Contacts of the helix formed by residues 522 - 538 (chain C) in PDB entry 4UQJ
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 ALA 522 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518C LEU 4.0 3.8 - - - -
519C ASP 3.8 6.4 + - - +
520C PRO 3.7 4.4 + - - -
521C LEU* 1.3 74.9 - - - +
523C TYR* 1.3 67.0 + - - +
524C GLU* 3.4 17.0 - - + +
525C ILE* 2.9 39.2 + - + +
526C TRP* 3.0 11.8 + - - -
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Residues in contact with TYR 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515C PHE* 3.4 30.1 - + - +
518C LEU* 3.5 45.9 - - + +
519C ASP* 4.3 10.9 + - - -
521C LEU 3.7 0.6 + - - -
522C ALA* 1.3 73.1 - - - +
524C GLU* 1.3 71.7 + - - +
526C TRP* 3.5 11.6 + + - +
527C MET* 3.0 33.0 + - + +
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Residues in contact with GLU 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C ALA* 3.4 19.7 - - + +
523C TYR* 1.3 88.2 + - - +
525C ILE* 1.3 59.7 + - + +
527C MET* 3.5 8.6 + - - +
528C CYS* 3.2 32.7 + - - -
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Residues in contact with ILE 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520C PRO 5.4 1.8 - - - +
521C LEU* 3.3 26.5 - - + -
522C ALA* 2.9 29.5 + - + +
524C GLU* 1.3 77.4 - - + +
526C TRP* 1.3 64.4 + - - +
527C MET 3.1 1.8 - - - -
528C CYS* 3.4 4.6 + - - +
529C ILE* 3.0 24.1 + - - +
612C ILE* 4.8 5.2 - - + -
790D SER 6.0 3.4 - - - +
792D VAL* 3.5 48.9 - - + -
796D PHE* 4.5 5.6 - - + -
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Residues in contact with TRP 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B PHE* 3.9 35.9 - + - -
611B ILE* 4.8 5.8 - - + -
517C PHE* 4.2 27.8 - + - -
518C LEU* 4.2 19.8 + - + +
521C LEU* 2.6 68.2 + - + +
522C ALA 3.0 18.1 + - - -
523C TYR* 3.8 11.9 - + - +
525C ILE* 1.3 75.0 - - - +
527C MET* 1.3 60.0 + - + +
529C ILE* 2.9 37.3 - - + +
530C VAL* 3.1 20.6 - - + +
616C TYR* 4.6 6.3 - + - -
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Residues in contact with MET 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523C TYR* 3.0 23.3 + - + +
524C GLU* 3.5 10.1 - - - +
525C ILE 3.1 0.4 - - - -
526C TRP* 1.3 76.3 - - - +
528C CYS* 1.3 61.3 + - - +
530C VAL* 2.8 25.8 + - + +
531C PHE* 2.8 50.2 + - + -
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Residues in contact with CYS 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524C GLU* 3.2 18.3 + - - +
525C ILE* 3.4 2.7 + - - +
527C MET* 1.3 81.6 - - - +
529C ILE* 1.3 57.3 + - - +
531C PHE* 3.7 12.6 - - - +
532C ALA* 2.8 27.0 + - - +
796D PHE* 3.3 32.8 - - + -
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Residues in contact with ILE 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C LEU* 5.3 5.6 - - + -
525C ILE* 3.0 17.0 + - + +
526C TRP* 2.9 42.4 - - + +
528C CYS* 1.3 77.9 - - - +
530C VAL* 1.3 61.6 + - + +
532C ALA* 4.7 0.4 - - - -
533C TYR* 3.1 23.7 + - - +
605C TRP* 4.0 8.4 - - + -
608C PHE* 3.8 13.7 - - + -
609C THR* 5.6 5.6 - - - +
612C ILE* 3.5 38.4 - - + -
796D PHE* 3.4 11.6 - - + -
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Residues in contact with VAL 530 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526C TRP* 3.1 20.9 - - + +
527C MET* 2.8 13.7 + - + +
529C ILE* 1.3 84.1 - - + +
531C PHE* 1.3 67.0 + - + +
532C ALA 3.3 0.2 - - - -
533C TYR* 3.1 22.7 - - + +
534C ILE* 3.1 21.0 + - + +
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Residues in contact with PHE 531 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527C MET* 2.8 64.4 + - + -
528C CYS* 3.7 13.0 - - - +
530C VAL* 1.3 79.7 - - + +
532C ALA* 1.3 57.3 + - - +
534C ILE* 3.2 21.9 - - + +
535C GLY* 2.8 24.3 + - - -
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Residues in contact with ALA 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528C CYS 2.8 16.2 + - - +
529C ILE 4.5 1.6 - - - +
531C PHE* 1.3 75.1 - - - +
533C TYR* 1.3 59.6 + - - +
535C GLY* 3.5 3.9 - - - +
536C VAL* 3.0 35.0 + - + +
605C TRP* 3.9 7.0 - - + -
608C PHE* 5.0 0.2 - - + -
796D PHE* 4.0 14.6 - - + -
799D LEU* 3.9 26.2 - - + -
803D LEU* 6.2 2.0 - - + -
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Residues in contact with TYR 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529C ILE 3.1 18.7 + - - +
530C VAL* 3.1 18.2 - - + +
532C ALA* 1.3 79.7 - - - +
534C ILE* 1.3 77.4 + - + +
536C VAL* 3.3 4.0 + - - +
537C SER* 3.2 21.8 + - - -
580C SER* 3.3 10.3 + - - -
583C ALA* 3.2 39.2 - - + +
584C PHE* 2.9 26.5 + - - +
585C MET 5.2 0.4 - - - -
605C TRP* 3.6 24.4 - + + -
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Residues in contact with ILE 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530C VAL* 3.1 18.1 + - + +
531C PHE* 3.2 30.5 - - + +
533C TYR* 1.3 88.7 - - + +
535C GLY* 1.3 58.2 + - - +
536C VAL 3.1 1.1 - - - -
537C SER* 3.2 13.3 + - - +
538C VAL* 3.1 30.7 + - - +
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Residues in contact with GLY 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531C PHE 2.8 18.3 + - - -
532C ALA* 3.2 7.6 + - - -
533C TYR 3.1 1.0 - - - -
534C ILE* 1.3 80.2 - - - +
536C VAL* 1.3 57.7 + - - +
538C VAL* 3.2 10.4 - - - +
539C VAL* 3.1 26.3 - - - +
803D LEU* 4.4 6.8 - - - +
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Residues in contact with VAL 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532C ALA 3.0 18.6 + - - +
533C TYR 3.3 4.0 + - - +
535C GLY* 1.3 79.2 - - - +
537C SER* 1.3 56.9 + - - +
538C VAL 3.0 4.9 - - - -
539C VAL* 3.2 4.7 + - - +
540C LEU* 2.9 40.5 + - + +
583C ALA* 6.5 1.3 - - + -
601C VAL* 3.6 25.8 - - + -
605C TRP* 3.6 36.6 - - + -
799D LEU* 4.8 3.6 - - + -
803D LEU* 4.0 23.3 - - + -
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Residues in contact with SER 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533C TYR* 3.2 9.6 + - - -
534C ILE* 3.2 26.3 + - - +
536C VAL* 1.3 77.6 - - - +
538C VAL* 1.3 57.1 + - - +
540C LEU* 4.6 2.9 - - - -
541C PHE* 3.2 22.8 + - - +
576C SER* 5.4 2.9 - - - +
579C PHE* 3.5 37.6 - - - +
580C SER* 4.5 5.6 - - - -
583C ALA* 4.1 11.2 - - - +
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Residues in contact with VAL 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534C ILE 3.1 19.7 + - - +
535C GLY* 3.2 17.7 - - - +
537C SER* 1.3 79.8 - - - +
539C VAL* 1.3 69.9 + - + +
540C LEU 3.4 0.4 - - - -
541C PHE* 3.3 15.5 + - + +
542C LEU* 3.2 31.6 + - + +
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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