Contacts of the helix formed by residues 525 - 548 (chain A) in PDB entry 1OMW
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 VAL 525 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ILE* 4.1 19.5 - - + -
177A TRP* 4.7 1.3 - - + -
212A ASP 4.1 6.5 - - - +
213A THR* 3.8 43.7 - - + +
521A VAL* 3.2 11.7 + - + -
524A THR* 1.3 83.9 + - - +
526A PHE* 1.3 68.6 + - - +
527A ASP 3.4 1.6 - - - -
528A THR* 3.1 13.2 + - - +
529A ILE* 3.0 37.3 + - + +
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Residues in contact with PHE 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 3.8 28.5 - - + -
66A LEU* 3.7 35.7 - - + -
67A LEU* 4.3 17.3 - - + -
177A TRP* 3.5 44.0 - + - -
521A VAL* 3.1 34.9 + - + +
522A ALA* 3.8 10.3 - - - +
524A THR 3.5 1.4 - - - -
525A VAL* 1.3 77.9 - - - +
527A ASP* 1.3 74.8 + - - +
529A ILE* 3.9 0.7 - - - +
530A ASN* 3.0 50.8 + - - -
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Residues in contact with ASP 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 5.7 0.7 - - - +
522A ALA 5.5 3.1 + - - +
524A THR 5.0 1.6 + - - +
525A VAL 3.4 0.6 - - - -
526A PHE* 1.3 92.0 - - - +
528A THR* 1.3 60.7 + - + +
530A ASN* 3.3 5.8 + - - +
531A ALA* 3.0 28.8 + - - +
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Residues in contact with THR 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A THR 4.7 3.6 + - - +
525A VAL* 3.1 21.6 + - - +
527A ASP* 1.3 78.1 - - + +
529A ILE* 1.3 61.1 + - - +
531A ALA* 3.8 7.1 + - - +
532A GLU* 3.1 28.9 + - - +
535A ARG* 5.5 0.9 + - - -
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Residues in contact with ILE 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS* 3.7 31.6 - - + +
32A ILE* 4.3 20.2 - - + +
33A LEU* 6.0 0.4 - - - -
34A LEU* 4.1 18.4 - - + +
177A TRP* 3.7 25.4 - - + -
525A VAL* 3.0 37.4 + - + +
526A PHE 3.9 2.5 - - - +
528A THR* 1.3 80.5 - - - +
530A ASN* 1.3 57.0 + - - +
531A ALA 3.2 1.6 - - - -
532A GLU* 3.4 8.7 - - + +
533A THR* 2.7 43.9 + - + +
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Residues in contact with ASN 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 4.6 0.3 - - - +
67A LEU* 4.7 6.7 - - - +
173A ARG* 3.4 28.5 + - - +
177A TRP* 2.9 24.0 + - - -
526A PHE* 3.0 56.6 + - - +
527A ASP* 3.8 6.7 + - - +
529A ILE* 1.3 77.8 - - - +
531A ALA* 1.3 59.1 + - - +
533A THR* 4.2 0.2 - - - -
534A ASP* 3.1 33.4 + - - +
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Residues in contact with ALA 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ASP 3.0 16.5 + - - +
528A THR* 3.9 7.4 - - - +
530A ASN* 1.3 74.8 - - - +
532A GLU* 1.3 65.6 + - - +
534A ASP* 3.7 8.4 - - - +
535A ARG* 3.4 28.7 + - - +
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Residues in contact with GLU 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS* 3.6 25.3 + - - +
528A THR* 3.1 21.7 + - - +
529A ILE* 3.3 14.6 + - + +
531A ALA* 1.3 77.7 - - - +
533A THR* 1.3 66.8 + - + +
534A ASP 3.1 0.2 - - - -
535A ARG* 3.0 43.2 + - - +
536A LEU* 3.2 21.1 + - + +
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Residues in contact with THR 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 6.0 4.0 - - + -
34A LEU* 3.6 44.2 - - + +
173A ARG* 4.0 11.3 - - - -
529A ILE* 2.7 25.1 + - + +
532A GLU* 1.3 81.7 - - + +
534A ASP* 1.3 65.1 + - - +
536A LEU* 3.6 24.7 - - + +
537A GLU* 3.2 38.8 + - - +
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Residues in contact with ASP 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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170A LYS* 5.1 9.8 + - - -
173A ARG* 2.8 32.3 + - - +
530A ASN* 3.1 23.9 + - - +
531A ALA* 3.7 9.0 - - - +
532A GLU 3.1 0.4 - - - -
533A THR* 1.3 76.7 - - - +
535A ARG* 1.3 57.6 + - - +
537A GLU* 3.3 4.7 + - - +
538A ALA* 3.0 31.2 + - - +
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Residues in contact with ARG 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A THR 5.5 0.4 + - - -
531A ALA* 3.4 22.6 + - - +
532A GLU* 3.0 34.5 + - - +
534A ASP* 1.3 76.9 - - - +
536A LEU* 1.3 63.6 + - - +
538A ALA* 4.0 3.9 - - - +
539A ARG* 3.0 62.8 + - + +
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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
----------------------------------------------------------
33A LEU* 5.8 6.7 - - + -
532A GLU* 3.2 20.0 + - + +
533A THR* 3.6 35.2 - - + +
534A ASP 3.3 0.2 - - - -
535A ARG* 1.3 72.5 - - - +
537A GLU* 1.3 55.9 + - + +
539A ARG* 3.0 10.6 + - - +
540A LYS* 2.8 36.1 + - + +
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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
----------------------------------------------------------
35A PRO 4.9 0.7 - - - +
36A GLU* 5.3 0.5 - - - -
37A PRO* 3.4 33.7 - - + +
173A ARG* 3.5 17.7 + - - -
176A GLN* 2.9 23.7 + - - -
533A THR* 3.2 26.4 + - - +
534A ASP* 3.3 4.2 + - - +
535A ARG 3.3 0.4 - - - -
536A LEU* 1.3 83.0 - - + +
538A ALA* 1.3 58.4 + - - +
540A LYS* 3.3 8.8 + - + +
541A LYS* 3.0 28.3 + - - +
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Residues in contact with ALA 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A ASP 3.0 17.1 + - - +
535A ARG* 4.3 3.6 - - - +
537A GLU* 1.3 74.5 - - - +
539A ARG* 1.3 53.3 + - + +
540A LYS 3.3 0.2 - - - -
541A LYS* 3.8 11.8 - - + +
542A THR* 2.5 36.1 + - - -
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Residues in contact with ARG 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A ARG* 3.0 54.2 + - + +
536A LEU* 3.0 9.0 + - - +
538A ALA* 1.3 78.5 - - + +
540A LYS* 1.3 56.8 + - - +
542A THR* 3.7 9.3 + - - +
543A LYS* 3.3 27.0 + - - +
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Residues in contact with LYS 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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36A GLU* 3.2 38.3 + - - +
37A PRO* 5.3 5.1 - - - +
536A LEU* 2.8 12.7 + - + +
537A GLU* 3.3 13.2 + - + +
539A ARG* 1.3 76.0 - - - +
541A LYS* 1.3 55.3 + - - +
542A THR 3.2 0.7 - - - -
543A LYS* 3.3 9.9 + - + +
544A ASN* 2.5 53.4 + - - +
564A TYR* 6.0 0.9 - - - -
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Residues in contact with LYS 541 (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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537A GLU 3.0 18.3 + - - +
538A ALA* 3.8 11.2 - - + +
539A ARG 3.5 0.2 - - - -
540A LYS* 1.3 75.6 - - - +
542A THR* 1.3 58.3 + - - +
544A ASN* 3.8 9.0 - - - +
545A LYS* 3.3 31.9 + - - +
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Residues in contact with THR 542 (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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538A ALA 2.5 28.6 + - - -
539A ARG* 3.9 9.7 - - - +
540A LYS 3.2 0.2 - - - -
541A LYS* 1.3 77.4 - - - +
543A LYS* 1.3 62.3 + - - +
545A LYS* 3.5 6.5 + - + +
546A GLN* 3.4 43.7 + - + +
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Residues in contact with LYS 543 (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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539A ARG 3.3 14.1 + - - +
540A LYS* 3.4 14.6 - - + +
542A THR* 1.3 76.6 - - - +
544A ASN* 1.3 66.9 + - - +
546A GLN* 3.4 14.9 + - - +
547A LEU* 3.3 35.5 + - + +
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Residues in contact with ASN 544 (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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540A LYS* 2.5 56.1 + - - +
541A LYS* 3.8 7.7 - - - +
543A LYS* 1.3 78.1 - - - +
545A LYS* 1.3 54.8 + - - +
547A LEU* 4.3 9.3 - - - +
548A GLY 3.1 10.8 + - - -
549A HIS* 2.7 44.9 + - + -
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Residues in contact with LYS 545 (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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541A LYS* 3.3 26.2 + - - +
542A THR* 3.7 7.9 - - + +
543A LYS 3.2 0.6 - - - -
544A ASN* 1.3 79.2 - - - +
546A GLN* 1.3 59.8 + - + +
548A GLY* 4.2 4.1 + - - -
549A HIS* 4.6 29.0 + - + +
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Residues in contact with GLN 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A THR* 3.4 34.4 + - + +
543A LYS* 3.4 11.2 + - - +
544A ASN 3.3 0.6 - - - -
545A LYS* 1.3 80.8 - - + +
547A LEU* 1.3 67.3 + - + +
548A GLY 3.5 0.2 - - - -
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Residues in contact with LEU 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A LYS* 3.3 32.2 + - + +
544A ASN* 4.3 10.1 - - - +
546A GLN* 1.3 82.2 - - + +
548A GLY* 1.3 61.8 + - - +
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Residues in contact with GLY 548 (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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544A ASN 3.1 6.0 + - - -
545A LYS 4.2 4.6 + - - -
546A GLN 3.5 2.2 - - - -
547A LEU* 1.3 83.5 - - - +
549A HIS* 1.3 71.5 - - - +
550A GLU 3.7 0.9 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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