Contacts of the helix formed by residues 435 - 456 (chain L) in PDB entry 1F1H
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 435 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101L ASP* 3.5 36.0 + - + +
110L ARG* 4.0 11.9 - - - +
429L LYS* 4.7 2.5 - - - -
432L GLY* 4.6 4.9 - - - +
433L VAL 4.0 0.2 + - - -
434L PHE* 1.3 75.7 - - - +
436L ASP* 1.3 65.7 + - - +
437L GLU* 3.3 17.7 + - - -
438L ALA* 3.0 27.3 + - + +
439L ILE* 3.0 25.8 + - - +
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Residues in contact with ASP 436 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425L ARG* 3.1 26.5 + - - +
429L LYS* 2.8 40.9 + - - +
435L THR* 1.3 73.2 - - - +
437L GLU* 1.3 63.1 + - - +
439L ILE* 3.1 4.1 + - - +
440L ASP* 2.7 45.5 + - - +
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Residues in contact with GLU 437 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101L ASP* 3.8 14.0 - - - +
102L ARG* 3.5 23.5 + - - +
435L THR* 3.3 15.4 + - - -
436L ASP* 1.3 88.0 + - + +
438L ALA* 1.3 57.2 + - - +
440L ASP* 3.9 7.7 - - - +
441L ALA* 2.8 34.9 + - - +
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Residues in contact with ALA 438 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L THR* 5.8 0.7 - - - +
101L ASP 3.6 22.9 - - - +
102L ARG* 3.8 20.3 - - + +
107L ILE* 4.7 9.6 - - + -
434L PHE* 5.1 2.9 - - + -
435L THR* 3.0 30.2 + - - +
437L GLU* 1.3 75.7 - - - +
439L ILE* 1.3 63.9 + - + +
441L ALA* 3.6 2.6 - - - +
442L TYR* 3.1 22.7 + - - +
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Residues in contact with ILE 439 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421L LEU* 4.1 19.3 - - + +
425L ARG* 4.0 39.7 - - + +
428L LEU* 4.2 16.4 - - + -
429L LYS* 4.4 8.3 - - + -
434L PHE* 3.9 35.4 - - + -
435L THR 3.0 13.9 + - - +
436L ASP 3.5 6.1 - - - +
438L ALA* 1.3 74.1 - - - +
440L ASP* 1.3 60.7 + - - +
442L TYR* 3.3 7.7 + - - +
443L ILE* 2.9 46.2 + - + +
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Residues in contact with ASP 440 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425L ARG* 2.9 35.1 + - - -
436L ASP* 2.7 32.2 + - - +
437L GLU* 3.9 6.2 + - - +
439L ILE* 1.3 72.3 - - - +
441L ALA* 1.3 61.7 + - - +
443L ILE* 3.4 10.2 + - - +
444L ALA* 3.0 25.0 + - - +
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Residues in contact with ALA 441 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L THR* 5.5 2.0 - - + +
56L GLY* 4.0 24.2 - - - +
102L ARG* 4.0 19.3 - - + +
437L GLU 2.8 19.5 + - - +
438L ALA 3.6 4.5 - - - +
440L ASP* 1.3 77.8 - - - +
442L TYR* 1.3 62.1 + - - +
444L ALA* 3.3 7.3 + - - +
445L LEU* 3.1 27.5 + - - +
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Residues in contact with TYR 442 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L THR* 3.5 37.6 - - + +
310L ALA 2.6 32.2 + - - -
311L LEU* 3.7 18.6 + - + -
314L PRO* 3.2 21.3 - - - +
366L ASN* 5.6 3.4 + - + +
369L LEU* 3.8 25.4 - - + -
418L LEU* 4.6 4.0 - - + -
421L LEU* 4.1 18.4 - - + -
438L ALA 3.1 11.1 + - - +
439L ILE* 3.5 9.9 - - - +
441L ALA* 1.3 77.4 - - - +
443L ILE* 1.3 69.9 + - + +
445L LEU* 3.1 4.5 + - + +
446L ARG* 3.1 50.6 + - + +
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Residues in contact with ILE 443 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418L LEU* 3.9 24.9 - - + +
421L LEU* 3.7 17.0 - - + -
422L ASP* 3.9 33.9 - - + +
425L ARG* 4.4 5.8 - - - +
439L ILE* 2.9 32.9 + - + +
440L ASP* 3.7 8.1 - - - +
442L TYR* 1.3 78.6 - - - +
444L ALA* 1.3 57.9 + - - +
446L ARG 3.6 0.7 + - - -
447L ARG* 2.9 60.1 + - - +
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Residues in contact with ALA 444 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440L ASP 3.0 17.0 + - - +
441L ALA* 3.6 6.5 - - - +
442L TYR 3.1 0.2 - - - -
443L ILE* 1.3 78.2 - - - +
445L LEU* 1.3 66.0 + - - +
447L ARG* 3.2 7.2 + - - +
448L GLU* 3.2 23.1 + - - +
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Residues in contact with LEU 445 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L THR* 3.7 35.9 - - + -
25L LYS* 4.2 30.6 - - + +
55L GLY* 4.2 9.0 - - - +
56L GLY* 4.0 30.1 - - - +
441L ALA 3.1 15.0 + - - +
442L TYR* 3.1 7.0 + - + +
444L ALA* 1.3 74.2 - - - +
446L ARG* 1.3 67.5 + - + +
448L GLU* 3.1 38.4 + - - +
449L GLU* 3.4 10.3 + - - +
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Residues in contact with ARG 446 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465F TYR* 4.8 6.5 - - - -
468F VAL* 6.0 0.8 - - - +
25L LYS* 3.2 52.9 + - - +
310L ALA 5.3 0.4 - - - +
314L PRO* 3.4 40.6 + - + +
315L THR* 5.3 1.2 - - - +
364L ALA 4.4 1.6 + - - -
366L ASN* 5.2 2.4 - - - +
414L LEU* 4.0 10.1 - - + +
418L LEU* 4.0 21.8 - - + -
442L TYR* 3.1 51.5 + - + +
443L ILE 4.1 0.2 - - - +
445L LEU* 1.3 81.6 - - + +
447L ARG* 1.3 57.3 + - - +
449L GLU* 3.0 29.1 + - - +
450L ASP* 2.9 28.2 + - - +
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Residues in contact with ARG 447 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415L GLU* 3.5 33.7 + - - +
418L LEU* 3.8 27.6 + - + +
419L ASN* 3.9 17.4 + - - +
422L ASP* 5.0 9.3 + - - +
443L ILE* 2.9 39.7 + - - +
444L ALA* 3.6 9.0 - - - +
445L LEU 3.2 0.4 - - - -
446L ARG* 1.3 78.5 - - - +
448L GLU* 1.3 57.5 + - - +
450L ASP* 3.4 7.7 + - + +
451L ASP* 3.1 36.2 + - - +
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Residues in contact with GLU 448 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L LYS* 5.1 4.9 + - - +
444L ALA 3.2 11.2 + - - +
445L LEU* 3.1 37.6 - - - +
447L ARG* 1.3 75.1 - - - +
449L GLU* 1.3 67.4 - - + +
451L ASP* 3.4 12.7 + - - +
452L ARG* 3.4 24.3 + - - +
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Residues in contact with GLU 449 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464F LEU* 3.5 35.4 - - + +
465F TYR* 3.6 31.8 + - - +
25L LYS* 3.0 38.4 + - - +
314L PRO 4.5 0.5 - - - +
414L LEU* 5.6 0.4 - - + +
445L LEU 3.6 10.3 - - - +
446L ARG* 3.0 40.0 + - - +
448L GLU* 1.3 78.2 - - + +
450L ASP* 1.3 66.6 + - - +
452L ARG* 3.1 12.8 + - - +
453L VAL* 3.4 9.0 + - - +
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Residues in contact with ASP 450 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465F TYR* 4.6 0.6 + - - -
316L THR* 3.2 26.7 - - - +
414L LEU* 4.0 17.3 + - + +
415L GLU* 3.8 26.2 + - - +
418L LEU* 5.2 2.0 - - + -
446L ARG 2.9 16.8 + - - +
447L ARG* 3.6 10.8 - - + +
448L GLU 3.4 0.2 - - - -
449L GLU* 1.3 76.9 - - - +
451L ASP* 1.3 58.1 + - - +
453L VAL* 3.2 3.5 + - - +
454L ARG* 2.9 53.2 + - - +
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Residues in contact with ASP 451 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447L ARG* 3.1 23.1 + - - +
448L GLU* 3.5 16.2 - - - +
449L GLU 3.1 0.2 - - - -
450L ASP* 1.3 77.9 - - - +
452L ARG* 1.3 58.0 + - + +
454L ARG* 3.4 26.3 + - - -
455L MET* 2.8 54.0 + - - +
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Residues in contact with ARG 452 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261F PHE* 6.1 6.5 - - - -
460F VAL* 3.9 31.3 - - + +
463F GLU* 2.7 39.2 + - - +
464F LEU* 4.0 21.2 - - + +
142L ALA* 4.4 8.3 + - - +
448L GLU 3.4 13.2 + - - +
449L GLU* 3.1 9.0 + - - +
451L ASP* 1.3 75.9 - - + +
453L VAL* 1.3 63.4 + - - +
455L MET* 4.9 2.9 - - - -
456L THR* 2.8 37.6 + - - -
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Residues in contact with VAL 453 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320F LYS* 4.1 4.3 + - - -
458F HIS* 4.0 20.8 + - + +
460F VAL* 4.1 10.3 - - + -
461F GLU* 4.0 20.0 - - + +
464F LEU* 3.7 25.8 - - + -
316L THR* 3.5 34.8 - - + +
320L LYS* 5.0 4.0 - - - +
449L GLU 3.7 4.7 - - - +
450L ASP* 3.2 7.1 + - - +
451L ASP 3.2 0.2 - - - -
452L ARG* 1.3 79.8 - - - +
454L ARG* 1.3 62.9 + - + +
455L MET 3.5 0.2 + - - -
456L THR 3.8 13.3 - - - +
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Residues in contact with ARG 454 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319F TYR* 4.7 8.2 + - - +
320F LYS* 3.1 30.9 + - - +
322F LEU 5.9 0.2 + - - -
323F VAL* 4.3 24.1 - - - +
324F PRO* 5.4 6.3 - - - +
412F GLY* 4.1 18.1 + - - -
415L GLU* 3.9 19.0 + - - -
450L ASP* 2.9 41.0 + - - +
451L ASP* 3.4 25.6 + - - +
453L VAL* 1.3 78.1 - - + +
455L MET* 1.3 61.0 + - - +
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Residues in contact with MET 455 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258F LYS* 5.1 1.7 - - - -
261F PHE* 3.6 40.9 - - + -
320F LYS* 3.9 18.2 - - - +
323F VAL* 3.5 44.0 - - + -
324F PRO 6.1 0.4 - - - +
451L ASP* 2.8 44.0 + - - +
452L ARG* 4.3 2.0 - - - +
454L ARG* 1.3 79.5 - - - +
456L THR* 1.3 59.5 + - - +
457L PRO* 3.7 5.7 - - - +
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Residues in contact with THR 456 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261F PHE* 4.3 19.8 - - + -
320F LYS* 3.3 11.0 - - - -
458F HIS* 2.8 37.2 - - - +
460F VAL* 3.7 16.7 - - + +
142L ALA* 4.9 7.2 - - + -
146L GLY 6.1 0.2 - - - +
147L SER* 4.6 7.2 - - - +
452L ARG* 2.8 30.7 + - - -
453L VAL 3.8 0.4 + - - +
454L ARG 3.6 0.4 - - - -
455L MET* 1.3 76.4 - - - +
457L PRO* 1.3 80.3 - - + +
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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