Contacts of the helix formed by residues 574 - 595 (chain B) in PDB entry 2FJU
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 GLU 574 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573B THR* 1.3 72.1 - - - +
575B LEU* 1.3 67.3 + - + +
578B TYR* 3.0 28.8 + - - +
599B ILE* 4.0 10.3 - - - -
600B TYR 2.9 13.8 + - - +
602B LYS* 3.1 39.1 + - + +
605B ARG* 2.8 45.4 + - - -
611B TYR* 3.4 32.4 - - + +
616B PHE* 3.7 13.8 - - + -
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Residues in contact with LEU 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B SER 4.6 6.1 - - - +
528B ASP* 3.9 21.3 - - + +
573B THR* 2.9 6.8 - - + +
574B GLU* 1.3 84.9 - - + +
576B LYS* 1.3 60.5 + - - +
578B TYR* 3.3 8.5 + - + +
579B ASP* 2.9 29.0 + - - +
602B LYS* 3.9 45.5 - - + +
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Residues in contact with LYS 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B ASP* 5.1 2.6 + - - +
529B GLU* 6.5 0.7 - - + -
554B PHE* 4.7 8.5 - - - -
572B PHE* 3.6 26.2 - - + -
573B THR* 3.0 26.1 - - + +
575B LEU* 1.3 76.5 - - - +
577B ALA* 1.3 58.4 + - - +
579B ASP* 3.2 18.3 + - + +
580B LEU* 2.9 56.7 + - + +
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Residues in contact with ALA 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B PHE* 3.8 8.2 - - + +
573B THR 2.9 16.9 + - - +
576B LYS* 1.3 78.6 - - - +
578B TYR* 1.3 62.1 + - - +
580B LEU* 3.3 4.5 + - - +
581B LEU* 3.1 27.2 + - - +
588B PHE* 3.7 13.5 - - + -
599B ILE* 3.7 24.9 - - + -
616B PHE* 3.5 23.8 - - + -
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Residues in contact with TYR 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B GLU 3.0 21.6 + - - +
575B LEU* 3.6 9.2 - - + +
576B LYS 3.2 0.2 - - - -
577B ALA* 1.3 77.0 - - - +
579B ASP* 1.3 66.1 + - - +
581B LEU* 3.2 8.7 + - + +
582B SER* 3.1 29.3 + - - -
615B MET* 3.4 39.5 - - + -
616B PHE* 4.0 8.4 - + + -
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Residues in contact with ASP 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B LEU 2.9 17.2 + - - +
576B LYS* 3.5 20.2 + - + +
578B TYR* 1.3 82.0 - - + +
580B LEU* 1.3 60.5 + - - +
582B SER* 2.7 26.7 + - - -
583B LYS* 3.0 47.4 + - - +
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Residues in contact with LEU 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B PHE* 4.0 20.0 - - + -
557B PHE* 4.1 15.5 - - + -
572B PHE* 3.6 42.8 - - + -
576B LYS* 2.9 37.4 + - + +
577B ALA* 3.6 5.4 - - - +
578B TYR 3.2 0.2 - - - -
579B ASP* 1.3 78.5 - - + +
581B LEU* 1.3 55.4 + - - +
583B LYS* 4.5 5.8 - - + +
584B ALA* 2.7 41.3 + - + +
588B PHE* 3.8 21.5 - - + -
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Residues in contact with LEU 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B ALA 3.1 19.9 + - - +
578B TYR* 3.2 8.5 + - + +
580B LEU* 1.3 76.3 - - - +
582B SER* 1.3 60.3 - - - +
583B LYS 3.3 0.2 - - - -
585B SER* 3.2 33.7 - - - +
588B PHE* 3.3 29.6 - - + -
589B VAL* 5.8 0.9 - - + -
615B MET* 3.7 46.7 - - + +
616B PHE* 4.3 12.3 - - + -
619B ALA* 3.8 21.1 - - + -
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Residues in contact with SER 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B TYR* 3.1 22.4 + - - -
579B ASP* 2.7 27.5 + - - -
581B LEU* 1.3 78.9 - - - +
583B LYS* 1.3 65.4 + - - +
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Residues in contact with LYS 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B ASP* 3.0 46.7 + - - +
580B LEU* 4.3 6.5 - - + +
582B SER* 1.3 86.3 - - - +
584B ALA* 1.3 61.8 + - + +
585B SER 3.9 1.1 - - - -
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Residues in contact with ALA 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B PHE* 3.9 12.9 - - + -
580B LEU* 2.7 20.4 + - + +
583B LYS* 1.3 78.2 - - + +
585B SER* 1.3 65.0 + - - +
586B VAL 3.3 2.9 - - - -
587B GLN* 3.2 31.5 + - + -
588B PHE* 3.0 21.8 + - - +
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Residues in contact with SER 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B LEU 3.6 1.4 + - - -
581B LEU* 3.2 34.3 + - - +
582B SER 5.2 0.2 - - - -
583B LYS 3.9 0.8 - - - -
584B ALA* 1.3 75.3 - - - +
586B VAL* 1.3 70.8 + - - +
588B PHE* 3.3 4.6 + - - +
589B VAL* 3.1 31.8 + - - +
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Residues in contact with VAL 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B ALA 3.3 0.4 - - - -
585B SER* 1.3 85.3 + - - +
587B GLN* 1.3 73.8 + - - +
589B VAL* 3.5 7.0 + - - +
590B ASP* 3.1 37.3 + - - +
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Residues in contact with GLN 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B PHE* 3.5 28.2 - - + +
558B GLU* 4.9 11.6 + - - +
584B ALA* 3.2 37.9 - - + +
586B VAL* 1.3 93.5 + - - +
588B PHE* 1.3 58.8 + - - +
590B ASP* 3.2 8.5 + - - +
591B TYR* 2.8 31.4 + - - +
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Residues in contact with PHE 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B PHE* 3.4 26.9 - + + -
572B PHE* 3.9 26.0 - + - -
577B ALA* 3.7 25.8 - - + -
580B LEU* 3.8 22.0 - - + -
581B LEU* 3.3 29.2 - - + -
584B ALA 3.0 16.4 + - - +
585B SER 3.3 5.4 + - - +
587B GLN* 1.3 75.8 - - - +
589B VAL* 1.3 63.1 + - - +
591B TYR* 3.2 4.1 + + - +
592B ASN* 3.2 40.1 + - - -
597B SER* 4.0 10.8 - - - -
599B ILE* 4.6 0.2 - - + -
619B ALA* 4.9 1.8 - - + -
621B CYS* 3.8 19.7 - - - -
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Residues in contact with VAL 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B LEU* 5.8 0.9 - - + -
585B SER* 3.1 20.0 + - - +
586B VAL* 3.7 6.7 - - - +
588B PHE* 1.3 78.0 - - - +
590B ASP* 1.3 64.6 + - - +
592B ASN* 3.5 10.6 + - - +
593B LYS* 3.8 24.9 + - - +
618B ASN 5.1 2.2 - - - +
619B ALA* 3.7 31.9 - - + +
657B MET* 6.1 6.3 - - + -
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Residues in contact with ASP 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B VAL* 3.1 27.9 + - - +
587B GLN* 3.2 10.9 + - - +
589B VAL* 1.3 77.3 - - - +
591B TYR* 1.3 66.8 + - - +
593B LYS* 3.1 37.1 + - - +
594B ARG* 3.8 13.6 + - - +
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Residues in contact with TYR 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554B PHE* 4.8 3.6 - + - -
557B PHE* 3.7 28.7 - + + -
560B SER* 3.8 17.0 - - - -
568B VAL 3.9 0.5 + - - -
570B SER* 2.6 30.8 + - - -
572B PHE* 5.4 0.9 - + - -
587B GLN 2.8 17.9 + - - +
588B PHE* 3.2 7.6 + + - +
590B ASP* 1.3 75.4 - - - +
592B ASN* 1.3 70.2 + - - +
593B LYS 3.1 0.2 - - - -
594B ARG* 3.0 29.4 + - - +
595B GLN* 2.8 61.3 + - + +
596B MET 2.8 35.2 + - - -
597B SER* 3.9 9.0 - - - -
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Residues in contact with ASN 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B ASN* 3.2 11.8 - - - +
588B PHE* 3.2 27.5 + - - -
589B VAL 3.9 4.0 - - - +
590B ASP 3.3 0.4 - - - -
591B TYR* 1.3 81.1 - - - +
593B LYS* 1.3 61.7 + - - +
594B ARG 3.2 0.2 - - - -
595B GLN 3.3 10.2 - - - +
597B SER* 2.7 26.6 + - - -
619B ALA 2.8 26.4 + - - +
620B GLY* 3.4 23.8 - - - +
621B CYS* 3.3 11.3 - - - +
622B GLN* 3.3 6.6 + - - -
653B LYS* 3.4 15.8 + - - +
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Residues in contact with LYS 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B ASN* 2.8 14.2 + - - +
320B HIS* 2.9 24.9 + - - +
589B VAL* 3.8 26.9 - - - +
590B ASP* 3.1 24.8 + - - +
591B TYR 3.1 1.0 + - - -
592B ASN* 1.3 75.8 - - - +
594B ARG* 1.3 58.9 + - + +
656B PHE 3.9 17.7 + - - -
657B MET* 3.4 26.5 - - - +
658B ARG 4.5 4.9 - - - +
659B ARG 3.3 25.9 + - - +
660B PRO* 5.1 7.1 - - + +
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Residues in contact with ARG 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B ASN* 3.4 11.9 + - - +
557B PHE 5.0 1.0 + - - -
560B SER* 3.7 7.5 + - - -
561B ALA* 3.5 34.6 - - - +
564B ASN* 3.8 32.8 + - - +
566B SER* 3.3 30.0 - - - +
590B ASP* 3.8 8.9 + - - +
591B TYR* 3.0 27.6 + - - +
593B LYS* 1.3 81.2 - - + +
595B GLN* 1.3 100.5 + - + +
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Residues in contact with GLN 595 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ASN* 4.0 8.3 - - - -
560B SER* 3.7 16.9 + - - +
565B ARG 3.1 26.1 + - - +
566B SER* 3.9 5.2 - - - -
568B VAL* 3.1 30.8 - - - +
570B SER* 4.8 0.3 + - - -
591B TYR* 2.8 41.4 + - + -
592B ASN* 3.3 26.9 - - - +
594B ARG* 1.3 117.4 - - - +
596B MET* 1.3 63.5 + - - +
622B GLN* 3.6 4.0 - - - +
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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