Contacts of the helix formed by residues 383 - 401 (chain B) in PDB entry 3FO5
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 ASN 383 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A ARG* 3.1 51.1 + - - +
350A ARG* 2.9 32.4 - - - +
351A GLU* 3.2 20.2 + - - -
380B ASP* 2.8 19.5 + - + +
382B SER* 1.3 80.9 + - - +
384B GLN* 1.3 59.6 + - - +
385B VAL 3.2 0.6 + - - -
386B TYR* 3.3 3.1 + - - +
387B LEU* 2.9 41.7 + - + +
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Residues in contact with GLN 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A GLU* 3.1 2.8 + - - +
379B TRP* 3.4 37.2 - - + -
380B ASP 3.3 2.9 + - - -
381B PRO* 3.0 25.9 + - - +
383B ASN* 1.3 78.5 - - - +
385B VAL* 1.3 79.6 + - + +
387B LEU* 4.1 0.7 - - - +
388B SER* 3.1 25.5 + - - -
465B VAL* 3.6 31.9 + - + +
466B ASP* 4.4 9.8 + - - +
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Residues in contact with VAL 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A GLU* 2.9 22.2 + - + +
354A ALA* 3.4 23.8 - - + -
355A ARG* 3.8 20.9 - - + +
358A ILE* 3.5 30.5 - - + -
384B GLN* 1.3 92.3 - - + +
386B TYR* 1.3 62.1 + - - +
388B SER* 3.6 4.9 - - - -
389B TYR* 3.1 20.6 + - - +
495B ARG* 5.1 1.4 + - - -
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Residues in contact with TYR 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ARG* 3.3 60.4 - - + +
351A GLU* 3.1 19.7 + - - +
354A ALA* 3.7 6.2 - - + +
565A LEU* 4.0 23.8 - - + -
383B ASN* 3.3 2.2 + - - +
385B VAL* 1.3 74.5 - - - +
387B LEU* 1.3 73.3 + - + +
389B TYR* 2.9 24.8 + + - +
390B ASN* 2.8 61.1 + - + +
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ARG* 5.7 0.7 - - - +
377B VAL* 4.2 26.2 - - + -
378B PRO 3.7 22.2 - - - +
379B TRP* 4.0 25.6 - - + -
380B ASP* 4.1 6.5 - - + +
383B ASN* 2.9 34.7 + - + +
384B GLN 4.1 2.9 - - - +
386B TYR* 1.3 85.8 - - + +
388B SER* 1.3 57.7 + - - +
390B ASN* 3.8 5.8 - - + +
391B ASN* 2.9 30.1 + - - +
491B LEU* 4.0 15.9 - - + +
509B ARG* 5.4 3.0 - - - +
511B VAL* 5.7 0.7 - - + -
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Residues in contact with SER 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B TRP* 6.2 0.2 - - - -
384B GLN 3.1 20.0 + - - -
385B VAL* 3.6 5.4 - - - -
387B LEU* 1.3 74.6 - - - +
389B TYR* 1.3 64.3 + - - +
391B ASN* 3.3 2.3 + - - +
392B VAL* 3.1 27.0 + - - +
466B ASP* 5.8 0.2 - - - -
469B ASP* 2.6 30.9 + - - -
491B LEU* 4.2 5.4 - - - +
493B SER* 3.6 10.0 + - - -
495B ARG* 2.5 30.9 + - - -
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Residues in contact with TYR 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ALA* 4.6 9.2 - - + +
357A LYS* 3.9 26.9 - - + -
560A THR* 3.2 24.5 - - + +
565A LEU* 3.8 42.8 + - + +
566A SER* 5.2 0.5 - - - -
385B VAL 3.1 13.8 + - - +
386B TYR* 2.9 33.9 + + - +
388B SER* 1.3 75.6 + - - +
390B ASN* 1.3 66.6 + - + +
392B VAL* 3.3 5.4 + - + +
393B SER* 2.8 59.1 + - - -
495B ARG* 4.1 8.0 - - - +
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Residues in contact with ASN 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B TYR* 2.8 53.1 + - + +
387B LEU* 3.8 8.5 - - + +
389B TYR* 1.3 77.8 - - + +
391B ASN* 1.3 65.3 + - - +
393B SER* 4.2 4.0 - - - -
394B SER* 2.8 44.2 + - - -
509B ARG* 4.9 14.2 + - - -
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Residues in contact with ASN 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LEU 2.9 15.4 + - - +
388B SER 3.3 9.9 - - - +
390B ASN* 1.3 79.6 + - - +
392B VAL* 1.3 62.2 + - - +
394B SER* 3.5 4.9 + - - -
395B LEU* 3.4 12.5 + - - +
491B LEU* 2.9 33.7 + - + +
493B SER* 3.0 20.5 + - - +
507B ALA* 3.1 33.2 + - - +
508B LEU 3.5 5.5 - - - +
509B ARG* 3.4 29.0 - - + +
529B CYS* 5.0 2.1 - - - -
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Residues in contact with VAL 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LYS* 6.1 1.6 - - - +
388B SER 3.1 16.9 + - - +
389B TYR* 3.7 5.2 - - + +
391B ASN* 1.3 73.2 - - - +
393B SER* 1.3 68.0 + - - +
395B LEU* 3.2 5.4 + - - +
396B LYS* 3.1 47.4 + - - +
493B SER* 3.6 30.5 - - - +
495B ARG* 3.9 34.5 - - + +
505B VAL* 4.1 12.4 - - + +
507B ALA* 3.8 7.2 - - + -
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Residues in contact with SER 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B TYR* 2.8 56.3 + - - -
390B ASN* 3.9 4.9 - - - -
392B VAL* 1.3 75.1 - - - +
394B SER* 1.3 56.6 + - - +
396B LYS* 3.4 10.6 + - - +
397B MET* 2.9 40.6 + - - +
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Residues in contact with SER 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ASN* 2.8 37.6 + - - -
391B ASN* 3.7 5.6 - - - -
392B VAL 3.2 0.2 - - - -
393B SER* 1.3 76.8 - - - +
395B LEU* 1.3 56.3 + - - +
397B MET* 3.3 7.3 + - - +
398B LEU* 2.9 28.9 + - - +
509B ARG* 5.9 0.7 + - - -
528B LEU 5.8 0.7 - - - -
529B CYS* 3.7 18.5 - - - -
549B GLN* 5.8 0.4 - - - -
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Residues in contact with LEU 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ASN 3.4 2.6 + - - +
392B VAL 3.2 8.8 + - - +
394B SER* 1.3 73.8 - - - +
396B LYS* 1.3 67.5 + - - +
398B LEU* 3.1 12.7 + - + +
399B VAL* 3.0 26.1 + - + +
505B VAL* 3.9 7.6 - - + -
506B ILE 3.4 25.4 - - - +
507B ALA* 3.7 16.2 - - + -
529B CYS* 3.6 13.1 - - - -
530B SER 3.7 14.8 - - - +
531B GLY 3.8 9.9 - - - -
532B PHE 3.9 11.4 - - - +
533B CYS* 4.2 8.7 - - - -
547B TYR* 3.7 37.5 - - + -
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Residues in contact with LYS 396 (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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357A LYS* 4.4 5.3 - - - +
480A GLY* 3.4 17.0 - - - +
481A GLY* 2.8 37.0 + - - +
556A ASN* 3.0 42.1 + - - +
392B VAL* 3.1 36.7 + - + +
393B SER* 3.6 11.0 - - - +
395B LEU* 1.3 74.9 - - - +
397B MET* 1.3 62.8 + - + +
399B VAL* 3.3 11.5 + - - +
400B ALA 3.3 5.0 + - - -
495B ARG* 5.7 4.6 - - - +
502B ASP* 5.1 6.3 + - - -
503B PRO* 5.4 5.8 - - + -
505B VAL* 4.0 24.9 - - + -
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Residues in contact with MET 397 (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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480A GLY* 4.1 21.1 - - - +
568A GLU* 6.0 2.0 - - - +
393B SER* 2.9 29.3 + - - +
394B SER* 3.7 6.7 - - - +
396B LYS* 1.3 73.6 - - - +
398B LEU* 1.3 66.2 + - - +
400B ALA* 3.1 17.2 + - + +
401B LYS* 3.2 17.3 + - - +
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Residues in contact with LEU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B SER 2.9 14.2 + - - +
395B LEU* 3.1 9.8 + - + +
397B MET* 1.3 77.2 - - - +
399B VAL* 1.3 61.5 + - - +
400B ALA 3.3 0.3 + - - -
401B LYS* 3.3 17.3 + - + +
404B TRP* 3.0 40.2 + - + -
418B LEU* 4.1 15.5 - - + -
425B SER* 4.7 0.7 - - - +
529B CYS* 4.1 16.4 - - - +
547B TYR* 3.8 30.1 - - + -
548B ASN 4.8 0.9 - - - -
549B GLN* 3.9 48.5 - - + +
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Residues in contact with VAL 399 (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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481A GLY* 3.7 24.0 - - - -
482A HIS 3.9 1.3 - - - +
483A THR* 3.8 28.1 - - + +
395B LEU* 3.0 20.9 + - + +
396B LYS* 3.4 9.4 - - - +
397B MET 3.2 0.2 - - - -
398B LEU* 1.3 76.6 - - - +
400B ALA* 1.3 60.2 + - - +
401B LYS 3.5 1.6 + - - +
404B TRP* 3.8 11.6 + - - -
533B CYS* 3.5 30.5 - - - -
535B TRP* 3.9 8.5 - - + -
547B TYR* 3.6 36.4 + - + +
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Residues in contact with ALA 400 (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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478A ALA* 4.0 14.9 - - + +
479A LEU 3.5 32.1 - - - +
480A GLY* 4.0 2.0 - - - -
482A HIS 3.4 11.7 - - - +
483A THR* 5.4 0.4 - - - +
396B LYS 3.3 6.4 + - - +
397B MET* 3.1 14.8 + - + +
399B VAL* 1.3 78.6 - - - +
401B LYS* 1.3 66.1 + - - +
402B ASP* 3.6 2.9 + - - +
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Residues in contact with LYS 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B MET 3.2 18.2 + - - +
398B LEU* 3.3 20.8 + - + +
399B VAL 3.4 0.9 - - - +
400B ALA* 1.3 79.3 - - - +
402B ASP* 1.3 59.8 + - - +
403B ASN* 3.4 10.8 - - - +
404B TRP* 3.4 18.0 - - - +
418B LEU* 3.6 28.0 - - + -
420B ASP* 2.7 31.9 + - - +
549B GLN* 4.2 16.8 - - - +
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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
------------------------------------------------------------
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