Contacts of the helix formed by residues 412 - 430 (chain A) in PDB entry 2FY4
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 SER 412 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A GLN* 3.6 11.2 + - - -
411A CYS* 1.3 71.6 - - - +
413A PRO* 1.3 69.2 - - - +
414A ASP* 4.0 1.6 - - - +
415A ALA* 3.0 19.8 + - - +
416A PHE* 2.9 22.7 + - - +
486A ILE* 4.5 4.4 - - - +
490A THR* 3.7 19.2 + - - -
2000A COA 3.2 42.5 + - - -
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Residues in contact with PRO 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A LYS* 4.0 38.1 - - + -
406A ILE* 3.6 22.2 - - + -
407A LYS* 4.4 7.6 - - + -
411A CYS 3.4 7.8 - - - +
412A SER* 1.3 78.2 - - - +
414A ASP* 1.4 52.6 + - - +
416A PHE* 2.8 5.2 + - + +
417A ILE* 2.7 45.5 + - + +
566A PRO* 5.0 3.6 - - + -
2000A COA 2.8 44.0 - - - +
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Residues in contact with ASP 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A SER* 4.0 2.5 - - - +
413A PRO* 1.4 72.5 - - - +
415A ALA* 1.3 57.5 + - - +
417A ILE* 3.2 8.4 + - - +
418A GLN* 2.8 34.5 + - - +
437A GLU* 2.5 29.6 - - - +
489A GLN* 4.8 0.2 + - - -
493A THR* 4.7 6.5 + - + +
541A GLN* 2.7 32.1 + - - +
564A TYR* 2.6 21.8 + - - -
2000A COA 2.5 43.5 + - - +
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Residues in contact with ALA 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A SER* 3.0 22.5 + - - +
414A ASP* 1.3 75.8 + - - +
416A PHE* 1.3 57.5 + - - +
418A GLN* 3.2 2.6 + - - +
419A VAL* 2.9 35.9 + - - +
486A ILE* 3.9 10.1 - - + +
489A GLN* 3.4 28.2 - - + +
490A THR* 3.4 22.9 - - - +
493A THR* 5.4 1.3 - - - +
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Residues in contact with PHE 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A TYR* 3.3 38.1 - + - -
405A PHE* 4.9 3.4 - + - -
406A ILE* 3.6 33.4 - - + -
409A GLN* 5.0 6.5 - - + -
411A CYS* 4.3 4.3 - - + -
412A SER 2.9 12.3 + - - +
413A PRO 2.8 8.4 + - - +
415A ALA* 1.3 76.1 - - - +
417A ILE* 1.3 59.7 + - - +
419A VAL 3.4 0.7 + - - -
420A ALA* 3.0 22.3 + - - +
482A LEU* 5.2 0.4 - - + -
486A ILE* 3.6 31.3 - - + +
597A LEU* 3.9 15.7 - - + -
600A MET* 3.3 36.6 - - + +
601A ARG 4.7 0.2 - - - -
604A CYS* 4.3 21.3 - - - -
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Residues in contact with ILE 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ILE* 4.5 7.0 - - + -
413A PRO* 2.7 29.7 + - + +
414A ASP 3.7 3.4 - - - +
416A PHE* 1.3 73.9 - - + +
418A GLN* 1.3 65.6 + - - +
420A ALA* 3.0 7.4 + - + +
421A LEU* 2.9 25.8 + - + +
564A TYR* 3.8 35.0 - - + -
566A PRO* 3.7 29.8 - - + -
571A ILE* 3.9 27.4 - - + -
573A PHE* 3.9 25.6 - - + -
597A LEU* 5.3 1.1 - - + -
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Residues in contact with GLN 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A ASP* 2.8 20.1 + - - +
415A ALA 3.5 4.7 - - - +
417A ILE* 1.3 76.8 - - - +
419A VAL* 1.3 62.1 + - - +
421A LEU* 3.3 12.2 + - - +
422A GLN* 3.1 26.3 + - - +
435A THR* 4.6 4.3 - - - +
437A GLU* 3.0 31.2 - - - +
454A SER* 2.5 25.7 + - - +
489A GLN* 3.4 22.0 - - - +
537A LEU* 6.0 0.2 - - - +
539A THR* 3.1 28.1 + - - +
564A TYR* 2.8 30.4 + - - +
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Residues in contact with VAL 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ALA 2.9 19.9 + - - +
416A PHE 3.6 5.2 - - - +
417A ILE 3.2 0.2 - - - -
418A GLN* 1.3 73.2 - - - +
420A ALA* 1.3 67.4 + - - +
422A GLN* 3.1 10.7 + - + +
423A LEU* 3.0 20.6 + - - +
459A ALA* 5.7 6.1 - - + -
462A PHE* 3.9 32.0 - - + -
482A LEU* 5.2 1.3 - - + +
485A ALA* 4.0 17.9 - - + +
486A ILE* 3.9 30.3 - - + +
489A GLN* 4.3 8.3 - - + +
600A MET* 3.9 11.0 - - + -
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Residues in contact with ALA 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A PHE 3.0 12.7 + - - +
417A ILE* 3.0 11.4 + - + +
419A VAL* 1.3 76.3 - - - +
421A LEU* 1.3 58.0 + - + +
423A LEU* 3.2 2.1 + - - -
424A ALA* 2.8 28.9 + - - +
573A PHE* 5.9 0.4 - - + -
593A VAL* 5.2 4.7 - - + +
596A SER* 3.5 11.0 - - - -
597A LEU* 3.6 35.4 - - + -
600A MET* 3.5 17.2 - - - -
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Residues in contact with LEU 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A ILE* 2.9 23.3 + - + +
418A GLN* 3.5 20.2 - - - +
419A VAL 3.2 0.2 - - - -
420A ALA* 1.3 78.3 - - + +
422A GLN* 1.3 56.1 + - - +
424A ALA* 3.3 4.1 + - - +
425A PHE* 2.9 30.3 + - - +
537A LEU* 4.3 16.4 - - + +
539A THR* 4.3 14.6 - - + -
562A ALA* 4.5 9.0 - - + -
564A TYR* 4.1 29.2 - - + -
573A PHE* 4.1 13.9 - - + -
589A PHE* 4.0 18.5 - - + -
593A VAL* 3.9 25.1 - - + -
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Residues in contact with GLN 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A GLN* 3.1 16.3 + - - +
419A VAL* 3.1 12.0 + - + +
421A LEU* 1.3 76.4 - - - +
423A LEU* 1.3 57.2 + - - +
425A PHE* 3.3 5.6 + - - +
426A TYR* 2.9 30.3 + - - +
432A LEU* 3.2 29.2 - - + +
433A VAL 4.8 0.5 + - - +
435A THR* 3.1 37.7 + - - +
454A SER* 3.6 27.6 - - - +
455A ALA* 3.4 17.8 - - - +
459A ALA* 4.2 13.5 - - + -
463A VAL* 4.0 5.8 - - + -
537A LEU* 3.8 9.2 - - - +
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Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A VAL 3.0 12.7 + - - +
420A ALA* 3.6 7.2 - - - +
422A GLN* 1.3 75.2 - - - +
424A ALA* 1.3 65.9 + - - +
426A TYR 3.3 0.2 + - - -
427A ARG* 2.9 38.3 + - + +
462A PHE* 4.0 23.1 - - + -
463A VAL* 3.5 26.8 - - + +
466A VAL* 3.7 33.0 - - + -
467A THR* 4.2 10.3 - - + -
596A SER* 3.5 34.3 - - - +
599A ASP* 4.6 4.9 - - + -
600A MET* 4.5 3.8 - - + -
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Residues in contact with ALA 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A ALA 2.8 17.1 + - - +
421A LEU 3.6 5.6 - - - +
423A LEU* 1.3 77.4 - - - +
425A PHE* 1.3 64.0 + - - +
427A ARG* 3.3 4.7 - - - +
428A LEU* 3.2 20.8 + - - +
589A PHE* 4.0 7.1 - - + -
592A ALA* 3.5 35.6 - - + +
593A VAL* 3.6 18.8 - - + +
596A SER* 3.1 7.9 + - - -
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Residues in contact with PHE 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A LEU 2.9 18.0 + - - +
422A GLN* 3.6 7.2 - - - +
424A ALA* 1.3 77.6 - - - +
426A TYR* 1.3 57.3 + - - +
428A LEU 3.3 0.2 + - - -
429A HIS* 2.9 60.6 + + + +
431A ARG* 3.0 33.9 - - + -
432A LEU* 4.6 5.2 - - + -
433A VAL* 3.7 40.8 - - + -
536A VAL* 4.0 16.2 - - + -
537A LEU* 4.2 21.3 - - + -
560A TYR* 3.8 24.9 - + - -
589A PHE* 3.8 10.2 - + + -
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Residues in contact with TYR 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A GLN 2.9 17.0 + - - +
423A LEU 3.9 1.1 - - - +
425A PHE* 1.3 75.8 - - - +
427A ARG* 1.3 61.5 - - - +
430A ARG* 2.7 50.7 + - + -
431A ARG* 3.4 44.0 - - - -
432A LEU* 3.7 5.6 - - + +
460A LEU* 4.0 16.4 - - + -
463A VAL* 3.5 35.7 - - + -
464A ARG* 3.6 25.2 + - + +
467A THR* 3.2 29.8 - - + -
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Residues in contact with ARG 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A LEU* 2.9 25.4 + - + +
424A ALA* 3.3 11.4 - - - +
426A TYR* 1.3 73.3 - - - +
428A LEU* 1.3 63.5 + - - +
430A ARG* 3.1 24.2 + - - +
466A VAL* 5.2 4.4 - - - +
467A THR* 3.9 25.7 - - + +
592A ALA* 3.8 19.3 - - + +
595A GLU* 3.4 24.4 + - - +
596A SER* 3.3 41.9 + - - +
599A ASP* 2.9 29.7 + - - -
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Residues in contact with LEU 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A ALA 3.2 16.6 + - - +
425A PHE 3.8 1.8 - - - +
426A TYR 3.1 0.6 - - - -
427A ARG* 1.3 81.2 - - - +
429A HIS* 1.3 88.7 + - + +
430A ARG* 3.7 3.7 + - - +
560A TYR* 3.4 12.6 - - - +
585A SER* 5.3 0.9 - - - +
588A LYS* 3.9 35.9 - - + +
589A PHE* 4.1 25.4 - - + +
592A ALA* 4.6 6.7 - - + -
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Residues in contact with HIS 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A PHE* 2.9 59.5 + + + +
428A LEU* 1.3 94.0 + - + +
430A ARG* 1.3 74.1 + - - +
431A ARG* 3.5 11.8 + - + +
560A TYR* 2.8 30.7 + + - -
583A ALA* 3.0 34.9 + - + +
584A THR* 4.4 1.3 - - + -
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Residues in contact with ARG 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A TYR* 2.7 43.7 + - - -
427A ARG* 3.1 30.6 + - - +
428A LEU 4.9 3.0 + - - +
429A HIS* 1.3 75.1 - - - +
431A ARG* 1.3 62.8 + - - +
467A THR* 3.3 41.3 + - - +
468A ASP* 5.7 0.2 - - - +
469A HIS* 6.1 1.0 + - - -
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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
------------------------------------------------------------
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