Contacts of the helix formed by residues 435 - 456 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E ASP* 3.5 36.2 - - + +
110E ARG* 4.0 11.0 - - - +
429E LYS* 4.7 1.8 - - - -
432E GLY* 4.6 4.5 - - - +
433E VAL 4.0 0.2 + - - -
434E PHE* 1.3 77.5 - - - +
436E ASP* 1.3 65.6 + - - +
437E GLU* 3.3 18.8 + - - -
438E ALA* 3.0 26.2 + - - +
439E ILE* 3.0 25.6 + - - +
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Residues in contact with ASP 436 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425E ARG* 3.1 25.9 + - - +
429E LYS* 2.8 39.8 + - - +
435E THR* 1.3 72.7 - - - +
437E GLU* 1.3 63.9 + - + +
439E ILE* 3.1 5.1 + - - +
440E ASP* 2.7 43.4 + - - +
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Residues in contact with GLU 437 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E ASP* 3.8 13.7 - - - +
102E ARG* 3.5 23.9 + - - +
435E THR* 3.3 16.1 + - - +
436E ASP* 1.3 88.2 + - + +
438E ALA* 1.3 57.2 + - - +
440E ASP* 3.9 7.6 - - - +
441E ALA* 2.8 35.1 + - - +
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Residues in contact with ALA 438 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E THR* 5.8 0.5 - - - +
101E ASP 3.6 23.1 - - - +
102E ARG* 3.8 20.6 - - + +
107E ILE* 4.7 9.6 - - + -
434E PHE* 5.1 2.7 - - + -
435E THR* 3.0 30.4 + - - +
437E GLU* 1.3 75.3 - - - +
439E ILE* 1.3 64.4 + - + +
441E ALA* 3.6 2.1 - - - +
442E TYR* 3.1 23.2 + - - +
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Residues in contact with ILE 439 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421E LEU* 4.1 20.4 - - + +
425E ARG* 4.0 39.5 - - + +
428E LEU* 4.2 16.4 - - + -
429E LYS* 4.4 8.3 - - + -
434E PHE* 3.9 35.7 - - + -
435E THR 3.0 12.8 + - - +
436E ASP 3.5 6.5 - - - +
438E ALA* 1.3 74.1 - - - +
440E ASP* 1.3 60.2 + - - +
442E TYR* 3.3 7.3 + - - +
443E ILE* 2.9 45.8 + - + +
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Residues in contact with ASP 440 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425E ARG* 2.9 33.1 + - - -
436E ASP* 2.7 32.4 + - - +
437E GLU* 3.9 6.3 + - - +
439E ILE* 1.3 72.9 - - - +
441E ALA* 1.3 63.3 + - - +
443E ILE* 3.4 9.1 + - - +
444E ALA* 3.0 24.3 + - - +
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Residues in contact with ALA 441 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E THR* 5.5 2.5 - - + +
56E GLY* 4.0 24.4 - - - +
102E ARG* 4.0 19.7 - - + +
437E GLU 2.8 19.3 + - - +
438E ALA 3.6 4.5 - - - +
440E ASP* 1.3 76.8 - - - +
442E TYR* 1.3 60.9 + - - +
444E ALA* 3.3 6.7 + - - +
445E LEU* 3.1 27.7 + - - +
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Residues in contact with TYR 442 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E THR* 3.5 37.6 - - + +
310E ALA 2.6 31.5 + - - -
311E LEU* 3.7 19.7 + - + -
314E PRO* 3.2 21.0 - - - +
366E ASN* 5.6 3.0 - - + +
369E LEU* 3.8 24.0 - - + -
418E LEU* 4.6 4.5 - - + -
421E LEU* 4.1 18.2 - - + -
438E ALA 3.1 10.5 + - - +
439E ILE* 3.5 9.2 - - - +
441E ALA* 1.3 76.6 - - - +
443E ILE* 1.3 67.7 + - - +
445E LEU* 3.1 5.2 + - + +
446E ARG* 3.1 51.1 + - + +
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Residues in contact with ILE 443 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418E LEU* 3.9 23.9 - - + +
421E LEU* 3.7 17.9 - - + -
422E ASP* 3.9 33.9 - - + +
425E ARG* 4.4 5.6 - - - +
439E ILE* 2.9 30.9 + - + +
440E ASP* 3.7 8.7 - - - +
442E TYR* 1.3 77.8 - - - +
444E ALA* 1.3 58.6 + - + +
446E ARG 3.9 0.7 - - - -
447E ARG* 2.9 60.0 + - - +
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Residues in contact with ALA 444 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440E ASP 3.0 17.3 + - - +
441E ALA* 3.6 7.0 - - - +
442E TYR 3.1 0.2 - - - -
443E ILE* 1.3 76.9 - - - +
445E LEU* 1.3 64.8 + - - +
447E ARG* 3.2 7.9 + - - +
448E GLU* 3.2 23.4 + - - +
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Residues in contact with LEU 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E THR* 3.7 36.6 - - + -
25E LYS* 4.2 30.8 - - + +
55E GLY* 4.2 8.3 - - - +
56E GLY* 4.0 29.6 - - - +
441E ALA 3.1 15.3 + - - +
442E TYR* 3.1 6.8 + - + +
444E ALA* 1.3 74.7 - - - +
446E ARG* 1.3 67.5 + - + +
448E GLU* 3.1 37.6 - - - +
449E GLU* 3.4 10.1 + - - +
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Residues in contact with ARG 446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E LYS* 3.2 53.8 + - - +
310E ALA 5.3 0.2 - - - +
314E PRO* 3.4 40.5 + - - +
315E THR* 5.3 1.8 - - - +
364E ALA 4.4 1.8 + - - -
366E ASN* 5.2 2.4 - - - +
414E LEU* 4.0 10.1 - - + +
418E LEU* 4.0 23.3 - - + -
442E TYR* 3.1 52.1 + - + +
445E LEU* 1.3 80.2 - - + +
447E ARG* 1.3 57.2 + - - +
449E GLU* 3.0 30.3 + - - +
450E ASP* 2.9 28.8 + - - +
465K TYR* 4.8 6.3 - - - -
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Residues in contact with ARG 447 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415E GLU* 3.5 33.3 + - - +
418E LEU* 3.8 27.0 + - + +
419E ASN* 3.9 18.0 + - - +
422E ASP* 5.0 9.7 + - - +
443E ILE* 2.9 40.4 + - - +
444E ALA* 3.6 9.0 - - - +
445E LEU 3.2 0.4 - - - -
446E ARG* 1.3 78.7 - - - +
448E GLU* 1.3 56.3 + - - +
450E ASP* 3.4 7.8 + - + +
451E ASP* 3.1 36.7 + - - +
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Residues in contact with GLU 448 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LYS* 5.1 5.0 + - - +
444E ALA 3.2 12.0 + - - +
445E LEU* 3.1 37.2 - - - +
447E ARG* 1.3 73.9 - - - +
449E GLU* 1.3 68.7 + - + +
451E ASP* 3.4 12.5 + - - +
452E ARG* 3.4 24.4 + - - +
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Residues in contact with GLU 449 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E LYS* 3.0 37.6 + - - +
314E PRO 4.5 0.9 - - - +
414E LEU* 5.6 0.4 - - + +
445E LEU 3.6 11.0 - - - +
446E ARG* 3.0 40.6 + - - +
448E GLU* 1.3 78.7 - - + +
450E ASP* 1.3 64.9 + - - +
452E ARG* 3.1 16.9 + - - +
453E VAL* 3.4 8.7 + - - +
464K LEU* 3.6 31.4 - - + +
465K TYR* 3.7 32.3 + - - +
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Residues in contact with ASP 450 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316E THR* 3.2 27.8 - - - +
414E LEU* 4.0 17.5 + - + +
415E GLU* 3.8 25.8 + - - +
418E LEU* 5.2 2.0 - - + +
446E ARG 2.9 14.9 + - - +
447E ARG* 3.6 11.9 - - + +
449E GLU* 1.3 77.1 - - - +
451E ASP* 1.3 56.6 + - - +
453E VAL* 3.2 3.6 + - - +
454E ARG* 2.9 53.9 + - - +
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Residues in contact with ASP 451 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447E ARG* 3.1 23.2 + - - +
448E GLU* 3.5 14.7 - - - +
449E GLU 3.1 0.2 - - - -
450E ASP* 1.3 78.0 - - - +
452E ARG* 1.3 58.6 + - + +
454E ARG* 3.4 25.6 + - - +
455E MET* 2.8 53.0 + - - +
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Residues in contact with ARG 452 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E ALA* 4.4 8.5 + - - +
448E GLU 3.4 13.6 + - - +
449E GLU* 3.1 10.6 + - - +
451E ASP* 1.3 76.1 - - + +
453E VAL* 1.3 62.7 + - - +
455E MET* 4.9 2.9 - - - -
456E THR* 2.8 38.5 + - - -
261K PHE* 6.1 7.7 - - - -
460K VAL* 3.9 28.5 - - + +
463K GLU* 2.7 39.5 + - - +
464K LEU* 4.1 20.3 - - + +
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Residues in contact with VAL 453 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316E THR* 3.5 34.5 - - + +
320E LYS* 5.0 4.7 - - - +
449E GLU 3.7 4.3 - - - +
450E ASP 3.2 6.2 + - - +
451E ASP 3.2 0.8 - - - -
452E ARG* 1.3 79.2 - - - +
454E ARG* 1.3 62.2 + - + +
455E MET 3.5 0.2 + - - -
456E THR 3.8 13.5 - - - +
320K LYS* 4.1 4.3 - - - -
458K HIS* 4.0 21.2 + - + +
460K VAL* 4.0 11.4 - - + -
461K GLU* 4.1 17.0 - - + +
464K LEU* 3.7 26.0 - - + -
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Residues in contact with ARG 454 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415E GLU* 3.9 19.2 + - - -
450E ASP* 2.9 40.2 + - - +
451E ASP* 3.4 25.9 + - - +
453E VAL* 1.3 78.2 - - + +
455E MET* 1.3 61.8 + - - +
319K TYR* 4.7 7.7 + - - +
320K LYS* 3.0 31.7 + - - +
322K LEU 5.7 0.4 + - - -
323K VAL* 4.2 26.0 - - - +
324K PRO* 5.3 6.7 - - - +
412K GLY* 4.2 18.8 + - - -
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Residues in contact with MET 455 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451E ASP* 2.8 43.7 + - - +
452E ARG* 4.3 2.7 - - - +
454E ARG* 1.3 78.6 - - - +
456E THR* 1.3 59.5 + - - +
457E PRO* 3.7 5.9 - - - +
258K LYS* 5.0 2.3 - - - -
261K PHE* 3.5 42.1 - - + +
320K LYS* 3.9 18.7 - - - +
323K VAL* 3.5 42.6 - - + -
324K PRO 6.1 0.7 - - - +
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Residues in contact with THR 456 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E ALA* 4.9 7.9 - - + -
146E GLY 6.1 0.2 - - - +
147E SER* 4.6 7.2 - - - +
452E ARG* 2.8 31.8 + - - -
453E VAL 3.8 0.4 + - - +
454E ARG 3.6 0.6 - - - -
455E MET* 1.3 76.5 - - - +
457E PRO* 1.3 83.3 - - + +
458E HIS 3.3 0.9 + - - -
261K PHE* 4.2 20.2 - - + -
320K LYS* 3.3 10.2 - - - -
458K HIS* 2.9 34.3 - - - +
460K VAL* 3.7 16.7 - - + +
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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