
445B VAL* 1.3 77.0 - - - +
447B SER* 1.3 56.4 + - - +
449B GLY 2.7 21.1 + - - -
450B ILE* 3.0 28.5 + - + +
463B TYR* 4.4 13.3 + - - -
475B VAL* 4.4 11.4 - - + -
480B ARG* 3.7 30.7 - - - -
498B CYS 3.4 11.8 + - - +
499B TRP* 3.2 50.2 + + + -
500B ARG 4.1 1.6 - - - -
501B LYS* 4.9 1.6 - - - -
506B ARG* 3.7 26.0 - - - +
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Residues in contact with SER 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ARG 5.7 2.4 + - - -
387B LEU* 3.3 32.5 + - - +
428B TRP* 2.6 30.2 + - - +
429B THR* 4.4 3.1 - - - -
443B SER 3.1 12.8 + - - -
444B ASP* 3.5 9.9 + - - -
446B TRP* 1.3 74.0 - - - +
448B PHE* 1.3 57.1 + - - +
450B ILE* 3.0 7.0 + - - +
451B LEU* 2.6 36.6 + - - +
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Residues in contact with PHE 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ALA* 3.7 18.2 - - + -
370B ILE* 4.1 13.7 - - + -
371B ALA* 3.8 26.7 - - + -
374B MET* 5.2 0.2 - - + -
387B LEU* 3.9 13.8 - - + +
444B ASP 3.0 13.8 + - - +
445B VAL 3.2 9.6 - - - +
447B SER* 1.3 77.5 - - - +
449B GLY* 1.3 58.6 + - - +
451B LEU* 3.1 14.9 + - + +
452B LEU* 2.9 61.4 + - + +
498B CYS* 4.4 1.8 - - - -
509B PHE* 3.8 19.7 - + + -
512B LEU* 4.0 26.2 - - + -
516B LEU* 3.9 19.1 - - + -
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Residues in contact with GLY 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B VAL 3.0 6.5 + - - -
446B TRP 2.7 12.5 + - - -
448B PHE* 1.3 72.0 - - - +
450B ILE* 1.3 59.0 + - - +
452B LEU* 3.1 28.2 - - - +
453B THR 3.4 2.3 + - - -
495B MET* 3.8 2.9 - - - +
498B CYS* 3.8 15.5 - - - -
499B TRP* 3.1 31.5 - - - -
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Residues in contact with ILE 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LYS 3.7 19.3 - - - +
428B TRP* 3.5 31.2 - - + +
446B TRP* 3.0 30.2 + - + +
447B SER* 3.0 6.9 + - - +
449B GLY* 1.3 75.1 - - - +
451B LEU* 1.3 53.6 + - - +
453B THR* 2.6 37.0 + - - +
454B GLU* 3.2 3.6 + - + +
462B PRO* 3.8 18.8 - - + -
463B TYR* 3.4 25.1 - - - +
481B MET* 3.5 15.5 - - + -
499B TRP* 3.0 20.4 - - + +
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Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 4.7 5.4 - - + -
370B ILE* 3.9 19.3 - - + -
387B LEU* 3.8 27.4 - - + -
388B ARG* 3.7 26.5 - - - +
389B ALA* 3.9 13.0 - - + +
392B ILE* 4.2 10.3 - - + -
428B TRP* 4.5 0.8 - - - +
447B SER 2.6 15.9 + - - +
448B PHE* 3.4 18.6 - - + +
450B ILE* 1.3 70.5 - - - +
452B LEU* 1.3 63.2 + - + +
454B GLU* 3.1 17.5 + - - +
455B LEU* 3.1 42.9 + - + +
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Residues in contact with LEU 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ALA* 4.0 23.6 - - + -
448B PHE* 2.9 52.8 + - + +
449B GLY* 3.1 19.3 - - - +
451B LEU* 1.3 73.3 - - + +
453B THR* 1.3 52.0 + - - +
455B LEU* 3.2 10.6 + - + +
456B THR* 2.7 34.9 + - - +
491B LEU* 4.9 15.7 - - + -
494B LEU* 3.8 21.3 - - + -
495B MET* 3.8 27.1 - - + +
498B CYS* 4.7 2.7 - - - -
516B LEU* 4.9 3.1 - - + -
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Residues in contact with THR 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B ILE* 2.6 24.8 + - - +
452B LEU* 1.3 69.8 - - - +
454B GLU* 1.4 56.6 + - - +
456B THR* 3.1 7.8 + - - -
457B THR* 2.8 44.8 + - - +
460B ARG 5.2 1.3 + - - -
462B PRO* 4.3 8.8 - - - +
481B MET* 3.7 39.6 - - + +
482B PRO 5.8 0.7 - - - +
484B PRO* 5.0 7.4 - - + -
495B MET* 3.8 13.2 - - + -
499B TRP* 3.7 22.9 - - + -
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Residues in contact with GLU 454 (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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347B LEU* 4.0 15.6 - - - +
350B LEU* 3.8 4.4 - - + +
389B ALA* 2.9 45.9 + - + +
390B ALA 4.8 1.4 + - - -
428B TRP* 3.0 41.9 + - + +
450B ILE 3.2 6.0 + - - +
451B LEU* 3.1 14.9 + - - +
453B THR* 1.4 84.6 + - - +
455B LEU* 1.3 61.5 + - - +
457B THR* 3.9 6.1 - - - -
458B LYS* 3.4 3.1 + - - -
459B GLY* 2.7 35.2 + - - +
460B ARG 4.1 14.8 - - - +
461B VAL* 5.9 0.3 - - - -
462B PRO* 4.6 2.7 - - + -
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Residues in contact with LEU 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 3.8 25.1 - - + -
350B LEU* 4.0 10.8 - - + -
363B LEU* 2.9 63.8 - - + +
366B MET* 4.6 8.1 - - + -
367B ALA* 3.7 32.3 - - + +
370B ILE* 4.6 2.2 - - + -
451B LEU* 3.1 32.9 + - + +
452B LEU* 3.5 14.6 - - + +
453B THR 3.1 0.2 - - - -
454B GLU* 1.3 78.2 - - - +
456B THR* 1.3 62.8 + - + +
457B THR 3.7 0.2 + - - -
458B LYS* 3.8 6.6 + - - -
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Residues in contact with THR 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LEU* 4.3 13.0 - - + -
363B LEU* 4.6 3.4 - - + -
452B LEU 2.7 21.7 + - - +
453B THR* 3.1 13.9 + - - -
455B LEU* 1.3 84.8 - - + +
457B THR* 1.3 58.7 + - - +
458B LYS* 3.4 2.9 + - - +
484B PRO* 3.9 16.0 - - - +
485B PRO* 5.1 1.4 - - - +
487B CYS* 4.1 9.4 - - - -
491B LEU* 3.9 27.8 - - + -
495B MET* 3.6 7.9 - - + +
533B LEU* 3.5 30.7 - - + +
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Residues in contact with THR 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B THR* 2.8 25.8 + - - +
454B GLU 3.5 0.7 + - - -
455B LEU 3.4 0.2 - - - -
456B THR* 1.3 78.1 - - - +
458B LYS* 1.3 71.6 + - - +
459B GLY 3.1 2.1 + - - -
460B ARG* 3.0 53.4 + - + +
484B PRO* 4.7 17.0 - - + -
485B PRO* 5.5 6.1 - - + -
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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