Contacts of the helix formed by residues 542 - 559 (chain A) in PDB entry 5UFL
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 PRO 542 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505A GLN 5.5 6.7 - - - +
507A PRO* 5.0 12.3 - - + -
510A ILE* 4.0 16.4 - - + +
540A ASP 3.4 8.5 - - - +
541A PHE* 1.3 92.6 - - + +
543A ALA* 1.3 64.1 + - - +
544A LEU* 3.2 3.4 - - + +
545A VAL* 3.4 27.5 - - + +
546A LEU* 3.3 19.8 + - - +
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Residues in contact with ALA 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A PHE* 2.9 24.9 + - + +
542A PRO* 1.3 71.9 - - - +
544A LEU* 1.3 58.9 + - + +
546A LEU* 3.5 2.4 + - - +
547A GLY* 3.0 22.5 + - - -
526B GLN* 4.0 2.6 - - - +
529B LEU* 3.4 17.6 - - + +
533B LEU* 4.0 26.5 - - + -
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Residues in contact with LEU 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A PRO* 3.2 2.0 - - + -
543A ALA* 1.3 77.6 - - + +
545A VAL* 1.3 64.3 + - - +
547A GLY 3.3 0.3 + - - -
548A GLU* 3.1 19.2 + - - +
526B GLN* 3.1 42.3 + - - +
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Residues in contact with VAL 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A THR* 6.2 3.4 - - + -
507A PRO* 6.2 1.3 - - + -
510A ILE* 3.9 17.3 - - + -
542A PRO* 3.4 37.1 + - + +
544A LEU* 1.3 76.1 - - - +
546A LEU* 1.3 63.7 + - - +
548A GLU* 3.4 18.3 + - + +
549A SER* 2.9 28.4 + - - -
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Residues in contact with LEU 546 (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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510A ILE* 3.6 37.5 - - + +
513A LEU* 4.0 17.0 - - + -
514A ALA* 4.2 2.9 - - + +
517A LEU* 4.8 0.9 - - + -
532A LEU* 3.4 35.9 - - + -
541A PHE* 3.9 11.9 - - + -
542A PRO 3.3 9.3 + - - +
543A ALA* 3.6 7.2 - - - +
544A LEU 3.3 0.2 - - - -
545A VAL* 1.3 79.6 - - - +
547A GLY* 1.3 56.3 + - - +
549A SER* 3.7 0.2 - - - -
550A ILE* 2.8 62.7 + - + +
529B LEU* 4.2 15.5 - - + -
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Residues in contact with GLY 547 (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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543A ALA 3.0 14.7 + - - -
544A LEU 3.3 4.9 + - - -
546A LEU* 1.3 76.3 - - - +
548A GLU* 1.3 60.1 + - - +
551A ALA* 3.1 26.3 + - - +
522B ARG* 5.0 1.1 - - - +
525B VAL* 3.5 15.0 - - - +
526B GLN* 3.9 16.6 - - - -
529B LEU* 3.8 14.3 - - - +
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Residues in contact with GLU 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A THR* 4.4 21.3 + - + +
544A LEU* 3.1 19.1 + - - +
545A VAL* 3.6 19.7 - - + +
546A LEU 3.3 0.2 - - - -
547A GLY* 1.3 74.2 - - - +
549A SER* 1.3 58.0 + - - +
551A ALA* 3.5 3.9 + - - +
552A ALA* 3.0 31.8 + - - +
522B ARG* 4.2 24.7 - - - +
526B GLN* 4.0 4.7 + - - +
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Residues in contact with SER 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A THR* 4.9 8.6 - - - -
465A LYS 4.0 8.0 + - - -
510A ILE* 4.1 13.2 - - - -
511A THR* 4.1 13.0 + - - -
514A ALA* 3.2 20.6 - - - +
545A VAL* 2.9 18.1 + - - -
546A LEU 3.2 4.0 + - - -
548A GLU* 1.3 74.0 - - - +
550A ILE* 1.3 58.9 + - - +
552A ALA* 3.8 4.3 - - - +
553A ASN* 2.7 43.3 + - - +
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Residues in contact with ILE 550 (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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514A ALA* 4.1 13.9 - - - -
517A LEU* 3.9 25.1 - - + -
518A THR* 3.4 13.6 - - + +
546A LEU* 2.8 50.4 + - + +
547A GLY 4.0 3.6 - - - +
549A SER* 1.3 71.2 - - - +
551A ALA* 1.3 60.4 + - - +
553A ASN 3.3 0.7 + - - -
554A ASN* 2.8 51.2 + - - +
517B LEU* 3.4 19.5 - - + +
525B VAL* 3.8 11.9 - - + -
529B LEU* 4.6 14.1 - - + -
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Residues in contact with ALA 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A GLY 3.1 18.1 + - - +
548A GLU* 3.9 3.6 - - - +
550A ILE* 1.3 76.8 - - - +
552A ALA* 1.3 57.9 + - - +
554A ASN* 3.3 2.1 + - - +
555A ALA* 2.9 29.3 + - - +
519B SER 4.1 11.0 - - - -
520B ASP 3.9 14.7 - - - +
522B ARG* 3.9 30.5 - - + -
525B VAL* 4.0 8.9 - - + +
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Residues in contact with ALA 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A THR* 3.4 24.2 - - + +
466A VAL* 4.0 15.3 - - + +
548A GLU 3.0 19.0 + - - +
549A SER* 3.8 4.0 - - - +
551A ALA* 1.3 76.3 - - - +
553A ASN* 1.3 57.8 + - - +
555A ALA* 3.3 8.4 + - - +
556A TYR* 3.0 28.1 + - - +
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Residues in contact with ASN 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A LYS 3.2 22.6 + - - -
466A VAL* 4.1 4.4 - - - +
467A ALA* 3.0 32.4 + - - +
514A ALA* 3.6 8.9 - - - +
515A PHE* 3.3 16.9 - - - -
518A THR* 3.6 21.8 + - + +
549A SER* 2.7 36.9 + - - +
550A ILE 3.8 2.7 - - - +
552A ALA* 1.3 73.6 - - - +
554A ASN* 1.3 59.5 + - - +
556A TYR* 4.0 2.2 - - - +
557A ARG* 3.1 36.1 + - - +
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Residues in contact with ASN 554 (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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518A THR* 3.2 15.8 - - - +
550A ILE* 2.8 28.9 + - - +
551A ALA 3.6 2.0 - - - +
553A ASN* 1.3 73.9 - - - +
555A ALA* 1.3 65.2 + - - +
557A ARG* 4.9 2.0 - - - -
558A GLN* 3.1 42.8 + - - +
517B LEU 2.9 26.7 + - - -
518B THR* 3.4 9.7 - - - +
519B SER 3.1 26.9 + - - +
520B ASP* 4.4 0.2 - - - -
554B ASN* 3.3 20.4 - - - +
558B GLN* 5.2 1.3 + - - +
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Residues in contact with ALA 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A ALA 2.9 13.8 + - - +
552A ALA* 3.4 12.1 - - - +
554A ASN* 1.3 77.5 - - - +
556A TYR* 1.3 62.3 + - - +
558A GLN* 3.6 3.3 + - - +
559A GLN* 3.3 20.8 + - - +
520B ASP* 3.8 22.3 - - + +
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Residues in contact with TYR 556 (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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466A VAL* 3.1 33.0 - - + -
467A ALA 3.3 23.5 + - - -
468A ASP* 3.5 29.6 + - + +
552A ALA 3.0 11.6 + - - +
553A ASN 4.0 2.0 - - - +
554A ASN 3.4 0.2 - - - -
555A ALA* 1.3 75.0 - - - +
557A ARG* 1.3 75.3 + - + +
559A GLN* 2.9 49.0 + - - +
560A GLU* 3.4 17.5 + - - +
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Residues in contact with ARG 557 (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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467A ALA* 3.4 30.8 + - + +
473A LYS* 4.3 18.0 - - - +
515A PHE* 3.2 27.5 + - - +
518A THR* 2.9 43.1 + - - -
519A SER* 4.5 10.1 + - - +
520A ASP* 5.5 1.0 + - - +
524A GLN* 5.3 2.4 + - - +
553A ASN* 3.1 18.4 + - - +
554A ASN* 4.4 2.0 - - - +
556A TYR* 1.3 91.4 - - + +
558A GLN* 1.3 62.0 + - - +
560A GLU* 3.2 24.8 + - - +
558B GLN* 3.4 34.0 + - - +
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Residues in contact with GLN 558 (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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554A ASN* 3.1 30.8 + - - +
555A ALA 4.0 2.9 - - - +
557A ARG* 1.3 75.7 - - - +
559A GLN* 1.3 56.0 + - - +
560A GLU 3.5 2.9 + - - -
518B THR* 2.8 29.1 + - - -
520B ASP* 3.9 21.7 + - - +
554B ASN* 5.1 1.6 + - - +
557B ARG* 3.5 46.7 + - + +
558B GLN* 3.9 23.6 - - + +
560B GLU* 5.2 5.1 + - - +
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Residues in contact with GLN 559 (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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555A ALA 3.3 10.7 + - - +
556A TYR* 2.9 34.3 + - - +
558A GLN* 1.3 73.4 - - - +
560A GLU* 1.3 75.7 + - - +
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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
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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