Contacts of the helix formed by residues 435 - 456 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101F ASP* 3.5 35.6 + - + +
110F ARG* 4.0 11.7 - - - +
429F LYS* 4.7 2.2 - - - -
432F GLY* 4.6 4.7 - - - +
434F PHE* 1.3 76.2 - - - +
436F ASP* 1.3 63.1 + - - +
437F GLU* 3.3 18.5 + - - -
438F ALA* 3.0 27.5 + - + +
439F ILE* 3.0 26.1 + - - +
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Residues in contact with ASP 436 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425F ARG* 3.1 25.7 + - - +
429F LYS* 2.8 39.3 + - - +
435F THR* 1.3 72.2 - - - +
437F GLU* 1.3 62.7 + - + +
439F ILE* 3.1 4.7 + - - +
440F ASP* 2.7 44.0 + - - +
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Residues in contact with GLU 437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F ASP* 3.8 14.1 - - + +
102F ARG* 3.5 23.3 - - - +
435F THR* 3.3 16.0 + - - +
436F ASP* 1.3 88.2 + - + +
438F ALA* 1.3 55.1 + - - +
440F ASP* 3.9 7.5 - - - +
441F ALA* 2.8 34.4 + - - +
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Residues in contact with ALA 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F THR* 5.8 0.7 - - - +
101F ASP 3.6 22.4 - - - +
102F ARG* 3.8 20.4 - - + +
107F ILE* 4.7 9.6 - - + -
434F PHE* 5.0 2.9 - - + -
435F THR* 3.0 31.3 + - - +
437F GLU* 1.3 75.3 - - - +
439F ILE* 1.3 64.1 + - + +
441F ALA* 3.6 2.1 - - - +
442F TYR* 3.1 23.4 + - - +
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Residues in contact with ILE 439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421F LEU* 4.1 19.1 - - + +
425F ARG* 4.0 39.0 - - + +
428F LEU* 4.2 15.9 - - + -
429F LYS* 4.4 8.3 - - + -
434F PHE* 3.9 35.4 - - + -
435F THR 3.0 12.6 + - - +
436F ASP 3.5 6.7 - - - +
438F ALA* 1.3 74.1 - - - +
440F ASP* 1.3 58.8 + - - +
442F TYR* 3.3 6.4 + - - +
443F ILE* 2.9 45.8 + - + +
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Residues in contact with ASP 440 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425F ARG* 2.9 33.1 + - - -
436F ASP* 2.7 32.0 + - - +
437F GLU* 3.9 6.7 + - - +
439F ILE* 1.3 72.9 - - - +
441F ALA* 1.3 62.2 + - - +
443F ILE* 3.4 9.7 + - - +
444F ALA* 3.0 23.9 + - - +
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Residues in contact with ALA 441 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F THR* 5.5 2.2 - - + +
56F GLY* 4.0 24.6 - - - +
102F ARG* 4.0 19.5 - - + +
437F GLU 2.8 19.9 + - - +
438F ALA 3.6 4.9 - - - +
440F ASP* 1.3 75.5 - - - +
442F TYR* 1.3 60.6 + - - +
444F ALA* 3.3 6.9 + - - +
445F LEU* 3.1 28.2 + - - +
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Residues in contact with TYR 442 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F THR* 3.5 37.6 - - + +
310F ALA 2.6 31.8 + - - -
311F LEU* 3.7 18.3 + - + -
314F PRO* 3.2 20.6 - - - +
366F ASN* 5.6 3.4 + - + +
369F LEU* 3.8 25.6 - - + -
418F LEU* 4.6 3.8 - - + -
421F LEU* 4.1 18.2 - - + -
438F ALA 3.1 11.3 + - - +
439F ILE* 3.5 9.6 - - - +
441F ALA* 1.3 76.6 - - - +
443F ILE* 1.3 67.7 + - + +
445F LEU* 3.1 4.8 + - + +
446F ARG* 3.1 50.9 + - + +
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Residues in contact with ILE 443 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418F LEU* 3.9 24.5 - - + +
421F LEU* 3.7 17.5 - - + -
422F ASP* 3.9 34.5 - - + +
425F ARG* 4.4 5.4 - - - +
439F ILE* 2.9 32.0 + - + +
440F ASP* 3.7 8.7 - - - +
442F TYR* 1.3 79.3 - - - +
444F ALA* 1.3 58.9 + - - +
446F ARG 3.6 0.5 + - - -
447F ARG* 2.9 59.6 + - - +
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Residues in contact with ALA 444 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440F ASP 3.0 17.7 + - - +
441F ALA* 3.6 7.0 - - - +
442F TYR 3.1 0.4 - - - -
443F ILE* 1.3 77.1 - - - +
445F LEU* 1.3 65.1 + - - +
447F ARG* 3.2 8.0 + - - +
448F GLU* 3.2 22.9 + - - +
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Residues in contact with LEU 445 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F THR* 3.7 36.6 - - + -
25F LYS* 4.2 30.6 - - + +
55F GLY* 4.1 7.9 - - - +
56F GLY* 4.0 29.8 - - - +
441F ALA 3.1 13.9 + - - +
442F TYR* 3.1 6.8 + - + +
444F ALA* 1.3 74.7 - - - +
446F ARG* 1.3 66.9 + - + +
448F GLU* 3.1 40.2 + - - +
449F GLU* 3.4 10.4 + - - +
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Residues in contact with ARG 446 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F LYS* 3.2 53.7 + - - +
310F ALA 5.3 0.2 - - - +
314F PRO* 3.4 39.8 + - - +
315F THR* 5.3 1.8 - - - +
364F ALA 4.4 1.6 + - - -
366F ASN* 5.2 2.0 - - - +
414F LEU* 4.0 9.1 - - + +
418F LEU* 4.0 22.7 - - + -
442F TYR* 3.1 52.9 + - + +
445F LEU* 1.3 82.1 - - + +
447F ARG* 1.3 56.3 + - - +
449F GLU* 3.0 30.3 + - - +
450F ASP* 2.9 29.1 + - - +
465L TYR* 4.8 6.1 - - - -
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Residues in contact with ARG 447 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415F GLU* 3.5 32.9 + - - +
418F LEU* 3.8 27.2 + - + +
419F ASN* 3.9 17.6 + - - +
422F ASP* 5.0 9.5 + - - -
443F ILE* 2.9 41.3 + - - +
444F ALA* 3.6 9.4 - - - +
445F LEU 3.2 0.2 - - - -
446F ARG* 1.3 78.6 - - - +
448F GLU* 1.3 56.5 + - - +
450F ASP* 3.4 8.1 + - + +
451F ASP* 3.1 36.9 + - - +
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Residues in contact with GLU 448 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F LYS* 5.1 5.0 + - - +
444F ALA 3.2 10.5 + - - +
445F LEU* 3.1 37.0 - - - +
447F ARG* 1.3 74.7 - - - +
449F GLU* 1.3 68.5 + - + +
451F ASP* 3.4 13.4 + - + +
452F ARG* 3.4 23.9 + - - +
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Residues in contact with GLU 449 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F LYS* 3.0 37.6 + - - +
314F PRO 4.5 0.9 - - - +
414F LEU* 5.6 0.4 - - + +
445F LEU 3.6 10.5 - - - +
446F ARG* 3.0 40.6 + - - +
448F GLU* 1.3 78.3 - - + +
450F ASP* 1.3 65.5 + - - +
452F ARG* 3.1 17.1 + - - +
453F VAL* 3.4 8.3 + - - +
464L LEU* 3.6 30.3 - - + +
465L TYR* 3.7 32.5 + - - +
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Residues in contact with ASP 450 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F THR* 3.2 27.4 - - - +
414F LEU* 4.0 17.2 + - + +
415F GLU* 3.8 26.8 + - - +
418F LEU* 5.2 2.0 - - + +
446F ARG 2.9 16.3 + - - +
447F ARG* 3.6 12.3 - - + +
449F GLU* 1.3 76.9 - - - +
451F ASP* 1.3 57.3 + - - +
453F VAL* 3.2 3.8 + - - +
454F ARG* 2.9 53.1 + - - +
465L TYR* 4.7 0.2 + - - -
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Residues in contact with ASP 451 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447F ARG* 3.1 24.4 + - - +
448F GLU* 3.5 14.9 - - - +
449F GLU 3.1 0.4 - - - -
450F ASP* 1.3 77.4 - - - +
452F ARG* 1.3 57.9 + - + +
454F ARG* 3.4 26.9 + - - +
455F MET* 2.8 52.7 + - - +
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Residues in contact with ARG 452 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F ALA* 4.4 8.5 + - - +
448F GLU 3.4 13.2 + - - +
449F GLU* 3.1 9.9 + - - +
451F ASP* 1.3 77.6 - - + +
453F VAL* 1.3 63.3 + - - +
455F MET* 4.9 2.7 - - - -
456F THR* 2.8 37.5 + - - -
261L PHE* 6.1 8.3 - - - -
460L VAL* 4.0 29.0 - - + +
463L GLU* 2.7 38.3 + - - +
464L LEU* 4.0 20.9 - - + +
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Residues in contact with VAL 453 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F THR* 3.5 34.5 - - + +
320F LYS* 5.0 4.7 - - - +
449F GLU 3.7 11.7 - - - +
450F ASP 3.2 5.7 + - - +
451F ASP 3.2 0.6 - - - -
452F ARG* 1.3 79.7 - - - +
454F ARG* 1.3 62.5 + - + +
455F MET 3.5 0.3 + - - -
456F THR 3.8 13.0 - - - +
320L LYS* 4.1 4.7 + - - -
458L HIS* 4.0 21.7 + - + +
460L VAL* 4.1 9.0 - - + -
461L GLU* 4.1 20.0 - - + +
464L LEU* 3.7 18.4 - - + -
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Residues in contact with ARG 454 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415F GLU* 3.9 18.5 + - - -
450F ASP* 2.9 40.4 + - - +
451F ASP* 3.4 25.9 + - - +
453F VAL* 1.3 79.0 - - + +
455F MET* 1.3 61.1 + - - +
456F THR 3.6 0.2 - - - -
319L TYR* 4.7 7.3 + - - +
320L LYS* 3.1 30.3 + - - +
322L LEU 5.8 0.6 + - - -
323L VAL* 4.3 24.9 - - - +
324L PRO* 5.4 6.1 - - - +
412L GLY* 4.1 18.7 + - - -
413L SER* 6.5 0.2 - - - -
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Residues in contact with MET 455 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451F ASP* 2.8 44.4 + - - +
452F ARG* 4.3 2.7 - - - +
454F ARG* 1.3 80.2 - - - +
456F THR* 1.3 59.3 + - - +
457F PRO* 3.7 5.4 - - - +
258L LYS* 5.1 1.6 - - - -
261L PHE* 3.6 41.1 - - + -
320L LYS* 3.8 18.2 - - - +
323L VAL* 3.4 43.5 - - + -
324L PRO 6.0 0.7 - - - +
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Residues in contact with THR 456 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142F ALA* 4.9 7.0 - - + -
146F GLY 6.1 0.2 - - - +
147F SER* 4.6 7.2 - - - +
452F ARG* 2.8 31.2 + - - -
454F ARG 3.6 0.6 - - - -
455F MET* 1.3 76.0 - - - +
457F PRO* 1.3 79.5 - - + +
261L PHE* 4.3 20.7 - - + -
320L LYS* 3.2 11.5 - - - -
458L HIS* 2.8 37.5 - - - +
460L VAL* 3.8 17.0 - - + +
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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
------------------------------------------------------------
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