Contacts of the helix formed by residues 435 - 456 (chain D) in PDB entry 1FPY
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101D ASP* 3.1 36.1 + - + +
110D ARG* 3.5 18.2 - - - +
429D LYS* 4.8 1.3 - - - -
432D GLY 4.8 3.6 - - - +
434D PHE* 1.3 80.1 - - - +
436D ASP* 1.3 64.2 + - - +
437D GLU* 2.7 19.4 + - - -
438D ALA* 3.1 19.2 + - + +
439D ILE* 3.0 27.2 + - - +
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Residues in contact with ASP 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425D ARG* 3.1 21.7 + - - +
429D LYS* 3.0 40.7 + - - +
435D THR* 1.3 72.0 - - - +
437D GLU* 1.3 56.3 + - + +
439D ILE* 3.0 6.8 + - - +
440D ASP* 2.6 47.8 + - - +
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Residues in contact with GLU 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D ASP* 3.4 21.1 - - - +
102D ARG* 3.6 24.9 + - - +
435D THR* 2.7 25.4 + - - -
436D ASP* 1.3 76.0 + - + +
438D ALA* 1.3 59.5 + - - +
440D ASP* 3.7 11.9 + - + +
441D ALA* 2.7 36.0 + - - +
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Residues in contact with ALA 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D THR* 6.0 0.3 - - - +
101D ASP 3.4 25.1 - - - +
102D ARG* 3.7 18.6 - - + +
107D ILE* 4.7 10.3 - - + -
434D PHE* 5.1 2.7 - - + -
435D THR* 3.1 29.8 + - - +
437D GLU* 1.3 78.5 + - - +
439D ILE* 1.3 63.4 + - + +
441D ALA* 3.6 3.1 - - - +
442D TYR* 3.2 20.6 + - - +
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Residues in contact with ILE 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421D LEU* 4.1 21.5 - - + +
425D ARG* 4.0 25.6 - - + +
428D LEU* 4.2 16.6 - - + -
429D LYS* 4.2 14.6 - - + -
434D PHE* 3.6 41.1 - - + -
435D THR 3.0 11.6 + - - +
436D ASP 3.0 7.5 + - - +
438D ALA* 1.3 74.4 - - - +
440D ASP* 1.3 62.4 + - - +
442D TYR* 3.5 6.1 + - - +
443D ILE* 3.1 40.1 + - + +
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Residues in contact with ASP 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425D ARG* 3.0 32.7 + - - -
436D ASP* 2.6 35.9 + - - +
437D GLU* 3.7 9.6 + - + -
439D ILE* 1.3 73.6 - - - +
441D ALA* 1.3 57.0 + - - +
443D ILE* 3.6 8.8 + - - +
444D ALA* 3.1 26.3 + - - +
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Residues in contact with ALA 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D THR* 6.1 2.0 - - + +
56D GLY* 4.1 22.8 - - - +
102D ARG* 4.3 17.7 - - + +
437D GLU 2.7 21.3 + - - +
438D ALA* 3.6 4.3 - - - +
440D ASP* 1.3 71.1 - - - +
442D TYR* 1.3 66.0 + - - +
444D ALA* 3.1 16.3 + - - +
445D LEU* 3.1 20.2 + - + +
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Residues in contact with TYR 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D THR* 3.7 32.6 - - + +
310D ALA* 2.8 31.1 + - + -
311D LEU* 3.6 21.8 + - + -
314D PRO* 3.3 19.2 - - - +
366D ASN* 5.3 3.3 - - + +
369D LEU* 3.5 34.3 - - + -
418D LEU* 4.5 5.6 - - + -
421D LEU* 4.4 10.1 - - + -
438D ALA 3.2 10.6 + - - +
439D ILE* 3.7 10.3 - - - +
441D ALA* 1.3 78.4 - - - +
443D ILE* 1.3 67.2 + - - +
445D LEU* 3.1 15.7 + - + +
446D ARG* 3.1 45.1 + - + +
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Residues in contact with ILE 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418D LEU* 4.0 18.7 - - + +
421D LEU* 3.8 19.1 - - + -
422D ASP* 4.0 30.5 - - + +
425D ARG* 4.4 6.3 - - - +
439D ILE* 3.1 34.8 + - + +
440D ASP* 3.8 8.3 - - - +
442D TYR* 1.3 80.5 - - - +
444D ALA* 1.3 58.4 + - - +
446D ARG* 3.5 1.2 + - - +
447D ARG* 2.9 67.3 + - + +
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Residues in contact with ALA 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440D ASP 3.1 14.6 + - - +
441D ALA* 3.1 14.0 + - - +
443D ILE* 1.3 77.6 - - - +
445D LEU* 1.3 62.5 + - + +
447D ARG* 3.3 7.8 + - - +
448D GLU* 3.2 22.2 + - - +
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Residues in contact with LEU 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D THR* 3.6 35.4 - - + -
25D LYS* 4.2 27.0 + - + +
55D GLY* 4.1 15.7 - - - -
56D GLY* 3.8 22.9 - - - +
441D ALA 3.1 12.9 + - - +
442D TYR* 3.1 7.4 + - + +
444D ALA* 1.3 76.2 - - + +
446D ARG* 1.3 69.5 + - + +
448D GLU* 2.9 40.4 - - - +
449D GLU* 3.2 11.5 + - - +
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Residues in contact with ARG 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LYS* 3.1 47.7 + - - +
314D PRO* 3.3 37.4 + - + +
315D THR* 5.3 1.2 - - - +
364D ALA 4.6 2.6 + - - -
366D ASN 5.3 0.2 - - - +
414D LEU* 4.2 8.0 - - + +
418D LEU* 3.9 23.1 - - + -
442D TYR* 3.1 51.9 + - + +
443D ILE 3.9 0.2 - - - +
445D LEU* 1.3 82.5 - - + +
447D ARG* 1.3 60.8 + - - +
449D GLU* 3.0 38.8 + - - +
450D ASP* 2.8 31.2 + - - +
465J TYR* 4.5 6.3 - - - -
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Residues in contact with ARG 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415D GLU* 3.7 19.7 + - - +
418D LEU* 3.6 16.6 - - + +
419D ASN* 3.5 39.8 - - - +
422D ASP* 5.7 4.0 + - - +
443D ILE* 2.9 46.0 + - + +
444D ALA* 3.4 9.2 - - - +
445D LEU 3.1 0.2 - - - -
446D ARG* 1.3 77.6 - - - +
448D GLU* 1.3 56.9 + - - +
450D ASP* 3.5 10.7 + - - +
451D ASP* 3.0 36.6 + - - +
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Residues in contact with GLU 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LYS* 5.0 3.5 + - - +
444D ALA 3.2 8.9 + - - +
445D LEU* 2.9 43.1 - - - +
447D ARG* 1.3 75.6 - - - +
449D GLU* 1.3 67.9 + - + +
451D ASP* 3.3 25.1 - - + +
452D ARG* 3.3 13.7 + - - +
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Residues in contact with GLU 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LYS* 2.7 31.9 + - - +
314D PRO 4.0 0.7 - - - +
414D LEU* 5.4 0.4 - - + +
445D LEU 3.2 10.4 + - - +
446D ARG* 3.0 43.7 + - - +
448D GLU* 1.3 76.9 - - + +
450D ASP* 1.3 66.0 + - - +
452D ARG* 3.0 17.9 + - - +
453D VAL* 3.4 9.2 + - - +
464J LEU* 3.6 28.2 - - + +
465J TYR* 3.4 33.1 + - - +
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Residues in contact with ASP 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D THR* 3.6 24.6 - - - +
413D SER* 6.0 0.3 - - - -
414D LEU* 3.8 23.2 + - + +
415D GLU* 4.3 20.0 + - - +
418D LEU* 5.4 1.8 - - + -
446D ARG 2.8 16.8 + - - +
447D ARG* 3.8 12.9 - - - +
449D GLU* 1.3 75.2 - - - +
451D ASP* 1.3 58.0 + - - +
453D VAL* 3.2 2.9 + - - +
454D ARG* 2.8 67.3 + - - +
465J TYR* 4.6 0.6 + - - -
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Residues in contact with ASP 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447D ARG* 3.0 27.1 + - - +
448D GLU* 3.3 17.8 - - - +
449D GLU 3.1 0.4 - - - -
450D ASP* 1.3 77.4 - - - +
452D ARG* 1.3 54.1 + - + +
454D ARG* 2.8 28.5 + - - +
455D MET* 2.7 55.2 + - - +
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Residues in contact with ARG 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ALA* 4.6 7.1 + - - +
448D GLU 3.5 14.6 - - - +
449D GLU* 3.0 10.1 + - - +
451D ASP* 1.3 76.8 - - + +
453D VAL* 1.3 62.6 + - - +
455D MET* 3.8 3.4 - - - +
456D THR* 2.9 39.4 + - - -
261J PHE* 6.0 8.2 - - - -
460J VAL* 4.0 21.9 - - + +
463J GLU* 2.5 40.0 + - - -
464J LEU* 3.5 29.2 - - + +
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Residues in contact with VAL 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D THR* 3.5 29.6 - - + +
320D LYS* 4.4 7.4 - - - +
449D GLU 3.9 4.3 - - - +
450D ASP 3.2 5.6 + - - +
452D ARG* 1.3 76.3 - - - +
454D ARG* 1.3 63.4 + - + +
455D MET 3.3 0.5 + - - -
456D THR* 3.6 15.4 - - - +
320J LYS* 4.1 6.1 + - - -
458J HIS* 4.2 22.1 + - + +
460J VAL* 4.0 13.7 - - + -
461J GLU* 4.0 22.9 - - + +
464J LEU* 3.8 23.6 - - + -
465J TYR* 4.7 0.2 - - + -
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Residues in contact with ARG 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D THR* 6.2 0.4 - - + -
415D GLU* 4.2 18.3 + - - -
450D ASP* 2.8 45.2 + - - +
451D ASP* 2.8 30.4 + - - +
453D VAL* 1.3 79.5 - - + +
455D MET* 1.3 69.1 + - - +
319J TYR 4.9 7.7 + - - +
320J LYS* 3.3 27.0 + - - +
323J VAL* 5.5 5.1 - - - +
412J GLY 5.2 8.7 + - - -
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Residues in contact with MET 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451D ASP* 2.7 41.6 + - - +
452D ARG* 4.1 2.5 - - - +
454D ARG* 1.3 89.0 - - - +
456D THR* 1.3 57.6 - - - +
457D PRO* 3.7 5.5 - - - +
258J LYS* 5.3 1.6 - - - +
261J PHE* 3.7 32.8 - - + +
320J LYS* 3.4 24.1 - - - +
323J VAL* 4.3 37.5 - - + -
324J PRO* 5.9 1.8 - - + +
326J TYR* 5.0 9.9 - - + +
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Residues in contact with THR 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ALA* 4.8 7.5 - - + +
147D SER* 4.7 7.6 - - - +
452D ARG* 2.9 28.8 + - - -
453D VAL 3.6 0.9 + - - +
455D MET* 1.3 77.1 - - - +
457D PRO* 1.3 73.7 - - + +
261J PHE* 4.5 19.7 - - + -
320J LYS* 3.3 11.8 - - - -
458J HIS* 2.8 45.9 - - - +
460J VAL* 3.7 17.7 - - + +
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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
------------------------------------------------------------
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