Contacts of the helix formed by residues 526 - 543 (chain A) in PDB entry 1M10
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 526 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523A SER 4.0 3.0 + - - -
525A LEU* 1.3 76.3 - - - +
527A GLU* 1.3 54.0 + - - +
528A ALA* 3.3 11.2 + - - +
529A GLU* 2.7 52.0 + - - +
530A PHE 2.7 30.3 + - - -
586A TYR* 3.4 4.7 - - - -
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Residues in contact with GLU 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A SER* 1.3 73.0 - - - +
528A ALA* 1.3 58.5 + - - +
530A PHE* 2.8 19.6 + - - +
531A GLU* 3.1 27.4 + - + +
586A TYR* 3.3 48.7 - - + +
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Residues in contact with ALA 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A SER* 3.3 9.8 + - - +
527A GLU* 1.3 82.1 - - - +
529A GLU* 1.3 60.6 + - + +
531A GLU* 3.5 15.9 - - - +
532A VAL* 3.4 17.5 - - - +
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Residues in contact with GLU 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A ARG 4.3 2.8 - - - +
525A LEU* 3.4 18.3 - - - +
526A SER* 2.7 52.9 + - - +
528A ALA* 1.3 72.3 - - + +
530A PHE* 1.3 65.5 + - - +
531A GLU 3.2 0.7 - - - -
532A VAL* 3.4 14.2 + - - +
533A LEU* 3.4 8.3 + - - +
679A SER* 5.6 3.6 - - - -
680A VAL* 3.5 37.4 - - + +
681A ASP* 5.6 1.6 - - - +
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Residues in contact with PHE 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A LEU* 4.4 14.1 - - + -
520A ASP 3.5 26.2 - - - -
521A GLY* 4.4 6.1 - - - -
522A SER 6.0 0.4 - - - -
525A LEU* 4.8 7.6 - - + -
526A SER 2.7 10.3 + - - +
527A GLU 2.8 10.5 + - - +
529A GLU* 1.3 73.5 - - - +
531A GLU* 1.3 55.2 + - - +
533A LEU* 2.8 40.8 + - + +
534A LYS* 2.8 34.6 + - + +
557A GLU* 4.5 11.0 - - + -
584A VAL* 3.4 39.7 - - + -
585A LYS 4.1 1.8 - - - -
586A TYR* 3.4 46.0 - + + -
587A ALA 5.2 0.4 - - - -
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Residues in contact with GLU 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A GLU* 3.3 30.0 - - + +
528A ALA* 3.5 13.9 - - - +
530A PHE* 1.3 82.9 - - - +
532A VAL* 1.3 53.3 + - + +
534A LYS* 3.1 41.2 + - - +
535A ALA* 2.7 34.9 + - - +
582A SER 4.8 1.0 - - - +
586A TYR* 5.1 1.6 - - - +
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Residues in contact with VAL 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A ALA 3.4 17.5 - - - +
529A GLU* 3.7 12.1 - - - +
530A PHE 3.2 0.6 - - - -
531A GLU* 1.3 75.0 - - + +
533A LEU* 1.3 63.2 + - - +
535A ALA* 3.8 9.4 - - + +
536A PHE* 3.4 12.8 + - - +
680A VAL* 3.6 36.3 - - + +
681A ASP* 4.4 11.7 - - - +
683A LEU* 3.6 9.9 - - + +
684A GLU* 6.5 1.1 - - + -
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Residues in contact with LEU 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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519A LEU* 3.9 29.2 - - + -
520A ASP* 4.4 7.9 - - + +
525A LEU* 4.0 21.3 - - + -
529A GLU 3.4 9.1 + - - +
530A PHE* 2.8 20.9 + - + +
532A VAL* 1.3 76.4 - - - +
534A LYS* 1.3 68.3 + - - +
536A PHE* 3.0 23.4 + - + +
537A VAL* 3.1 11.1 + - - +
621A LEU* 3.7 33.7 - - + -
653A ILE* 4.4 9.0 - - + -
680A VAL* 4.9 4.0 - - + -
683A LEU* 3.8 22.4 - - + -
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Residues in contact with LYS 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A LEU* 4.7 6.3 - - + -
530A PHE* 2.8 29.9 + - + +
531A GLU* 3.1 47.7 + - - +
533A LEU* 1.3 73.5 - - - +
535A ALA* 1.3 67.7 + - - +
537A VAL* 3.0 18.6 + - - +
538A VAL* 3.0 17.0 + - - +
581A ALA 4.0 9.8 - - - +
582A SER* 3.0 31.7 + - - +
583A GLN 4.2 1.8 - - - -
584A VAL* 2.8 43.2 + - + +
585A LYS* 5.1 0.6 - - - +
586A TYR 5.1 1.0 - - - +
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Residues in contact with ALA 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A GLU 2.7 20.2 + - - +
532A VAL* 3.8 11.7 - - + +
534A LYS* 1.3 71.6 - - - +
536A PHE* 1.3 65.1 + - - +
538A VAL* 2.9 19.7 + - - +
539A ASP* 3.0 22.1 + - - +
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Residues in contact with PHE 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A PHE* 4.9 1.1 - + - -
532A VAL 3.4 3.7 + - - +
533A LEU* 3.0 21.0 + - + +
535A ALA* 1.3 78.1 - - - +
537A VAL* 1.3 66.0 + - + +
539A ASP* 3.5 7.3 + - - +
540A MET* 3.1 57.0 + - + +
619A LEU* 4.2 10.5 - - + -
621A LEU* 4.0 22.0 - - + -
651A VAL* 5.8 0.4 - - + -
683A LEU* 3.5 51.8 - - + -
684A GLU* 5.5 1.3 - - - +
686A GLN* 6.2 0.2 - - + -
687A ARG* 3.9 34.3 - - + +
690A ILE* 4.5 16.6 - - + -
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Residues in contact with VAL 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A PHE* 3.5 42.0 - - + -
519A LEU* 4.2 22.0 - - + -
533A LEU 3.1 16.8 - - - +
534A LYS* 3.0 12.3 + - - +
536A PHE* 1.3 78.8 - - + +
538A VAL* 1.3 68.2 + - + +
539A ASP 3.0 1.3 - - - -
540A MET* 2.9 10.4 + - - +
541A MET* 2.8 32.9 + - - +
555A VAL* 4.6 9.6 - - + -
581A ALA* 5.0 5.2 - - + +
621A LEU* 4.8 2.7 - - + -
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Residues in contact with VAL 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A LYS 3.0 14.2 + - - +
535A ALA* 2.9 12.4 + - - +
537A VAL* 1.3 75.3 - - - +
539A ASP* 1.3 62.3 + - - +
541A MET* 3.4 11.6 + - - +
542A GLU* 2.9 47.5 + - + +
578A ARG* 3.6 37.4 - - + +
581A ALA* 4.7 3.6 - - + -
582A SER* 3.9 21.1 - - - +
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Residues in contact with ASP 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 ALA* 3.0 18.3 + - - +
536A PHE* 3.6 6.3 - - - +
537A VAL 3.0 0.8 - - - -
538A VAL* 1.3 76.7 - - - +
540A MET* 1.3 67.6 + - - +
541A MET 2.9 1.6 - - - -
542A GLU* 2.7 33.7 + - - +
543A GLN* 3.0 17.8 + - + +
684A GLU* 3.8 10.4 - - - +
687A ARG* 2.4 49.6 + - - +
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Residues in contact with MET 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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515A LEU* 4.4 4.9 - - + -
517A PHE* 3.6 20.4 - - + -
536A PHE* 3.1 45.9 + - + +
537A VAL 2.9 8.0 + - - +
539A ASP* 1.3 79.4 - - - +
541A MET* 1.3 61.8 + - - +
543A GLN* 3.7 11.2 + - - +
544A LEU* 3.6 23.7 - - + +
619A LEU* 3.2 33.0 - - + -
687A ARG* 4.7 8.7 - - + +
690A ILE* 4.2 9.4 - - + -
691A VAL* 4.1 22.6 - - - +
694A LEU* 4.0 22.0 - - + -
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Residues in contact with MET 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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517A PHE* 4.3 15.5 - - + -
537A VAL* 2.8 23.1 + - - +
538A VAL* 3.4 11.7 - - - +
539A ASP 2.8 0.4 + - - -
540A MET* 1.3 76.0 - - - +
542A GLU* 1.3 65.7 + - - +
544A LEU* 2.8 29.1 + - - +
546A ILE* 3.5 38.4 - - + +
553A VAL* 4.2 15.3 - - + -
555A VAL* 5.0 3.1 - - + -
566A ILE* 4.1 14.1 - - + -
577A LEU* 3.6 26.5 - - + -
578A ARG* 3.7 16.6 - - + +
581A ALA* 3.8 20.6 - - - -
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Residues in contact with GLU 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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505A HIS* 6.2 2.0 - - + -
508A TYR* 4.1 11.8 + - - -
538A VAL* 2.9 34.1 + - - +
539A ASP* 2.7 34.1 + - - +
541A MET* 1.3 71.9 - - - +
543A GLN* 1.3 55.0 + - + +
544A LEU* 2.5 17.7 + - - +
578A ARG* 3.7 23.1 + - - +
687A ARG* 5.5 0.2 + - - -
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Residues in contact with GLN 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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505A HIS* 3.9 11.1 + - - +
507A PHE 3.4 20.0 + - - -
508A TYR* 3.1 28.4 - - + +
509A CYS 3.1 9.9 + - - +
539A ASP* 3.0 15.4 + - + +
540A MET* 4.0 6.3 - - - +
541A MET 3.2 0.2 - - - -
542A GLU* 1.3 73.9 - - + +
544A LEU* 1.3 75.1 + - - +
687A ARG* 3.3 29.7 + - - +
688A ASP* 3.2 16.7 + - - +
691A VAL* 3.2 37.9 - - + +
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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
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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