Contacts of the helix formed by residues 522 - 540 (chain A) in PDB entry 5LGT
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 522 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519A VAL* 4.2 13.4 - - - +
521A LEU* 1.3 77.6 - - - +
523A SER* 1.3 66.8 + - - +
524A ARG* 2.8 21.7 + - - +
525A ASP* 2.8 25.6 + - - -
526A ARG* 3.0 19.9 + - - +
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Residues in contact with SER 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A SER* 1.3 71.6 + - - +
524A ARG* 1.3 66.9 + - - -
526A ARG* 3.3 6.8 + - - +
527A GLN* 2.9 34.5 + - - +
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Residues in contact with ARG 524 (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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364A GLU* 2.6 46.4 + - + +
366A ASN* 5.7 1.6 - - - +
368A GLN* 6.0 1.4 - - - +
369A ALA 5.2 0.6 + - - -
371A PRO* 4.2 18.0 - - - +
374A LYS* 3.2 35.0 - - - +
522A SER* 2.8 13.6 + - - +
523A SER* 1.3 73.8 - - - +
525A ASP* 1.3 69.0 + - - +
527A GLN* 3.1 17.3 + - - +
528A ILE* 3.1 27.7 + - + +
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Residues in contact with ASP 525 (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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374A LYS* 2.5 36.8 + - - +
378A VAL* 4.1 14.9 - - + +
519A VAL* 5.4 1.7 - - - +
520A TYR 4.8 1.0 - - - +
521A LEU* 3.4 27.5 - - + +
522A SER* 2.8 35.4 + - - +
523A SER 3.2 0.6 - - - -
524A ARG* 1.3 75.4 - - - +
526A ARG* 1.3 51.7 + - - +
528A ILE* 3.1 5.4 + - - +
529A LEU* 2.8 35.5 + - - +
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Residues in contact with ARG 526 (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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413A GLU* 6.1 4.4 - - - +
416A ILE* 3.3 34.4 - - - +
521A LEU* 4.3 16.3 - - + +
522A SER 3.0 17.2 + - - +
523A SER* 3.8 6.1 - - - +
525A ASP* 1.3 75.3 - - - +
527A GLN* 1.3 57.9 + - + +
529A LEU* 3.7 12.5 - - - +
530A ASP* 2.9 57.8 + - - +
533A PHE* 3.9 10.9 - - - -
685A THR* 3.5 25.7 + - - +
688A ARG* 4.4 4.8 - - - +
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Residues in contact with GLN 527 (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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364A GLU* 6.0 4.9 - - + +
365A ALA* 5.6 4.6 - - - +
523A SER* 2.9 29.0 + - - +
524A ARG* 3.1 23.9 + - - +
526A ARG* 1.3 74.0 - - + +
528A ILE* 1.3 65.6 + - + +
530A ASP* 3.4 12.6 + - - +
531A TRP 3.3 14.7 + - - -
681A VAL* 3.3 17.9 - - + +
682A GLY 4.1 13.0 + - - +
683A SER* 3.7 36.6 + - - +
684A THR* 5.7 1.8 - - - +
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Residues in contact with ILE 528 (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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362A LEU* 4.1 23.1 - - + -
364A GLU* 4.5 12.1 - - + +
370A VAL* 3.8 39.0 - - + -
374A LYS* 4.2 20.2 - - + -
375A ASP* 5.5 3.1 - - - -
378A VAL* 3.8 24.7 - - + -
524A ARG 3.3 14.4 - - - +
525A ASP 3.1 6.8 + - - +
527A GLN* 1.3 75.3 - - + +
529A LEU* 1.3 66.4 + - - +
531A TRP* 2.9 20.2 + - - +
532A HIS* 3.3 9.4 + - + +
681A VAL* 4.1 15.5 - - + -
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Residues in contact with LEU 529 (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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378A VAL* 3.5 16.9 - - + +
381A GLU* 5.3 1.8 - - + -
382A PHE* 3.7 40.2 - - + +
385A LEU* 3.7 18.8 - - + -
416A ILE* 4.2 7.2 - - + -
521A LEU* 4.0 25.8 - - + -
525A ASP 2.8 16.7 + - - +
526A ARG* 3.7 12.3 - - - +
528A ILE* 1.3 78.0 - - - +
530A ASP* 1.3 61.4 + - - +
532A HIS* 3.1 6.1 + - - +
533A PHE* 3.1 46.9 + - + -
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Residues in contact with ASP 530 (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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526A ARG* 2.9 48.4 + - - +
527A GLN* 3.4 15.2 - - - +
528A ILE 3.2 0.4 - - - -
529A LEU* 1.3 74.7 - - - +
531A TRP* 1.3 57.8 + - - +
533A PHE* 3.3 4.8 + - - -
534A ALA 2.8 22.9 + - - -
682A GLY 5.6 0.2 - - - +
684A THR 3.6 4.7 - - - +
685A THR* 2.8 41.1 + - - -
688A ARG* 3.2 37.5 + - + +
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Residues in contact with TRP 531 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A CYS* 4.2 15.7 - - + -
362A LEU* 3.5 34.5 - - + -
527A GLN 3.3 7.9 + - - +
528A ILE* 2.9 16.1 + - - +
530A ASP* 1.3 76.7 - - - +
532A HIS* 1.3 97.1 + + + +
534A ALA* 2.8 23.2 + - - +
535A ASN* 2.8 32.8 + - + -
679A GLY* 3.9 9.8 - - - -
680A HIS 3.0 30.6 + - - +
681A VAL* 4.2 11.9 - - + -
682A GLY 5.4 1.1 - - - +
688A ARG* 4.7 3.1 - - - +
692A PHE* 2.8 42.0 + + + -
693A LEU* 4.6 6.3 - - + -
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Residues in contact with HIS 532 (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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362A LEU* 4.0 12.5 - - + +
375A ASP* 4.7 4.7 + - - -
378A VAL* 4.4 5.2 - - + -
379A GLU* 3.5 47.6 + - + +
382A PHE* 3.6 53.9 - + + -
528A ILE* 3.3 25.6 - - + +
529A LEU* 3.1 8.1 + - - +
531A TRP* 1.3 105.2 - + - +
533A PHE* 1.3 59.8 + - - +
535A ASN* 3.5 7.5 - - - +
536A LEU 3.4 14.7 + - - -
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Residues in contact with PHE 533 (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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382A PHE* 4.0 26.9 - + - -
385A LEU* 4.4 7.2 - - + -
412A LEU* 3.5 31.4 - - + -
416A ILE* 4.3 10.8 - - + -
526A ARG* 3.9 14.6 - - - -
529A LEU* 3.1 52.4 + - + -
530A ASP* 3.5 7.4 - - - +
532A HIS* 1.3 73.8 - - - +
534A ALA* 1.3 65.2 + - - +
536A LEU* 3.0 16.0 + - + +
537A GLU* 3.0 17.9 + - - +
544A LEU* 3.9 16.3 - - + +
688A ARG* 3.0 36.8 - - - +
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Residues in contact with ALA 534 (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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530A ASP 2.8 13.3 + - - +
531A TRP* 2.8 13.8 + - - +
533A PHE* 1.3 70.3 - - - +
535A ASN* 1.3 52.4 + - - +
537A GLU* 2.8 14.8 + - - +
538A PHE* 2.6 34.7 + - - +
688A ARG* 3.5 37.8 - - + +
689A GLY* 4.1 4.7 - - - +
692A PHE* 3.7 16.0 - - + -
708A ALA* 4.1 1.6 - - - +
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Residues in contact with ASN 535 (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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382A PHE* 6.3 0.4 - - + -
531A TRP* 2.8 26.6 + - + +
532A HIS* 3.5 14.8 - - - +
534A ALA* 1.3 78.2 - - - +
536A LEU* 1.3 56.4 + - - +
538A PHE* 3.2 18.2 - - - +
539A ALA* 2.9 26.3 + - - +
692A PHE* 3.3 27.5 - - + -
693A LEU* 3.6 18.8 - - - +
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Residues in contact with LEU 536 (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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382A PHE* 4.3 20.2 - - + -
386A LEU* 4.3 21.1 - - + -
408A LEU* 3.9 20.6 - - + -
412A LEU* 5.3 0.7 - - + -
532A HIS 3.4 7.6 + - - +
533A PHE* 3.0 11.7 + - + +
535A ASN* 1.3 75.0 - - - +
537A GLU* 1.3 60.6 + - - +
539A ALA* 3.5 5.1 + - + +
540A ASN* 2.8 44.0 + - - +
544A LEU* 3.9 27.0 - - + +
552A TRP* 4.2 20.6 - - + -
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Residues in contact with GLU 537 (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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533A PHE 3.0 17.0 - - - +
534A ALA* 2.8 9.3 + - - +
536A LEU* 1.3 73.6 - - - +
538A PHE* 1.3 59.9 + - - +
541A ALA* 2.9 26.9 + - - -
542A THR 3.2 17.4 + - - +
543A PRO* 3.1 10.1 - - - +
544A LEU* 2.6 41.2 + - + +
688A ARG* 3.2 36.1 + - - +
689A GLY 5.6 0.3 + - - -
708A ALA* 4.1 2.4 - - - +
709A GLY* 3.6 28.3 + - - +
710A GLU* 4.3 5.6 + - - +
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Residues in contact with PHE 538 (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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534A ALA 2.6 9.3 + - - +
535A ASN* 3.2 30.1 - - - +
537A GLU* 1.3 71.3 - - - +
539A ALA* 1.3 76.0 + - + +
541A ALA* 3.0 12.7 + - - +
659A LEU* 3.6 21.1 - - + +
661A LYS* 6.0 0.4 - - - -
692A PHE* 3.4 24.9 - + + -
693A LEU* 4.6 4.0 - - + -
695A TRP* 3.7 16.8 - + - -
706A LEU* 3.1 27.8 - - + -
708A ALA* 3.6 11.1 - - + +
761A TYR* 3.5 7.3 + - - -
902A 6W3 3.4 62.6 - + - -
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Residues in contact with ALA 539 (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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535A ASN 2.9 12.4 + - - +
536A LEU* 3.5 8.7 + - + +
538A PHE* 1.3 78.3 - - + +
540A ASN* 1.3 69.6 + - - +
761A TYR* 2.7 19.9 + - - -
902A 6W3 3.2 54.1 - - + +
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Residues in contact with ASN 540 (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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536A LEU* 2.8 32.9 + - - +
539A ALA* 1.3 84.5 - - - +
541A ALA* 1.3 70.7 + - - +
542A THR* 3.1 10.3 + - + +
547A LEU* 4.0 32.3 - - + +
552A TRP* 3.8 34.1 - - - +
761A TYR* 4.0 5.5 - - - +
763A TYR* 3.9 14.0 - - + +
902A 6W3 4.0 24.3 - - - +
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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